diff --git a/files/galaxy-re.grid.cesnet.cz/README b/files/galaxy-re.grid.cesnet.cz/README new file mode 100644 index 00000000..28b14e04 --- /dev/null +++ b/files/galaxy-re.grid.cesnet.cz/README @@ -0,0 +1,120 @@ +# usegalaxy + +Simple galaxy installation steps. + +On fresh install of ubuntu: +``` +sudo apt-get update +sudo apt-get upgrade -y +sudo apt update +sudo apt upgrade -y +sudo apt install -y software-properties-common +sudo apt-add-repository --yes --update ppa:ansible/ansible +sudo apt install -y ansible +``` + +Clone the repo and instal required galaxy roles. +``` +git clone https://github.com/CESNET/usegalaxy.git +cd usegalaxy +ansible-galaxy install -p roles -r requirements.yml +``` +Note that the roles are already present in this repo. + +After the instalation, you should configure your [inventory file](https://training.galaxyproject.org/training-material/topics/admin/tutorials/ansible/tutorial.html#inventory-file) ([hosts](https://github.com/CESNET/usegalaxy/blob/main/hosts)) and set up a vault: +``` +openssl rand -base64 24 > .vault-password.txt +ansible-vault create group_vars/secret.yml +``` +The second command opens an editor wherein you should define variables eg.: +``` +vault_id_secret: "a-long-random-value" +rabbitmq_users_password: + mqadmin: "a-long-random-value" + galaxy: "a-long-random-value" + galaxy_gpu: "a-long-random-value" +``` +The value should be a long random value, which can be obtained by command `openssl rand -base64 24`, though you should avoid having a `/` or `\` in your password as galaxy will interpret this as a path. + +Make sure you have these ports enabled on your machine: +``` +80(HTTP) +443(HTTPS) +4369(TCP) +5671(TCP) +15672(TCP) +25672(TCP) +``` + +Once everything have been installed and configured, the ansible playbook can be run as follows: +``` +ansible-playbook galaxy.yml +``` + +## Usegalaxy tools + +Install ephemeris for tool management: +``` +virtualenv -p python3 ~/ephemeris_venv +. ~/ephemeris_venv/bin/activate +pip install ephemeris +``` +To obtain the list of tools from the [usegalaxy.eu](https://usegalaxy.eu) use: +``` +get-tool-list -g "https://usegalaxy.eu" -o "eu_tool_list.yaml" +``` +and then to install them: +``` +shed-tools install -g https://your-galaxy -a -t eu_tool_list.yaml +``` +The api key can be found in the User -> Preferences -> Manage API Key in Galaxy menu. + +... + +Later we should use this [role](https://github.com/galaxyproject/ansible-galaxy-tools) to automate this, but there are too many tools to be installed and it is very inpractical for testing purposes. + +## Debian 11 + +### TUS + +On ubuntu < 22.04 and Debian < 12 the GLIBC version is incompatible with the ```galaxyproject.tusd``` GLIBC, therfore playbook ends in error. +- in `roles/galaxyproject.tusd/defaults/main.yml` you have to set the `tusd_version:` to 'v1.8.0' (tested, possibly higher) + +### Ansible + +On Debian 11 the default version of `ansible` is 2.10.08 which fails to extract binaries for TUSd. +- workaround: + - because of Puppet, we need to create dedicated sources.list file for ansible + - `sudo vim /etc/apt/sources.list.d/ansible_ubuntu_focal_main.list` add this line : `deb http://ppa.launchpad.net/ansible/ansible/ubuntu focal main` + - then `sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 93C4A3FD7BB9C367` + - followed by `sudo apt-get update` and `sudo apt-get install ansible -y` +- Note that you might need to `sudo apt remove ansible` `sudo apt autoremove` before you try to install ansible. + +### Nginx Upload Module + +Our playbook makes use of `nginx-upload-module`, which is not included by default in any nginx-* distribution from `apt`. +This is a simple recipe for installing nginx with the upload-module. + +``` +sudo apt remove *nginx* -y && +sudo apt autoremove -y && + +wget http://nginx.org/download/nginx-1.24.0.tar.gz && +tar -xzf nginx-1.24.0.tar.gz && +cd nginx-1.24.0/ && +git clone https://github.com/hongzhidao/nginx-upload-module.git && +sudo apt-get install -y libpcre3 libpcre3-dev libssl-dev zlib1g-dev && +./configure --user=nginx --group=nginx --prefix=/etc/nginx --conf-path=/etc/nginx/nginx.conf --sbin-path=/usr/sbin/nginx --http-log-path=/var/log/nginx/access.log --error-log-path=/var/log/nginx/error.log --lock-path=/var/lock/nginx.lock --pid-path=/run/nginx.pid --modules-path=/usr/lib/nginx/modules --http-client-body-temp-path=/var/lib/nginx/body --http-fastcgi-temp-path=/var/lib/nginx/fastcgi --http-proxy-temp-path=/var/lib/nginx/proxy --http-scgi-temp-path=/var/lib/nginx/scgi --http-uwsgi-temp-path=/var/lib/nginx/uwsgi --with-compat --with-debug --with-pcre-jit --with-http_ssl_module --with-http_stub_status_module --with-http_realip_module --with-http_auth_request_module --with-http_v2_module --with-http_dav_module --with-http_slice_module --with-threads --with-http_addition_module --with-http_gunzip_module --with-http_gzip_static_module --with-http_sub_module --add-module=nginx-upload-module && +make && make install +``` + +Note that you might need to `sudo systemctl unmask nginx.service` and remove the `galaxy` and `redirect-ssl` from `/etc/nginx/sites-available and `/etc/nginx/sites-enabled` before running the playbook again. + +### Other issues + + +Use `sudo apt install python3-docker` before running the `usegalaxy.rabbitmqserver` role. + +For influxdb apt key error: https://www.influxdata.com/blog/linux-package-signing-key-rotation/ + +For proftpd add "LoadModule mod_tls.c" to roles/galaxyproject.proftpd/templates/tls.conf.j2 just before the TLSEngine diff --git a/files/galaxy-re.grid.cesnet.cz/all_tools.yml b/files/galaxy-re.grid.cesnet.cz/all_tools.yml new file mode 100644 index 00000000..cd10e148 --- /dev/null +++ b/files/galaxy-re.grid.cesnet.cz/all_tools.yml @@ -0,0 +1,128 @@ +# DEMON: This file is a copy from usegalaxy.cz, it wasn't adjusted to the needs of RE yet +name: Tools +type: generic +id: all_tools +items: +- sections: + - upload_file + - get_data + - data_source_tools + - send_data + - collection_operations + - expression_tools +- id: general_text_label + text: General Text Tools + type: label +- sections: + - text_manipulation + - filter_and_sort + - join__subtract_and_group + - convert + - convert_formats + - builtin_converters +- id: genomic_manip_label + text: Genomic File Manipulation + type: label +- sections: + - fasta_fastq + - fastq_quality_control + - quality_control + - sam_bam + - bed + - vcf_bcf + - nanopore + - lift_over + - extract_features + - operate_on_genomic_intervals + - fetch_sequences___alignments + - chromosome_conformation +- id: genomics_analysis_label + text: Genomics Analysis + type: label +- sections: + - assembly + - annotation + - mapping + - variant_calling + - rna_analysis + - multiple_alignments + - hgv + - evolution + - regional_variation + - biodiversity_data_exploration + - genome_diversity + - rna_seq + - peak_calling + - genome_editing + - epigenetics + - phylogenetics + - phenotype_association + - single_cell + - hca_single_cell + - hca-single_cell + - single-cell +- id: stats_viz + text: Statistics and Visualization + type: label +- sections: + - statistics + - machine_learning + - plots + - interactive_tools + - graph_display_data +- id: genomics_toolkits_label + text: Genomics Toolkits + type: label +- sections: + - mothur + - qiime + - qiime_2 + - picard + - deeptools + - emboss + - ncbi_blast + - mimodd + - scanpy + - hicexplorer + - gemini + - motif_tools + - gatk_tools + - rad_seq + - sanger_sequencing + - dna_metabarcoding + - apollo +- id: domain_tools_label + text: Domain Tools + type: label +- sections: + - virology + - metagenomic_analysis + - proteomics + - metabolomics + - muon_spectroscopy + - chemicaltoolbox + - astronomy + - imaging + - climate_analysis + - gis_data_handling + - spatial_omics + - ecoregionalization + - graphclust + - species_abundance + - data_and_metadata_management + - obo_ontology_manipulation + - ontology + - compute_indicators_for_satellite_remote_sensing + - compute_indicators_for_turnover_boulders_fields + - animal_detection_on_acoustic_recordings +# - id: other_tools_label +# text: Other Tools +# type: label +- sections: + - other_tools +# - id: testing_tools_label +# text: Testing Tools +# type: label +- sections: + - local_tools + - test_tools diff --git a/files/galaxy-re.grid.cesnet.cz/pulsar.pub b/files/galaxy-re.grid.cesnet.cz/pulsar.pub new file mode 100644 index 00000000..8e52ab8e --- /dev/null +++ b/files/galaxy-re.grid.cesnet.cz/pulsar.pub @@ -0,0 +1 @@ +ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPJ4pNj4pZBfm/hGSD04ZkuxtCbageNxwSD6EAZ+wyjQ galaxyelixir@galaxy-re.grid.cesnet.cz diff --git a/files/galaxy-re.grid.cesnet.cz/regalaxy_integrated_tool_panel.xml b/files/galaxy-re.grid.cesnet.cz/regalaxy_integrated_tool_panel.xml new file mode 100644 index 00000000..9190a82b --- /dev/null +++ b/files/galaxy-re.grid.cesnet.cz/regalaxy_integrated_tool_panel.xml @@ -0,0 +1,714 @@ + + + + + + + + + +
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+ + diff --git a/files/galaxy-re.grid.cesnet.cz/regalaxy_tool_list.yaml b/files/galaxy-re.grid.cesnet.cz/regalaxy_tool_list.yaml new file mode 100644 index 00000000..d84cccf8 --- /dev/null +++ b/files/galaxy-re.grid.cesnet.cz/regalaxy_tool_list.yaml @@ -0,0 +1,373 @@ +tools: +- name: ncbi_datasets + owner: iuc + revisions: + - 198c75abbf55 + tool_panel_section_id: getext + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: repeatexplorer2_testing + owner: petr-novak + revisions: + - 3d0ba5734776 + - 4308d3e572ee + - 792914356c37 + - 20ef42e81eeb + - 5cca2c9aa4ad + - a27646c27090 + tool_panel_section_id: repeatexplorer + tool_panel_section_label: RepeatExplorer + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dante + owner: petr-novak + revisions: + - 8f2bd3cae2de + - f0663cdbae66 + - ae4cebdccf74 + tool_panel_section_id: dante + tool_panel_section_label: DANTE + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dante_tir + owner: petr-novak + revisions: + - ce4d06c72092 + tool_panel_section_id: dante_tir + tool_panel_section_label: DANTE_TIR + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dante_ltr + owner: petr-novak + revisions: + - e61f06df42b9 + - 08b5e23859ed + - 27e5f58763f2 + - 8224e3d7b03a + - d5508ce50c49 + tool_panel_section_id: dante_ltr + tool_panel_section_label: DANTE_LTR + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tidecluster + owner: petr-novak + revisions: + - 440796be7576 + - a0f57cfa1bb7 + - 971dbc97e607 + - 30a8a954dd93 + tool_panel_section_id: tidecluster + tool_panel_section_label: TideCluster + tool_shed_url: toolshed.g2.bx.psu.edu +- name: repeat_annotation_pipeline3 + owner: petr-novak + revisions: + - 755a4d643184 + - 5366d5ea04bc + tool_panel_section_id: assembly_annotation_tools + tool_panel_section_label: Assembly annotation tools + tool_shed_url: toolshed.g2.bx.psu.edu +- name: re_utils + owner: petr-novak + revisions: + - 91996b991991 + tool_panel_section_id: repeatexplorer_utilities + tool_panel_section_label: RepeatExplorer utilities + tool_shed_url: toolshed.g2.bx.psu.edu +- name: long_reads_sampling + owner: petr-novak + revisions: + - 060fc04af21c + tool_panel_section_id: repeatexplorer_utilities + tool_panel_section_label: RepeatExplorer utilities + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastqc + owner: devteam + revisions: + - 5ec9f6bceaee + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_groomer + owner: devteam + revisions: + - 47e5dbc3e790 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_splitter + owner: devteam + revisions: + - e39cc71d3ed6 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_stats + owner: devteam 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tool_shed_url: toolshed.g2.bx.psu.edu +- name: trimmomatic + owner: pjbriggs + revisions: + - 32f1f56bd970 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: trim_galore + owner: bgruening + revisions: + - cd7e644cae1d + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqkit_stats + owner: iuc + revisions: + - 54a954ee64d4 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqtk + owner: iuc + revisions: + - 4b494533146a + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: various_galaxy_tools + owner: petr-novak + revisions: + - 1069776f7ae2 + tool_panel_section_id: genomic_file_utilities + tool_panel_section_label: Genomic file utilities + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gffread + owner: devteam + revisions: + - 3e436657dcd0 + tool_panel_section_id: bed + tool_panel_section_label: BED + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bedtools + owner: iuc + revisions: + - a1a923cd89e8 + tool_panel_section_id: bed + tool_panel_section_label: BED + tool_shed_url: toolshed.g2.bx.psu.edu +- name: jbrowse + owner: iuc + revisions: + - a6e57ff585c0 + tool_panel_section_id: jbrowse + tool_panel_section_label: Jbrowse + tool_shed_url: toolshed.g2.bx.psu.edu +- name: krona_text + owner: petr-novak + revisions: + - 04021cfd5170 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: histogram + owner: devteam + revisions: + - 6f134426c2b0 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_point + owner: iuc + revisions: + - 3b12bf9b4b87 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_histogram + owner: iuc + revisions: + - b0d96516e6a5 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_violin + owner: iuc + revisions: + - 0e7290688b50 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_pca + owner: iuc + revisions: + - b1268b7544d3 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_heatmap + owner: iuc + revisions: + - 10515715c940 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: text_processing + owner: bgruening + revisions: + - d698c222f354 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text manipulation + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/files/galaxy-re.grid.cesnet.cz/tpv_rules_local.yml b/files/galaxy-re.grid.cesnet.cz/tpv_rules_local.yml new file mode 100644 index 00000000..dac311e5 --- /dev/null +++ b/files/galaxy-re.grid.cesnet.cz/tpv_rules_local.yml @@ -0,0 +1,235 @@ +tools: + # DEMON: All Novak's tools (except 2) are not properly containerized, therefore, they need conda to deal with dependences + .*/petr-novak/.*: + cores: 2 + mem: 10 + context: + scratch: 15 + scheduling: + require: + - conda + + # DANTE_TIR toolset: https://toolshed.g2.bx.psu.edu/repos/petr-novak/dante_tir + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_tir/.*: + cores: 20 + mem: 32 + + # DANTE toolset: https://toolshed.g2.bx.psu.edu/repos/petr-novak/dante + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_filter/.*: + mem: 25 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_to_tabular/.*: + mem: 25 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_summary/.*: + mem: 25 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_extract/.*: + mem: 25 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/dante/.*: + cores: 32 + mem: 25 + context: + walltime: 336 + + # TideCluster tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster + toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tidecluster_annotation/.*: + cores: 16 + mem: 24 + toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tc_reannotate/.*: + cores: 32 + mem: 50 + context: + walltime: 96 + toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tidecluster/.*: + cores: 16 + mem: 64 + context: + scratch: 150 + walltime: 336 + + # repeat_annotation_pipeline tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3 +# toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/extract_re_contigs/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 +# toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/compare_gff/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 +# toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/summarize_gff_by_attribute/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 +# toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/annotate_contigs/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/repeat_annotate/.*: + cores: 32 + mem: 50 + context: + scratch: 50 + walltime: 96 + + # re_utils tools https://toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/RMsearch2/.*: + cores: 16 + mem: 32 + context: + scratch: 50 + walltime: 96 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/chip_seq_ratio_1/.*: + cores: 16 + mem: 32 + context: + scratch: 50 + walltime: 48 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/rename_sequences/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/pairScan/.*: + context: + scratch: 50 + walltime: 48 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/single_fastq_filtering/.*: + cores: 6 + context: + scratch: 50 + walltime: 24 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_affixer/.*: + context: + scratch: 50 +# toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/sampler/.*: +# context: +# scratch: 15 +# toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/plot_comparative/.*: +# context: +# scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/extract_var_files_from_re/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/summarize_annotation/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/names_affixer/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/cluster_table2krona_format/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_input/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_interlacer/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/paired_fastq_filtering/.*: +# mem: 10 #DEMON: old setting but there was job which used 78GB; the best would be to scale to input size + mem: 50 + context: + scratch: 50 +# walltime: 24 #DEMON: used to be 24h but if input is very big it could take more time, would be great to scale it to input size + walltime: 48 + + # DANTE_ltr tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr +# toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_summary/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/clean_dante_ltr/.*: + cores: 32 + mem: 64 + context: + scratch: 64 + walltime: 168 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_search/.*: + cores: 32 + mem: 64 + context: + scratch: 64 + walltime: 168 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_to_library/.*: + cores: 32 + mem: 64 + context: + scratch: 64 + walltime: 168 + + # ReapeatExplorer tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing + toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/repeatexplorer2/.*: + cores: 10 + mem: 4 + context: + scratch: 50 + walltime: 48 + scheduling: + reject: + - conda + require: + - singularity + container_resolvers: + - type: cached_explicit_singularity + cache_directory: "$SINGULARITY_CACHEDIR" + - type: explicit_singularity + - type: cached_mulled_singularity + cache_directory: "$SINGULARITY_CACHEDIR" + - auto_install: true + type: mulled_singularity + - auto_install: false + cache_directory: /mnt/galaxy-re/singularity/mulled + type: build_mulled_singularity + params: + singularity_default_container_id: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache/cache/library/sha256.660dda926394f3db2400f7800e064cf731c75566853cac43a30be44e3b5f5d73" + env: + SINGULARITY_CACHEDIR: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache" + rules: + - id: queue_definition_by_parameter + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_definition' in param_dict and 'queue_specification' in param_dict['queue_definition'] + cores: | + import re + int(re.search(r'ncpus=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + mem: | + import re + int(re.search(r'mem=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + context: + scratch: | + import re + int(re.search(r'scratch_local=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + walltime: | + import re + int(re.search(r'walltime=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + - id: basic_fast_queue_selected + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_select' in param_dict and param_dict['queue_select'].startswith('basic_fast_queue') + cores: 10 + mem: 16 + context: + scratch: 50 + walltime: 48 + - id: long_slow_queue_selected + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_select' in param_dict and param_dict['queue_select'].startswith('long_slow_queue') + cores: 16 + mem: 64 + context: + scratch: 50 + walltime: 336 + - id: extra_long_slow_queue_selected + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_select' in param_dict and param_dict['queue_select'].startswith('extra_long_slow_queue') + cores: 16 + mem: 64 + context: + scratch: 50 + walltime: 720 + + toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/tarean/.*: + inherits: toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/repeatexplorer2/.* diff --git a/files/galaxy/config/sanitize_allowlist.txt b/files/galaxy/config/sanitize_allowlist.txt new file mode 100644 index 00000000..49dfb6e6 --- /dev/null +++ b/files/galaxy/config/sanitize_allowlist.txt @@ -0,0 +1,44 @@ +toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc +toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc +toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona_text +toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse +toolshed.g2.bx.psu.edu/repos/petr-novak/dante/dante +toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_extract +toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_filter +toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_summary +toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_to_tabular +toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr 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This can be enabled by renaming this file to examples.py and adding + the following to the ``app:main`` section of ``galaxy.ini``: + + tool_filters = examples:restrict_testing_tools_to_admins + """ + if tool.id == "testing_html" or tool.id == "testing_pbs" or tool.id == "testing": + return context.trans.user_is_admin + return True diff --git a/files/galaxy/static/style/base.css b/files/galaxy/static/style/base.css new file mode 100644 index 00000000..6e893571 --- /dev/null +++ b/files/galaxy/static/style/base.css @@ -0,0 +1,60 @@ +@charset "UTF-8";.markdown-textarea{border:1px solid #ccc;border-top:none;border-bottom:none;resize:none;outline:none;background-color:#f6f6f6;font-size:14px;font-family:Monaco,courier,monospace;padding:20px;width:100%;height:95%}pre code{white-space:pre-wrap}.badge{padding:.2em .6em .3em;border-width:1px;border-style:solid;border-radius:.15rem;text-decoration:none}.nametags:empty{display:none}.nametags 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Server is down

+

Please, be patient and try to reach it in couple of minutes.

+ + + diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/README b/files/repeatexplorer-elixir.cerit-sc.cz/README new file mode 100644 index 00000000..28b14e04 --- /dev/null +++ b/files/repeatexplorer-elixir.cerit-sc.cz/README @@ -0,0 +1,120 @@ +# usegalaxy + +Simple galaxy installation steps. + +On fresh install of ubuntu: +``` +sudo apt-get update +sudo apt-get upgrade -y +sudo apt update +sudo apt upgrade -y +sudo apt install -y software-properties-common +sudo apt-add-repository --yes --update ppa:ansible/ansible +sudo apt install -y ansible +``` + +Clone the repo and instal required galaxy roles. +``` +git clone https://github.com/CESNET/usegalaxy.git +cd usegalaxy +ansible-galaxy install -p roles -r requirements.yml +``` +Note that the roles are already present in this repo. + +After the instalation, you should configure your [inventory file](https://training.galaxyproject.org/training-material/topics/admin/tutorials/ansible/tutorial.html#inventory-file) ([hosts](https://github.com/CESNET/usegalaxy/blob/main/hosts)) and set up a vault: +``` +openssl rand -base64 24 > .vault-password.txt +ansible-vault create group_vars/secret.yml +``` +The second command opens an editor wherein you should define variables eg.: +``` +vault_id_secret: "a-long-random-value" +rabbitmq_users_password: + mqadmin: "a-long-random-value" + galaxy: "a-long-random-value" + galaxy_gpu: "a-long-random-value" +``` +The value should be a long random value, which can be obtained by command `openssl rand -base64 24`, though you should avoid having a `/` or `\` in your password as galaxy will interpret this as a path. + +Make sure you have these ports enabled on your machine: +``` +80(HTTP) +443(HTTPS) +4369(TCP) +5671(TCP) +15672(TCP) +25672(TCP) +``` + +Once everything have been installed and configured, the ansible playbook can be run as follows: +``` +ansible-playbook galaxy.yml +``` + +## Usegalaxy tools + +Install ephemeris for tool management: +``` +virtualenv -p python3 ~/ephemeris_venv +. ~/ephemeris_venv/bin/activate +pip install ephemeris +``` +To obtain the list of tools from the [usegalaxy.eu](https://usegalaxy.eu) use: +``` +get-tool-list -g "https://usegalaxy.eu" -o "eu_tool_list.yaml" +``` +and then to install them: +``` +shed-tools install -g https://your-galaxy -a -t eu_tool_list.yaml +``` +The api key can be found in the User -> Preferences -> Manage API Key in Galaxy menu. + +... + +Later we should use this [role](https://github.com/galaxyproject/ansible-galaxy-tools) to automate this, but there are too many tools to be installed and it is very inpractical for testing purposes. + +## Debian 11 + +### TUS + +On ubuntu < 22.04 and Debian < 12 the GLIBC version is incompatible with the ```galaxyproject.tusd``` GLIBC, therfore playbook ends in error. +- in `roles/galaxyproject.tusd/defaults/main.yml` you have to set the `tusd_version:` to 'v1.8.0' (tested, possibly higher) + +### Ansible + +On Debian 11 the default version of `ansible` is 2.10.08 which fails to extract binaries for TUSd. +- workaround: + - because of Puppet, we need to create dedicated sources.list file for ansible + - `sudo vim /etc/apt/sources.list.d/ansible_ubuntu_focal_main.list` add this line : `deb http://ppa.launchpad.net/ansible/ansible/ubuntu focal main` + - then `sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 93C4A3FD7BB9C367` + - followed by `sudo apt-get update` and `sudo apt-get install ansible -y` +- Note that you might need to `sudo apt remove ansible` `sudo apt autoremove` before you try to install ansible. + +### Nginx Upload Module + +Our playbook makes use of `nginx-upload-module`, which is not included by default in any nginx-* distribution from `apt`. +This is a simple recipe for installing nginx with the upload-module. + +``` +sudo apt remove *nginx* -y && +sudo apt autoremove -y && + +wget http://nginx.org/download/nginx-1.24.0.tar.gz && +tar -xzf nginx-1.24.0.tar.gz && +cd nginx-1.24.0/ && +git clone https://github.com/hongzhidao/nginx-upload-module.git && +sudo apt-get install -y libpcre3 libpcre3-dev libssl-dev zlib1g-dev && +./configure --user=nginx --group=nginx --prefix=/etc/nginx --conf-path=/etc/nginx/nginx.conf --sbin-path=/usr/sbin/nginx --http-log-path=/var/log/nginx/access.log --error-log-path=/var/log/nginx/error.log --lock-path=/var/lock/nginx.lock --pid-path=/run/nginx.pid --modules-path=/usr/lib/nginx/modules --http-client-body-temp-path=/var/lib/nginx/body --http-fastcgi-temp-path=/var/lib/nginx/fastcgi --http-proxy-temp-path=/var/lib/nginx/proxy --http-scgi-temp-path=/var/lib/nginx/scgi --http-uwsgi-temp-path=/var/lib/nginx/uwsgi --with-compat --with-debug --with-pcre-jit --with-http_ssl_module --with-http_stub_status_module --with-http_realip_module --with-http_auth_request_module --with-http_v2_module --with-http_dav_module --with-http_slice_module --with-threads --with-http_addition_module --with-http_gunzip_module --with-http_gzip_static_module --with-http_sub_module --add-module=nginx-upload-module && +make && make install +``` + +Note that you might need to `sudo systemctl unmask nginx.service` and remove the `galaxy` and `redirect-ssl` from `/etc/nginx/sites-available and `/etc/nginx/sites-enabled` before running the playbook again. + +### Other issues + + +Use `sudo apt install python3-docker` before running the `usegalaxy.rabbitmqserver` role. + +For influxdb apt key error: https://www.influxdata.com/blog/linux-package-signing-key-rotation/ + +For proftpd add "LoadModule mod_tls.c" to roles/galaxyproject.proftpd/templates/tls.conf.j2 just before the TLSEngine diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/all_tools.yml b/files/repeatexplorer-elixir.cerit-sc.cz/all_tools.yml new file mode 100644 index 00000000..cd10e148 --- /dev/null +++ b/files/repeatexplorer-elixir.cerit-sc.cz/all_tools.yml @@ -0,0 +1,128 @@ +# DEMON: This file is a copy from usegalaxy.cz, it wasn't adjusted to the needs of RE yet +name: Tools +type: generic +id: all_tools +items: +- sections: + - upload_file + - get_data + - data_source_tools + - send_data + - collection_operations + - expression_tools +- id: general_text_label + text: General Text Tools + type: label +- sections: + - text_manipulation + - filter_and_sort + - join__subtract_and_group + - convert + - convert_formats + - builtin_converters +- id: genomic_manip_label + text: Genomic File Manipulation + type: label +- sections: + - fasta_fastq + - fastq_quality_control + - quality_control + - sam_bam + - bed + - vcf_bcf + - nanopore + - lift_over + - extract_features + - operate_on_genomic_intervals + - fetch_sequences___alignments + - chromosome_conformation +- id: genomics_analysis_label + text: Genomics Analysis + type: label +- sections: + - assembly + - annotation + - mapping + - variant_calling + - rna_analysis + - multiple_alignments + - hgv + - evolution + - regional_variation + - biodiversity_data_exploration + - genome_diversity + - rna_seq + - peak_calling + - genome_editing + - epigenetics + - phylogenetics + - phenotype_association + - single_cell + - hca_single_cell + - hca-single_cell + - single-cell +- id: stats_viz + text: Statistics and Visualization + type: label +- sections: + - statistics + - machine_learning + - plots + - interactive_tools + - graph_display_data +- id: genomics_toolkits_label + text: Genomics Toolkits + type: label +- sections: + - mothur + - qiime + - qiime_2 + - picard + - deeptools + - emboss + - ncbi_blast + - mimodd + - scanpy + - hicexplorer + - gemini + - motif_tools + - gatk_tools + - rad_seq + - sanger_sequencing + - dna_metabarcoding + - apollo +- id: domain_tools_label + text: Domain Tools + type: label +- sections: + - virology + - metagenomic_analysis + - proteomics + - metabolomics + - muon_spectroscopy + - chemicaltoolbox + - astronomy + - imaging + - climate_analysis + - gis_data_handling + - spatial_omics + - ecoregionalization + - graphclust + - species_abundance + - data_and_metadata_management + - obo_ontology_manipulation + - ontology + - compute_indicators_for_satellite_remote_sensing + - compute_indicators_for_turnover_boulders_fields + - animal_detection_on_acoustic_recordings +# - id: other_tools_label +# text: Other Tools +# type: label +- sections: + - other_tools +# - id: testing_tools_label +# text: Testing Tools +# type: label +- sections: + - local_tools + - test_tools diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/pulsar.pub b/files/repeatexplorer-elixir.cerit-sc.cz/pulsar.pub new file mode 100644 index 00000000..8e52ab8e --- /dev/null +++ b/files/repeatexplorer-elixir.cerit-sc.cz/pulsar.pub @@ -0,0 +1 @@ +ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPJ4pNj4pZBfm/hGSD04ZkuxtCbageNxwSD6EAZ+wyjQ galaxyelixir@galaxy-re.grid.cesnet.cz diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/regalaxy_integrated_tool_panel.xml b/files/repeatexplorer-elixir.cerit-sc.cz/regalaxy_integrated_tool_panel.xml new file mode 100644 index 00000000..9190a82b --- /dev/null +++ b/files/repeatexplorer-elixir.cerit-sc.cz/regalaxy_integrated_tool_panel.xml @@ -0,0 +1,714 @@ + + + + + + + + + +
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+ diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/regalaxy_tool_list.yaml b/files/repeatexplorer-elixir.cerit-sc.cz/regalaxy_tool_list.yaml new file mode 100644 index 00000000..d84cccf8 --- /dev/null +++ b/files/repeatexplorer-elixir.cerit-sc.cz/regalaxy_tool_list.yaml @@ -0,0 +1,373 @@ +tools: +- name: ncbi_datasets + owner: iuc + revisions: + - 198c75abbf55 + tool_panel_section_id: getext + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: repeatexplorer2_testing + owner: petr-novak + revisions: + - 3d0ba5734776 + - 4308d3e572ee + - 792914356c37 + - 20ef42e81eeb + - 5cca2c9aa4ad + - a27646c27090 + tool_panel_section_id: repeatexplorer + tool_panel_section_label: RepeatExplorer + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dante + owner: petr-novak + revisions: + - 8f2bd3cae2de + - f0663cdbae66 + - ae4cebdccf74 + tool_panel_section_id: dante + tool_panel_section_label: DANTE + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dante_tir + owner: petr-novak + revisions: + - ce4d06c72092 + tool_panel_section_id: dante_tir + tool_panel_section_label: DANTE_TIR + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dante_ltr + owner: petr-novak + revisions: + - e61f06df42b9 + - 08b5e23859ed + - 27e5f58763f2 + - 8224e3d7b03a + - d5508ce50c49 + tool_panel_section_id: dante_ltr + tool_panel_section_label: DANTE_LTR + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tidecluster + owner: petr-novak + revisions: + - 440796be7576 + - a0f57cfa1bb7 + - 971dbc97e607 + - 30a8a954dd93 + tool_panel_section_id: tidecluster + tool_panel_section_label: TideCluster + tool_shed_url: toolshed.g2.bx.psu.edu +- name: repeat_annotation_pipeline3 + owner: petr-novak + revisions: + - 755a4d643184 + - 5366d5ea04bc + tool_panel_section_id: assembly_annotation_tools + tool_panel_section_label: Assembly annotation tools + tool_shed_url: toolshed.g2.bx.psu.edu +- name: re_utils + owner: petr-novak + revisions: + - 91996b991991 + tool_panel_section_id: repeatexplorer_utilities + tool_panel_section_label: RepeatExplorer utilities + tool_shed_url: toolshed.g2.bx.psu.edu +- name: long_reads_sampling + owner: petr-novak + revisions: + - 060fc04af21c + tool_panel_section_id: repeatexplorer_utilities + tool_panel_section_label: RepeatExplorer utilities + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastqc + owner: devteam + revisions: + - 5ec9f6bceaee + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_groomer + owner: devteam + revisions: + - 47e5dbc3e790 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_splitter + owner: devteam + revisions: + - e39cc71d3ed6 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_stats + owner: devteam + revisions: + - f0e7deab6518 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_barcode_splitter + owner: devteam + revisions: + - 0b7ec11b3c7c + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_artifacts_filter + owner: devteam + revisions: + - 529bccd5e4a1 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_nucleotides_distribution + owner: devteam + revisions: + - b6b54ba71bd8 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_quality_statistics + owner: devteam + revisions: + - cc0fd298cc17 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_quality_boxplot + owner: devteam + revisions: + - 867ab348287d + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_quality_converter + owner: devteam + revisions: + - 045f0e1043f7 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_quality_filter + owner: devteam + revisions: + - 64e9a6afdd0c + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: multiqc + owner: iuc + revisions: + - abfd8a6544d7 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_compute_length + owner: devteam + revisions: + - 7d37cfda8e00 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_to_tabular + owner: devteam + revisions: + - e7ed3c310b74 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_formatter + owner: devteam + revisions: + - 516b97a23d7e + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_reverse_complement + owner: devteam + revisions: + - 177f0621c266 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_trimmer + owner: devteam + revisions: + - 73194cdd4f57 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_renamer + owner: devteam + revisions: + - f984bb114520 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tabular_to_fasta + owner: devteam + revisions: + - 0a7799698fe5 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tabular_to_fastq + owner: devteam + revisions: + - 2dcfbbf9071a + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_to_tabular + owner: devteam + revisions: + - 4b347702c4aa + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastqtofasta + owner: devteam + revisions: + - 297962e79f39 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_deinterlacer + owner: devteam + revisions: + - f3936d0632cb + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_interlacer + owner: devteam + revisions: + - 2ccb8dcabddc + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fasta_filter_by_length + owner: devteam + revisions: + - 8cacfcf96a52 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ucsc_fasplit + owner: iuc + revisions: + - bf04bd405d5b + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: trimmomatic + owner: pjbriggs + revisions: + - 32f1f56bd970 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: trim_galore + owner: bgruening + revisions: + - cd7e644cae1d + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqkit_stats + owner: iuc + revisions: + - 54a954ee64d4 + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: seqtk + owner: iuc + revisions: + - 4b494533146a + tool_panel_section_id: fasta/fastq_manipulation + tool_panel_section_label: FASTA/FASTQ manipulation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: various_galaxy_tools + owner: petr-novak + revisions: + - 1069776f7ae2 + tool_panel_section_id: genomic_file_utilities + tool_panel_section_label: Genomic file utilities + tool_shed_url: toolshed.g2.bx.psu.edu +- name: gffread + owner: devteam + revisions: + - 3e436657dcd0 + tool_panel_section_id: bed + tool_panel_section_label: BED + tool_shed_url: toolshed.g2.bx.psu.edu +- name: bedtools + owner: iuc + revisions: + - a1a923cd89e8 + tool_panel_section_id: bed + tool_panel_section_label: BED + tool_shed_url: toolshed.g2.bx.psu.edu +- name: jbrowse + owner: iuc + revisions: + - a6e57ff585c0 + tool_panel_section_id: jbrowse + tool_panel_section_label: Jbrowse + tool_shed_url: toolshed.g2.bx.psu.edu +- name: krona_text + owner: petr-novak + revisions: + - 04021cfd5170 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: histogram + owner: devteam + revisions: + - 6f134426c2b0 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_point + owner: iuc + revisions: + - 3b12bf9b4b87 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_histogram + owner: iuc + revisions: + - b0d96516e6a5 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_violin + owner: iuc + revisions: + - 0e7290688b50 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_pca + owner: iuc + revisions: + - b1268b7544d3 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ggplot2_heatmap + owner: iuc + revisions: + - 10515715c940 + tool_panel_section_id: visualisation + tool_panel_section_label: Visualisation + tool_shed_url: toolshed.g2.bx.psu.edu +- name: text_processing + owner: bgruening + revisions: + - d698c222f354 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text manipulation + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/static/images/umbr_programs_icons/ELIXIR_CZECHREPUBLIC_white_background_small.png b/files/repeatexplorer-elixir.cerit-sc.cz/static/images/umbr_programs_icons/ELIXIR_CZECHREPUBLIC_white_background_small.png new file mode 100644 index 00000000..c3042190 Binary files /dev/null and b/files/repeatexplorer-elixir.cerit-sc.cz/static/images/umbr_programs_icons/ELIXIR_CZECHREPUBLIC_white_background_small.png differ diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/static/images/umbr_programs_icons/RE_header.png b/files/repeatexplorer-elixir.cerit-sc.cz/static/images/umbr_programs_icons/RE_header.png new file mode 100644 index 00000000..752bb82a Binary files /dev/null and b/files/repeatexplorer-elixir.cerit-sc.cz/static/images/umbr_programs_icons/RE_header.png differ diff 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+global: + default_inherits: default + +tools: + default: + abstract: true + cores: 2 + mem: 10 + env: + # Ensuring a consistent collation environment is good for reproducibility. + LC_ALL: C + GALAXY_SLOTS: "{cores}" + GALAXY_MEMORY_MB: "{int(mem)*1000}" + context: + scratch: 15 + walltime: 24 + queue: galaxyre + scheduling: + require: + - pulsar + reject: + - offline + + # Tools for testing and playing + testing.*: + cores: 1 + mem: 1 + context: + scratch: 1 + walltime: 1 + + # DANTE_TIR toolset: https://toolshed.g2.bx.psu.edu/repos/petr-novak/dante_tir + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_tir/.*: + cores: 20 + mem: 32 + + # DANTE toolset: https://toolshed.g2.bx.psu.edu/repos/petr-novak/dante + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_filter/.*: + cores: 2 + mem: 25 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_to_tabular/.*: + cores: 2 + mem: 25 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_summary/.*: + cores: 2 + mem: 25 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_extract/.*: + cores: 2 + mem: 25 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/dante/.*: + cores: 32 + mem: 25 + context: + scratch: 15 + walltime: 336 + + # TideCluster tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster + toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tidecluster_annotation/.*: + cores: 16 + mem: 24 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tc_reannotate/.*: + cores: 32 + mem: 50 + context: + scratch: 15 + walltime: 96 + toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tidecluster/.*: + cores: 16 + mem: 64 + context: + scratch: 150 + walltime: 336 + + # repeat_annotation_pipeline tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3 + toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/extract_re_contigs/.*: + cores: 2 + mem: 10 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/compare_gff/.*: + cores: 2 + mem: 10 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/summarize_gff_by_attribute/.*: + cores: 2 + mem: 10 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/annotate_contigs/.*: + cores: 2 + mem: 10 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/repeat_annotate/.*: + cores: 32 + mem: 50 + context: + scratch: 50 + walltime: 96 + + # re_utils tools https://toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/RMsearch2/.*: + cores: 16 + mem: 32 + context: + scratch: 50 + walltime: 96 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/chip_seq_ratio_1/.*: + cores: 16 + mem: 32 + context: + scratch: 50 + walltime: 48 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/rename_sequences/.*: + cores: 2 + mem: 10 + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/pairScan/.*: + cores: 2 + mem: 10 + context: + scratch: 50 + walltime: 48 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/single_fastq_filtering/.*: + cores: 6 + mem: 10 + context: + scratch: 50 + walltime: 24 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_affixer/.*: + cores: 2 + mem: 10 + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/sampler/.*: + cores: 2 + mem: 10 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/plot_comparative/.*: + cores: 2 + mem: 10 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/extract_var_files_from_re/.*: + cores: 2 + mem: 10 + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/summarize_annotation/.*: + cores: 2 + mem: 10 + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/names_affixer/.*: + cores: 2 + mem: 10 + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/cluster_table2krona_format/.*: + cores: 2 + mem: 10 + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_input/.*: + cores: 2 + mem: 10 + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_interlacer/.*: + cores: 2 + mem: 10 + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/paired_fastq_filtering/.*: +# cores: 6 #DEMON: old setting but seems pointless + cores: 2 +# mem: 10 #DEMON: old setting but there was job which used 78GB; the best would be to scale to input size + mem: 50 + context: + scratch: 50 +# walltime: 24 #DEMON: used to be 24h but if input is very big it could take more time, would be great to scale it to input size + walltime: 48 + + # DANTE_ltr tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_summary/.*: + cores: 2 + mem: 10 + context: + scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/clean_dante_ltr/.*: + cores: 32 + mem: 64 + context: + scratch: 64 + walltime: 168 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_search/.*: + cores: 32 + mem: 64 + context: + scratch: 64 + walltime: 168 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_to_library/.*: + cores: 32 + mem: 64 + context: + scratch: 64 + walltime: 168 + + # ReapeatExplorer tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing + toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/repeatexplorer2/.*: + cores: 10 + mem: 4 + context: + scratch: 50 + walltime: 48 + scheduling: + require: + - pulsar + - singularity + container_resolvers: + - type: cached_explicit_singularity + cache_directory: "$SINGULARITY_CACHEDIR" + - type: explicit_singularity + - type: cached_mulled_singularity + cache_directory: "$SINGULARITY_CACHEDIR" + - auto_install: true + type: mulled_singularity + - auto_install: false + cache_directory: /mnt/galaxy-re/singularity/mulled + type: build_mulled_singularity + params: + singularity_default_container_id: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache/cache/library/sha256.660dda926394f3db2400f7800e064cf731c75566853cac43a30be44e3b5f5d73" + rules: + - id: queue_definition_by_parameter + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_definition' in param_dict and 'queue_specification' in param_dict['queue_definition'] + cores: | + import re + int(re.search(r'ncpus=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + mem: | + import re + int(re.search(r'mem=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + context: + scratch: | + import re + int(re.search(r'scratch_local=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + walltime: | + import re + int(re.search(r'walltime=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + - id: basic_fast_queue_selected + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_select' in param_dict and param_dict['queue_select'].startswith('basic_fast_queue') + cores: 10 + mem: 16 + context: + scratch: 50 + walltime: 48 + - id: long_slow_queue_selected + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_select' in param_dict and param_dict['queue_select'].startswith('long_slow_queue') + cores: 16 + mem: 64 + context: + scratch: 50 + walltime: 336 + - id: extra_long_slow_queue_selected + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_select' in param_dict and param_dict['queue_select'].startswith('extra_long_slow_queue') + cores: 16 + mem: 64 + context: + scratch: 50 + walltime: 720 + + toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/tarean/.*: + inherits: toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/repeatexplorer2/.* + + .*/fastq_groomer/.*: + cores: 1 + mem: 16 + +roles: + training.*: + max_cores: 2 + max_mem: "int(max_cores * 3.8)" + scheduling: + require: + - training + helper: + scheduling: + require: + - helper + highmem: + mem: 512 + context: + queue: elixircz + test: + scheduling: + require: + - test + +destinations: + tpv_local: + runner: local_runner + max_accepted_cores: 1 + max_accepted_mem: 4 + params: + tmp_dir: true + scheduling: + require: + - local + reject: + - singularity + tpv_local_singularity: + runner: local_runner + max_accepted_cores: 1 + max_accepted_mem: 4 + params: + singularity_enabled: true + singularity_default_container_id: "/cvmfs/singularity.galaxyproject.org/all/python:3.8.3" + env: + SINGULARITY_CACHEDIR: "/mnt/galaxy-re/singularity/" + SINGULARITY_TMPDIR: /mnt/galaxy-re/tmp + scheduling: + require: + - local + prefer: + - singularity + tpv_pulsar: + runner: pulsar_runner + max_accepted_cores: 32 + max_accepted_mem: 185 + max_accepted_gpus: 0 + max_cores: 32 + max_mem: 128 + max_gpus: 0 + params: + default_file_action: remote_rsync_transfer + transport: rsync + ssh_user: "galaxyelixir" + ssh_host: "repeatexplorer-elixir.cerit-sc.cz" + ssh_port: 22 + ssh_key: | + -----BEGIN OPENSSH PRIVATE KEY----- + b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAAAMwAAAAtzc2gtZW + QyNTUxOQAAACDyeKTY+KWQX5v4Rkg9OGZLsbQm2oHjccEg+hAGfsMo0AAAAKgS5zlWEuc5 + VgAAAAtzc2gtZWQyNTUxOQAAACDyeKTY+KWQX5v4Rkg9OGZLsbQm2oHjccEg+hAGfsMo0A + AAAECe7yi98nsOset8Jo7V2Gmh19TtINb+4Cnx8YFxJSgKafJ4pNj4pZBfm/hGSD04Zkux + tCbageNxwSD6EAZ+wyjQAAAAJWdhbGF4eWVsaXhpckBnYWxheHktcmUuZ3JpZC5jZXNuZX + QuY3o= + -----END OPENSSH PRIVATE KEY----- + dependency_resolution: remote + jobs_directory: /storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/staging + persistence_directory: /opt/pulsar/files/persistent + remote_metadata: false + rewrite_parameters: true + outputs_to_working_directory: false + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + env: + TMPDIR: $SCRATCHDIR + TMP: $SCRATCHDIR + TEMP: $SCRATCHDIR + scheduling: + require: + - pulsar + reject: + - singularity + tpv_pulsar_singularity: + inherits: tpv_pulsar + runner: pulsar_runner + params: + singularity_enabled: true + singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR:rw" + singularity_default_container_id: "/cvmfs/singularity.galaxyproject.org/all/python:3.8.3" + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + env: + SINGULARITY_CACHEDIR: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache" + SINGULARITY_TMPDIR: "$SCRATCHDIR" + XDG_CACHE_HOME: "$SCRATCHDIR" + scheduling: + require: + - pulsar + - singularity + tpv_pulsar_test: + inherits: tpv_pulsar + runner: pulsar_runner + params: + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + scheduling: + require: + - pulsar + - test + reject: + - singularity + tpv_pulsar_highmem: + inherits: tpv_pulsar + runner: pulsar_runner + max_accepted_mem: 512 + max_mem: 512 + + tpv_pulsar_helper: + runner: pulsar_helper + max_accepted_cores: 32 + max_accepted_mem: 185 + max_accepted_gpus: 0 + max_cores: 32 + max_mem: 128 + max_gpus: 0 + params: + default_file_action: remote_rsync_transfer + transport: rsync + ssh_user: "galaxyelixir" + ssh_host: "repeatexplorer-elixir.cerit-sc.cz" + ssh_port: 22 + ssh_key: | + -----BEGIN OPENSSH PRIVATE KEY----- + b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAAAMwAAAAtzc2gtZW + QyNTUxOQAAACDyeKTY+KWQX5v4Rkg9OGZLsbQm2oHjccEg+hAGfsMo0AAAAKgS5zlWEuc5 + VgAAAAtzc2gtZWQyNTUxOQAAACDyeKTY+KWQX5v4Rkg9OGZLsbQm2oHjccEg+hAGfsMo0A + AAAECe7yi98nsOset8Jo7V2Gmh19TtINb+4Cnx8YFxJSgKafJ4pNj4pZBfm/hGSD04Zkux + tCbageNxwSD6EAZ+wyjQAAAAJWdhbGF4eWVsaXhpckBnYWxheHktcmUuZ3JpZC5jZXNuZX + QuY3o= + -----END OPENSSH PRIVATE KEY----- + dependency_resolution: remote + jobs_directory: /storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/staging + persistence_directory: /opt/pulsar/files/persistent + remote_metadata: false + rewrite_parameters: true + outputs_to_working_directory: false + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + env: + TMPDIR: $SCRATCHDIR + TMP: $SCRATCHDIR + TEMP: $SCRATCHDIR + scheduling: + require: + - pulsar + - helper + reject: + - singularity + tpv_pulsar_singularity_helper: + inherits: tpv_pulsar_helper + runner: pulsar_helper + params: + singularity_enabled: true + singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR:rw" + singularity_default_container_id: "/cvmfs/singularity.galaxyproject.org/all/python:3.8.3" + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue}@pbs-m1.metacentrum.cz -N pulsar_re_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + env: + SINGULARITY_CACHEDIR: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache" + SINGULARITY_TMPDIR: "$SCRATCHDIR" + XDG_CACHE_HOME: "$SCRATCHDIR" + scheduling: + require: + - pulsar + - helper + - singularity diff --git a/files/repeatexplorer-elixir.cerit-sc.cz/tpv_rules_local.yml b/files/repeatexplorer-elixir.cerit-sc.cz/tpv_rules_local.yml new file mode 100644 index 00000000..1e153b83 --- /dev/null +++ b/files/repeatexplorer-elixir.cerit-sc.cz/tpv_rules_local.yml @@ -0,0 +1,250 @@ +tools: + .*/trimmomatic/.*: + rules: + - id: no_singularity + if: | + # versions without singularity container available + no_container = { + '0.39+galaxy0', + } + any(helpers.tool_version_eq(tool, version) for version in no_container) + scheduling: + require: + - conda + + # DEMON: All Novak's tools (except 2) are not properly containerized, therefore, they need conda to deal with dependences + .*/petr-novak/.*: + cores: 2 + mem: 10 + context: + scratch: 15 + scheduling: + require: + - conda + + # DANTE_TIR toolset: https://toolshed.g2.bx.psu.edu/repos/petr-novak/dante_tir + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_tir/.*: + cores: 20 + mem: 32 + context: + walltime: 48 + + # DANTE toolset: https://toolshed.g2.bx.psu.edu/repos/petr-novak/dante + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_filter/.*: + mem: 25 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_to_tabular/.*: + mem: 25 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/gff_summary/.*: + mem: 25 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/domains_extract/.*: + mem: 25 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante/dante/.*: + cores: 32 + mem: 25 + context: + walltime: 336 + + # TideCluster tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster + toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tidecluster_annotation/.*: + cores: 16 + mem: 24 + toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tc_reannotate/.*: + cores: 32 + mem: 50 + context: + walltime: 96 + toolshed.g2.bx.psu.edu/repos/petr-novak/tidecluster/tidecluster/.*: + cores: 16 + mem: 64 + context: + scratch: 150 + walltime: 336 + + # repeat_annotation_pipeline tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3 +# toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/extract_re_contigs/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 +# toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/compare_gff/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 +# toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/summarize_gff_by_attribute/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 +# toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/annotate_contigs/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/repeat_annotation_pipeline3/repeat_annotate/.*: + cores: 32 + mem: 50 + context: + scratch: 50 + walltime: 96 + + # re_utils tools https://toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/RMsearch2/.*: + cores: 16 + mem: 32 + context: + scratch: 50 + walltime: 96 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/chip_seq_ratio_1/.*: + cores: 16 + mem: 32 + context: + scratch: 50 + walltime: 48 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/rename_sequences/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/pairScan/.*: + context: + scratch: 50 + walltime: 48 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/single_fastq_filtering/.*: + cores: 6 + context: + scratch: 50 + walltime: 24 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_affixer/.*: + context: + scratch: 50 +# toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/sampler/.*: +# context: +# scratch: 15 +# toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/plot_comparative/.*: +# context: +# scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/extract_var_files_from_re/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/summarize_annotation/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/names_affixer/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/cluster_table2krona_format/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_input/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/fasta_interlacer/.*: + context: + scratch: 50 + toolshed.g2.bx.psu.edu/repos/petr-novak/re_utils/paired_fastq_filtering/.*: +# mem: 10 #DEMON: old setting but there was job which used 78GB; the best would be to scale to input size + mem: 50 + context: + scratch: 50 +# walltime: 24 #DEMON: used to be 24h but if input is very big it could take more time, would be great to scale it to input size + walltime: 48 + + # DANTE_ltr tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr +# toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_summary/.*: +# cores: 2 +# mem: 10 +# context: +# scratch: 15 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/clean_dante_ltr/.*: + cores: 32 + mem: 64 + context: + scratch: 64 + walltime: 168 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_search/.*: + cores: 32 + mem: 64 + context: + scratch: 64 + walltime: 168 + toolshed.g2.bx.psu.edu/repos/petr-novak/dante_ltr/dante_ltr_to_library/.*: + cores: 32 + mem: 64 + context: + scratch: 64 + walltime: 168 + + # ReapeatExplorer tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing + toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/repeatexplorer2/.*: + cores: 10 + mem: 4 + context: + scratch: 50 + walltime: 48 + scheduling: + reject: + - conda + require: + - singularity + container_resolvers: + - type: cached_explicit_singularity + cache_directory: "$SINGULARITY_CACHEDIR" + - type: explicit_singularity + - type: cached_mulled_singularity + cache_directory: "$SINGULARITY_CACHEDIR" + - auto_install: true + type: mulled_singularity + - auto_install: false + cache_directory: /mnt/galaxy-re/singularity/mulled + type: build_mulled_singularity + params: + singularity_default_container_id: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache/cache/library/sha256.660dda926394f3db2400f7800e064cf731c75566853cac43a30be44e3b5f5d73" + env: + SINGULARITY_CACHEDIR: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache" + rules: + - id: queue_definition_by_parameter + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_definition' in param_dict and 'queue_specification' in param_dict['queue_definition'] + cores: | + import re + int(re.search(r'ncpus=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + mem: | + import re + int(re.search(r'mem=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + context: + scratch: | + import re + int(re.search(r'scratch_local=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + walltime: | + import re + int(re.search(r'walltime=(\d)+', job.get_param_values(app)['queue_definition']['queue_specification']).group(0).split('=')[1]) + - id: basic_fast_queue_selected + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_select' in param_dict and param_dict['queue_select'].startswith('basic_fast_queue') + cores: 10 + mem: 16 + context: + scratch: 50 + walltime: 48 + - id: long_slow_queue_selected + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_select' in param_dict and param_dict['queue_select'].startswith('long_slow_queue') + cores: 16 + mem: 64 + context: + scratch: 50 + walltime: 336 + - id: extra_long_slow_queue_selected + if: | + param_dict = job.get_param_values(app) # get job input parameters as dictionary + 'queue_select' in param_dict and param_dict['queue_select'].startswith('extra_long_slow_queue') + cores: 16 + mem: 64 + context: + scratch: 50 + walltime: 720 + + toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/tarean/.*: + inherits: toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/repeatexplorer2/.* diff --git a/galaxy.yml b/galaxy.yml index bf0d956d..bb34c2e1 100644 --- a/galaxy.yml +++ b/galaxy.yml @@ -80,11 +80,11 @@ fstype: xfs opts: rw,_netdev state: mounted - - name: Create galaxy mutable data directory + - name: Create RBD data directory file: owner: "{{ galaxy_user_name }}" group: "{{ galaxy_user_group_name }}" - path: "{{ galaxy_mutable_data_dir }}" + path: "{{ rbd_data_dir }}" state: directory mode: '0755' @@ -100,6 +100,39 @@ - role: galaxyproject.postgresql_objects become: true become_user: postgres + post_tasks: + - name: Create pg_dump backup folder if needed + file: + path: "{{ postgresql_backup_dir }}/pg_dump" + state: directory + owner: postgres + group: "{{ galaxy_user_group_name }}" + mode: 0750 + - name: Create initial empty pg_dump file if needed # otherwise the following logrotate conf will not work + file: + path: "{{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql.gz" + state: touch + owner: postgres + group: "{{ galaxy_user_group_name }}" + mode: 0640 + - name: Set-up Galaxy DB backup using pg_dump and logrotate + ansible.builtin.blockinfile: + path: "/etc/logrotate.d/{{ postgresql_pg_dump_prefix }}" + create: true + block: | + {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql.gz { + daily + missingok + rotate 14 + nocompress + nocreate + postrotate + sudo -u postgres pg_dump {{ galaxy_db_name }} --file={{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql --verbose 2>&1 | logger -t {{ postgresql_pg_dump_prefix }} + echo "calling: postgres gzip {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql" && sudo -u postgres gzip {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql 2>&1 | logger -t {{ postgresql_pg_dump_prefix }} + echo "calling: chown postgres:{{ galaxy_user_group_name }} {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql" && chown postgres:{{ galaxy_user_group_name }} {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql 2>&1 | logger -t {{ postgresql_pg_dump_prefix }} + echo "calling: chmod 640 {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql" && chmod 640 {{ postgresql_backup_dir }}/pg_dump/{{ postgresql_pg_dump_prefix }}.sql 2>&1 | logger -t {{ postgresql_pg_dump_prefix }} + endscript + } - hosts: noletsencrypt become: true @@ -151,7 +184,7 @@ when: admin_ssh_keys - name: Install Dependencies package: - name: ['acl', 'bzip2', 'git', 'make', 'tar', 'python3-bioblend', 'python3-venv', 'python3-setuptools', 'python3-pip', 'python3-psycopg2', 'rsync', 'python3-docker', 'python3-passlib', 'nginx-full', 'logrotate', 'proftpd-mod-ldap', 'squashfs-tools', 'krb5-user'] # krb5-user is neccessary only if you need to mount NFS storage + name: ['acl', 'bzip2', 'git', 'make', 'tar', 'python3-bioblend', 'python3-venv', 'python3-setuptools', 'python3-pip', 'python3-psycopg2', 'rsync', 'python3-docker', 'python3-passlib', 'nginx-full', 'logrotate', 'proftpd-mod-ldap', 'squashfs-tools', 'libldap2-dev', 'libsasl2-dev']#, 'krb5-user'] # krb5-user is neccessary only if you need to mount NFS storage - name: Install RHEL/CentOS/Rocky specific dependencies package: name: ['tmpwatch'] @@ -198,9 +231,9 @@ - usegalaxy_eu.apptainer - galaxyproject.galaxy - usegalaxy_eu.tpv_auto_lint - - role: galaxyproject.miniconda - become: true - become_user: "{{ galaxy_user_name }}" +# - role: galaxyproject.miniconda +# become: true +# become_user: "{{ galaxy_user_name }}" - geerlingguy.redis - role: usegalaxy_eu.flower when: enable_flower | bool @@ -216,6 +249,22 @@ when: enable_telegraf | bool post_tasks: + - name: Add Nginx warning about maintenance + ansible.builtin.copy: + src: "{{ playbook_dir }}/files/nginx/warning.html" + dest: "/var/www/html/warning.html" + owner: www-data + group: www-data + mode: '0644' + + - name: Configure ProFTPd LDAP option + template: + src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/proftpd_ldap.conf.j2', 'templates/galaxy/config/proftpd_ldap.conf.j2']) }}" + dest: "{{ proftpd_config_include_dir }}/06_ldap.conf" + backup: yes + notify: + - reload proftpd + - name: Adds nginx's www-data user into galaxy user group ansible.builtin.user: name: www-data @@ -233,16 +282,32 @@ virtualenv: "{{ galaxy_venv_dir }}" when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz','usegalaxy.cz']" - - name: Creates entry in crontab "chmod on _files for ngnix access" + #DEMON: cleanup jobs from RE (maybe not needed) + - name: Creates entry in crontab "tmpreaper call in tus upload dir" ansible.builtin.cron: - name: "chmod on _files for ngnix access" - minute: "2" - hour: "*" # 2nd minute every hour - #DEMON: zvazit ci nepouzit find /rbd/data/datasets/*/*/*/dataset_*_files -type f ! -perm /g+rw -exec chmod g+rw '{}' ';' - job: "/usr/bin/find {{ galaxy_config.galaxy.file_path }}/*/*/*/dataset_*_files -type d -mmin -180 -maxdepth 0 -exec chmod -R g+rw '{}' ';'" + name: "tmpreaper in tus upload dir" + minute: "5" + hour: "*" + job: "/usr/sbin/tmpreaper --verbose=0 --showdeleted --all --mtime --mtime-dir --runtime=600 24h {{ galaxy_tus_upload_store }} >> {{ galaxy_data_dir }}/cleaning_tus_upload_dir.log" become: yes become_user: "{{ galaxy_user_name }}" - tags: cron + - name: Creates entry in crontab "tmpreaper call in galaxy tmp dir" + ansible.builtin.cron: + name: "tmpreaper in galaxy temp dir" + minute: "7" + hour: "*" + job: "/usr/sbin/tmpreaper --verbose=0 --showdeleted --all --mtime --mtime-dir --runtime=600 24h {{ galaxy_data_dir }}/tmp >> {{ galaxy_data_dir }}/cleaning_galaxy_temp_dir.log" + become: yes + become_user: "{{ galaxy_user_name }}" +# - name: Creates entry in crontab "tmpreaper call in galaxy jobs dir" +# ansible.builtin.cron: +# name: "tmpreaper in galaxy jobs dir" +# minute: "9" +# hour: "*" +# job: "/usr/sbin/tmpreaper --verbose=0 --showdeleted --all --mtime --mtime-dir --runtime=600 40d {{ galaxy_data_dir }}/jobs >> {{ galaxy_data_dir }}/cleaning_galaxy_jobs_dir.log" +# become: yes +# become_user: "{{ galaxy_user_name }}" + - name: Setup gxadmin cleanup task ansible.builtin.cron: @@ -250,7 +315,7 @@ user: "{{ galaxy_user_name }}" minute: "0" hour: "0" # midnight daily - job: "GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server /usr/local/bin/gxadmin galaxy cleanup 60" + job: "GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server /usr/local/bin/gxadmin galaxy cleanup 60 >> {{ galaxy_data_dir }}/cleaning_gxadmin_cleanup.log" tags: cron - name: Create a file with key for CRON jobs @@ -266,7 +331,7 @@ no_log: true # set up cron to propagate einfra users to einfra galaxy group - - name: Ensure the user_group cron script directory exists + - name: Ensure the user_group directory exists ansible.builtin.file: path: "{{ galaxy_root }}/cron/user_group" state: directory @@ -275,7 +340,7 @@ mode: '0755' when: "'usegalaxy.cz' in inventory_hostname" tags: cron - - name: Copy user - group association script + - name: Copy user-group association script ansible.builtin.copy: src: "{{ playbook_dir }}/extra_scripts/add_group_users.py" dest: "{{ galaxy_root }}/cron/user_group/add_group_users.py" @@ -290,7 +355,7 @@ append: yes when: "'usegalaxy.cz' in inventory_hostname" tags: cron - - name: Setup user - group association rutine + - name: Setup user-group association rutine ansible.builtin.cron: name: "Add E-infra users to E-infra group" user: postgres @@ -358,12 +423,15 @@ tags: cron when: "inventory_hostname in ['galaxy-qa1.galaxy.cloud.e-infra.cz', 'usegalaxy.cz', 'galaxy-umsa.grid.cesnet.cz']" - - - name: RE Galaxy instance patch in lib/galaxy/webapps/galaxy/api/job_files.py - replace: - path: "{{ galaxy_root }}/server/lib/galaxy/webapps/galaxy/api/job_files.py" - regexp: '^(\s*?)shutil\.move\(input_file\.name,\s*path\)\s*$' - replace: '\1os.chmod(shutil.move(input_file.name, path), 0o664)' + - name: Set-up pre-defined integrated_tool_panel config file on RE instance only + ansible.builtin.copy: + src: "{{ playbook_dir }}/files/{{ inventory_hostname }}/regalaxy_integrated_tool_panel.xml" + dest: "{{ galaxy_mutable_config_dir }}/integrated_tool_panel.xml" + owner: "{{ galaxy_user_name }}" + group: "{{ galaxy_user_group_name }}" + mode: '0644' + backup: true + when: "inventory_hostname in ['repeatexplorer-elixir.cerit-sc.cz', 'galaxy-re.grid.cesnet.cz']" - name: Add lines to logrotate config of ProFTPd lineinfile: @@ -372,6 +440,7 @@ insertbefore: BOF with_items: - /var/log/proftpd/tls.log + - /var/log/proftpd/ldap.log - /var/log/proftpd/sql.log - name: Add pulsar public ssh key diff --git a/group_vars/dbservers.yml b/group_vars/dbservers.yml index cb3183b2..219a889a 100644 --- a/group_vars/dbservers.yml +++ b/group_vars/dbservers.yml @@ -8,7 +8,7 @@ postgresql_objects_databases: - name: "{{ galaxy_db_name }}" owner: "{{ galaxy_user_name }}" postgresql_objects_privileges: - - database: galaxy + - database: "{{ galaxy_db_name }}" roles: telegraf privs: SELECT objs: ALL_IN_SCHEMA @@ -36,3 +36,4 @@ postgresql_objects_privileges: # # PostgreSQL Backups postgresql_backup_dir: "{{ galaxy_mutable_data_dir }}/backups" +postgresql_pg_dump_prefix: galaxy_db_backup diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index e9da4d92..2a6bf983 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -2,6 +2,7 @@ # defaults for host-specific vars csnt_brand: "" csnt_contact_email: "galaxy@cesnet.cz" +csnt_galaxy_url_prefix: '' csnt_short_term_storage_dir: short_term_web_storage csnt_enable_account_interface: true csnt_log_level: WARNING @@ -10,10 +11,13 @@ csnt_enable_notification_system: false csnt_enable_oidc: true csnt_oidc_config_file: "{{ galaxy_config_dir }}/oidc_config.xml" csnt_oidc_backends_config_file: "{{ galaxy_config_dir }}/oidc_backends_config.xml" +csnt_auth_config_file: "{{ galaxy_config_dir }}/auth_conf.xml" +csnt_smtp_server: "rs.cesnet.cz:25" csnt_enable_reports: false csnt_edam_panel_views: "" csnt_default_panel_view: default csnt_registered_user_jobs_limit: 10 +csnt_jobs_output_size_limit: 50GB csnt_tool_config_file: - "{{ galaxy_config_dir }}/tool_conf.xml" - "{{ galaxy_config_dir }}/local_tool_conf.xml" @@ -26,6 +30,13 @@ csnt_galaxy_tmpclean_dirs: - "{{ galaxy_config.galaxy.new_file_path }}" - "{{ galaxy_tus_upload_store if galaxy_config.gravity.tusd.enable else ' ' }}" csnt_require_login: true +csnt_toolbox_auto_sort: true +csnt_watch_job_rules: auto +csnt_retry_job_output_collection: 3 +csnt_gunicorn_workers: 2 +csnt_celery_concurrency: 2 +csnt_celery_memory_limit: 2 +csnt_handlers_processes: 2 admin_ssh_keys: false enable_telegraf: false @@ -46,9 +57,10 @@ galaxy_mutable_config_dir: "{{ galaxy_root }}/var/config" galaxy_gravity_state_dir: "{{ galaxy_root }}/var/gravity" galaxy_tool_dependency_dir: "{{ galaxy_root }}/var/dependencies" galaxy_user: {name: "{{ galaxy_user_name }}", shell: /bin/bash} -galaxy_commit_id: release_24.2 +galaxy_commit_id: release_25.0 galaxy_force_checkout: true galaxy_job_config_file: "{{ galaxy_config_dir }}/galaxy.yml" +galaxy_data_dir: "{{ galaxy_mutable_data_dir }}" # Miniconda miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda" @@ -66,7 +78,7 @@ galaxy_job_config: workers: 4 pulsar_tpv_runner: load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner - galaxy_url: "https://{{ rabbitmq_hostname }}" + galaxy_url: "https://{{ rabbitmq_hostname }}{{ csnt_galaxy_url_prefix }}" amqp_url: "pyamqp://{{ pulsar.user_name }}:{{ rabbitmq_users_password.pulsar }}@{{ rabbitmq_hostname }}:5671/pulsar?ssl=1" amqp_acknowledge: true amqp_ack_republish_time: 1200 @@ -102,7 +114,7 @@ galaxy_job_config: - type: anonymous_user_concurrent_jobs value: 1 - type: output_size - value: 50GB + value: "{{ csnt_jobs_output_size_limit }}" tools: - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc environment: local_env @@ -110,17 +122,18 @@ galaxy_job_config: galaxy_config: galaxy: # Main Configuration - # To not bother the main disk new_file_path: "{{ galaxy_mutable_data_dir }}/tmp" object_store_config_file: "{{ galaxy_config_dir }}/object_store_conf.xml" + auth_config_file: "{{ csnt_auth_config_file }}" enable_oidc: "{{ csnt_enable_oidc }}" - oidc_config_file: "{{ csnt_oidc_config_file }}" - oidc_backends_config_file: "{{ csnt_oidc_backends_config_file }}" + oidc_config_file: "{{ csnt_oidc_config_file if csnt_enable_oidc else '' }}" + oidc_backends_config_file: "{{ csnt_oidc_backends_config_file if csnt_enable_oidc else '' }}" logo_src: "https://www.e-infra.cz/img/logo.svg" themes_config_file: "{{ galaxy_config_dir }}/themes.yml" admin_users: "{{ vault_admin_users }}" + galaxy_url_prefix: "{{ csnt_galaxy_url_prefix }}" cleanup_job: onsuccess - smtp_server: "rs.cesnet.cz:25" + smtp_server: "{{ csnt_smtp_server }}" error_email_to: "{{ csnt_contact_email }}" allow_user_creation: false require_login: "{{ csnt_require_login }}" @@ -135,6 +148,7 @@ galaxy_config: tool_config_file: "{{ csnt_tool_config_file }}" tool_sheds_config_file: "{{ csnt_tool_sheds_config_file }}" sanitize_allowlist_file: "{{ galaxy_mutable_config_dir }}/sanitize_allowlist.txt" + toolbox_auto_sort: "{{ csnt_toolbox_auto_sort }}" # SQL Performance slow_query_log_threshold: 5 enable_per_request_sql_debugging: true @@ -144,7 +158,7 @@ galaxy_config: brand: "{{ csnt_brand }}" enable_account_interface: "{{ csnt_enable_account_interface }}" enable_notification_system: "{{ csnt_enable_notification_system }}" - watch_job_rules: 'auto' + watch_job_rules: "{{ csnt_watch_job_rules }}" allow_path_paste: "{{ csnt_allow_path_paste }}" enable_quotas: true allow_user_deletion: "{{ csnt_allow_user_deletion }}" @@ -157,7 +171,7 @@ galaxy_config: panel_views_dir: "{{ galaxy_config_dir }}/plugins/activities" file_source_templates_config_file: "{{ galaxy_config_dir }}/file_source_templates.yml" # NFS workarounds - retry_job_output_collection: 3 + retry_job_output_collection: "{{ csnt_retry_job_output_collection }}" # Debugging allow_user_impersonation: true log_level: "{{ csnt_log_level }}" @@ -165,27 +179,19 @@ galaxy_config: outputs_to_working_directory: true new_user_dataset_access_role_default_private: true # Make datasets private by default # TUS - galaxy_infrastructure_url: "https://{{ inventory_hostname }}" + galaxy_infrastructure_url: "https://{{ inventory_hostname }}{{ csnt_galaxy_url_prefix }}" tus_upload_store: "{{ galaxy_tus_upload_store }}" # CVMFS tool_data_table_config_path: - /cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml - /cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml # Tool Dependencies + dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml" container_resolvers: - type: explicit_singularity - type: cached_mulled_singularity cache_directory: /cvmfs/singularity.galaxyproject.org/all/ cache_directory_cacher_type: dir_mtime - # dependency_resolvers: - # - type: conda - # - type: tool_shed_packages - # - type: galaxy_packages - # - type: galaxy_packages - # versionless: true - # - type: conda - # versionless: true - # Data Library Directories library_import_dir: "{{ csnt_library_import_dir }}" user_library_import_dir: "{{ csnt_user_library_import_dir }}" @@ -209,7 +215,7 @@ galaxy_config: # listening options bind: "unix:{{ galaxy_mutable_config_dir }}/gunicorn.sock" # performance options - workers: 2 + workers: "{{ csnt_gunicorn_workers }}" # Other options that will be passed to gunicorn # This permits setting of 'secure' headers like REMOTE_USER (and friends) # https://docs.gunicorn.org/en/stable/settings.html#forwarded-allow-ips @@ -222,8 +228,8 @@ galaxy_config: enable: true queues: celery,galaxy.internal,galaxy.external pool: threads - memory_limit: 2 - concurrency: 2 + memory_limit: "{{ csnt_celery_memory_limit }}" + concurrency: "{{ csnt_celery_concurrency }}" loglevel: DEBUG tusd: enable: true @@ -231,7 +237,7 @@ galaxy_config: upload_dir: "{{ galaxy_tus_upload_store }}" handlers: handler: - processes: 2 + processes: "{{ csnt_handlers_processes }}" pools: - job-handlers - workflow-schedulers @@ -243,6 +249,8 @@ galaxy_config: galaxy_config_files_public: + - src: files/galaxy/config/sanitize_allowlist.txt + dest: "{{ galaxy_config.galaxy.sanitize_allowlist_file }}" - src: templates/{{ inventory_hostname }}/static/welcome.html dest: "{{ galaxy_mutable_config_dir }}/welcome.html" - src: files/galaxy/static/usegalaxycz_straight.svg @@ -267,10 +275,15 @@ galaxy_config_templates: dest: "{{ tpv_mutable_dir }}/tpv_rules_meta.yml" - src: "templates/galaxy/config/vault_conf.yml.j2" dest: "{{ galaxy_config_dir }}/vault_conf.yml" + - src: templates/galaxy/config/dependency_resolvers_conf.xml.j2 + dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}" - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/file_source_templates.yml.j2', 'templates/galaxy/config/file_source_templates.yml.j2']) }}" dest: "{{ galaxy_config_dir }}/file_source_templates.yml" + - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/auth_conf.xml.j2', 'templates/galaxy/config/auth_conf.xml.j2']) }}" + dest: "{{ galaxy_config.galaxy.auth_config_file }}" galaxy_extra_dirs: + - "{{ galaxy_data_dir }}" - "{{ tpv_config_dir }}" - "{{ galaxy_config_dir }}/plugins/activities" @@ -342,7 +355,7 @@ nginx_conf_ssl_certificate_key: /etc/letsencrypt/live/{{ inventory_hostname }}/p #Install pip docker package for ansible pip_install_packages: - - name: docker + - docker # RabbitMQ rabbitmq_hostname: "{{ inventory_hostname }}" @@ -356,7 +369,6 @@ rabbitmq_plugins: # ok for noletsencrypt #rabbitmq_conf_ssl_certificate: /etc/ssl/certs/cert.pem - rabbitmq_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem rabbitmq_conf_ssl_certificate_key: /etc/ssl/user/privkey-999:999.pem @@ -477,8 +489,6 @@ proftpd_options: - Port: 21 proftpd_sql_db: galaxy@/var/run/postgresql proftpd_sql_user: galaxy -#proftpd_conf_ssl_certificate: /etc/ssl/certs/cert.pem -#proftpd_conf_ssl_certificate_key: /etc/ssl/user/privkey-proftpd.pem proftpd_conf_ssl_certificate: /etc/letsencrypt/live/{{ inventory_hostname }}/cert.pem proftpd_conf_ssl_certificate_key: /etc/letsencrypt/live/{{ inventory_hostname }}/privkey.pem proftpd_global_options: diff --git a/group_vars/production.yaml b/group_vars/production.yaml index b0af65ed..2b39cd02 100644 --- a/group_vars/production.yaml +++ b/group_vars/production.yaml @@ -1,2 +1,3 @@ rbd_mount_point: /data +rbd_data_dir: "{{ rbd_mount_point }}/galaxy" rbd_cluster_code: CL4 diff --git a/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml b/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml index aaaf92cb..68f9724a 100644 --- a/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml +++ b/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml @@ -9,7 +9,7 @@ csnt_edam_panel_views: operations,topics csnt_default_panel_view: all_tools shed_tools_shadowing: true csnt_require_login: true -csnt_registered_user_jobs_limit: 1000 +csnt_registered_user_jobs_limit: 100 pulsar: user_name: galaxy-qa1 diff --git a/host_vars/galaxy-qa2.galaxy.cloud.e-infra.cz/vars.yml b/host_vars/galaxy-qa2.galaxy.cloud.e-infra.cz/vars.yml index 4ed0dfe9..c0435ac2 100644 --- a/host_vars/galaxy-qa2.galaxy.cloud.e-infra.cz/vars.yml +++ b/host_vars/galaxy-qa2.galaxy.cloud.e-infra.cz/vars.yml @@ -5,7 +5,7 @@ csnt_brand: QA2-TEST # csnt_enable_account_interface: false csnt_log_level: DEBUG csnt_enable_notification_system: true -csnt_registered_user_jobs_limit: 1000 +csnt_registered_user_jobs_limit: 100 pulsar: user_name: galaxy-qa1 diff --git a/host_vars/galaxy-re.grid.cesnet.cz/secret.yml b/host_vars/galaxy-re.grid.cesnet.cz/secret.yml new file mode 100644 index 00000000..3207edd3 --- /dev/null +++ b/host_vars/galaxy-re.grid.cesnet.cz/secret.yml @@ -0,0 +1,106 @@ +$ANSIBLE_VAULT;1.1;AES256 +35626631323763643938626366363165386262386133623038623236653231323737316366663537 +3132653761646564623938316438346437636432373638350a663430346338613961346464646130 +38313663353062343935343664393934306333346635663265363333623133343531303462383638 +6230373164353036370a393365623933333666613537646335303030303863633865303230323834 +33383866356632623532383234363035333266316436643538313135643234366631363262343437 +38396362643330653137646361353261613966376636646431303234623338613965656330383165 +33646261613738366531346164326365323735373166306432353564323635383461376664393731 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+#csnt_edam_panel_views: operations,topics +#csnt_default_panel_view: all_tools +csnt_allow_path_paste: true +csnt_allow_user_deletion: true +csnt_enable_oidc: false +csnt_auth_config_file: "{{ galaxy_config_dir }}/auth_conf.xml" +csnt_toolbox_auto_sort: false +csnt_contact_email: regalaxy@rt.cesnet.cz +csnt_watch_job_rules: 'polling' # used to be auto +csnt_retry_job_output_collection: 5 +csnt_gunicorn_workers: 9 +csnt_handlers_processes: 4 +csnt_celery_memory_limit: 4 +csnt_celery_concurrency: 8 + +enable_tiaas: false +shed_tools_shadowing: false + +galaxy_user_name: galaxyelixir +galaxy_user_id: 2469 +galaxy_user_group_name: galaxyelixir +galaxy_user_group_gid: 10145 +galaxy_db_name: galaxyelixir + +galaxy_user_group: + name: "{{ galaxy_user_group_name }}" + gid: "{{ galaxy_user_group_gid }}" +galaxy_user: + name: "{{ galaxy_user_name }}" + uid: "{{ galaxy_user_id }}" + group: "{{ galaxy_user_group.name }}" + shell: /bin/bash + +galaxy_users_domain: repeatexplorer-elixir.cerit-sc.cz + +extra_certbot_domains: + - "{{ galaxy_users_domain }}" + - galaxyelixir.vm.cesnet.cz + +#galaxy_commit_id: 72070dbd0a6d0f418d0b8f914825ea2b8e6a0a88 +galaxy_commit_id: release_25.0 +galaxy_build_client: false + +galaxy_systemd_nofile_limit: 150000 + +# Postgresql DB backup using dump is not implemented in main branch (find the code in galaxy-re branch) +#postgresql_pg_dump_prefix: galaxy_db_backup +postgresql_backup_local_dir: "{{ galaxy_data_dir }}/backups/scripts" + +miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/conda" +miniconda_version: 23.5.2 # 23.5.0 # 4.12.0 +miniconda_channels: ['conda-forge', 'bioconda', 'iuc', 'r', 'anaconda', 'petrnovak', 'defaults'] +miniconda_base_env_packages: ['mamba'] + +pulsar: + user_name: galaxyelixir + nfs_home: brno11-elixir + nfs_prefix: pulsar-re + pbs_queue: galaxyre + pbs_gpu_queue: galaxy_gpu + +#Install pip docker package for ansible +pip_install_packages: + - docker + - python-ldap + +galaxy_config_files: + - src: files/galaxy/themes.yml + dest: "{{ galaxy_config.galaxy.themes_config_file }}" + - src: "files/{{ inventory_hostname }}/tpv_rules_local.yml" + dest: "{{ tpv_mutable_dir }}/tpv_rules_{{ inventory_hostname }}.yml" + - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/config/tool_conf.xml', 'files/galaxy/config/tool_conf.xml']) }}" + dest: "{{ galaxy_config_dir }}/tool_conf.xml" + - src: files/galaxy/config/oidc_config.xml + dest: "{{ galaxy_config_dir }}/oidc_config.xml" + - src: "files/{{ inventory_hostname }}/all_tools.yml" + dest: "{{ galaxy_config_dir }}/plugins/activities/all_tools.yml" + +rabbitmq_vhosts: + - pulsar # DEMON: used to be /pulsar and Pulsar config must be changed before (or right after) the change is deployed + - galaxy_internal + +tusd_instances: + - name: uploads + # user that tusd will run as + user: "{{ galaxy_user.name }}" + # group that tusd will run as + group: "{{ galaxy_user.group }}" + # args passed to tusd + args: + - -host=localhost + - "-port={{ galaxy_tusd_port }}" + - "-upload-dir={{ galaxy_tus_upload_store }}" + - "-hooks-http=https://{{ inventory_hostname }}{{ csnt_galaxy_url_prefix }}/api/upload/hooks" + - -hooks-http-forward-headers=X-Api-Key,Cookie + - -hooks-enabled-events pre-create + +flower_bind_interface: localhost +flower_port: 5555 +flower_user: "{{ galaxy_user.name }}" +flower_group: "{{ galaxy_user.group }}" + +# PROFTPD specific setup +proftpd_galaxy_auth: no +proftpd_create_ftp_upload_dir: yes +galaxy_ftp_upload_dir: "{{ galaxy_config.galaxy.ftp_upload_dir }}" +proftpd_display_connect: | + {{ galaxy_users_domain }} FTP server + + Unauthorized access is prohibited +proftpd_galaxy_modules: + - mod_ldap.c + - mod_tls.c +proftpd_global_options: + - AllowOverwrite: 'on' + - AllowStoreRestart: 'on' + - PassivePorts: '56000 60000' +proftpd_options: + - AuthOrder: mod_ldap.c + - UseIPv6: 'off' + - RequireValidShell: 'off' + - User: "{{ galaxy_user_name }}" + - Group: "{{ galaxy_user_group_name }}" + - Port: '990' + - Umask: '037 037' + - DefaultRoot: "{{ galaxy_ftp_upload_dir }}/%u@{{ galaxy_users_domain }}" + - CreateHome: 'on 700 NoRootPrivs' +proftpd_conf_ssl_certificate: /etc/letsencrypt/live/{{ inventory_hostname }}/cert.pem +proftpd_conf_ssl_certificate_key: /etc/letsencrypt/live/{{ inventory_hostname }}/privkey.pem +proftpd_conf_ssl_certificate_type: 'EC' +proftpd_tls_protocol: TLSv1.2 TLSv1.3 +proftpd_tls_options: EnableDiags NoSessionReuseRequired UseImplicitSSL +proftpd_use_mod_tls_shmcache: false diff --git a/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml b/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml index d1c2920c..f1c98f7c 100644 --- a/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml +++ b/host_vars/galaxy-umsa.grid.cesnet.cz/vars.yml @@ -1,6 +1,7 @@ # where to put most of the data; we use RBD or NBD volumes rbd_mount_point: /rbd -galaxy_mutable_data_dir: "{{ rbd_mount_point }}/galaxy-umsa_data" +rbd_data_dir: "{{ rbd_mount_point }}/galaxy-umsa_data" +galaxy_mutable_data_dir: 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250GB +csnt_tool_config_file: +- "{{ galaxy_config_dir }}/local_tool_conf.xml" +- "{{ galaxy_root }}/server/config/tool_conf.xml.sample" +#csnt_edam_panel_views: operations,topics +#csnt_default_panel_view: all_tools +csnt_allow_path_paste: true +csnt_allow_user_deletion: true +csnt_enable_oidc: false +csnt_auth_config_file: "{{ galaxy_config_dir }}/auth_conf.xml" +csnt_toolbox_auto_sort: false +csnt_contact_email: regalaxy@rt.cesnet.cz +csnt_watch_job_rules: 'polling' # used to be auto +csnt_retry_job_output_collection: 5 +csnt_gunicorn_workers: 9 +csnt_handlers_processes: 4 +csnt_celery_memory_limit: 4 +csnt_celery_concurrency: 8 + +enable_tiaas: false +shed_tools_shadowing: false + +galaxy_user_name: galaxyelixir +galaxy_user_id: 2469 +galaxy_user_group_name: galaxyelixir +galaxy_user_group_gid: 10145 +galaxy_db_name: galaxyelixir + +galaxy_user_group: + name: "{{ galaxy_user_group_name }}" + gid: "{{ galaxy_user_group_gid }}" +galaxy_user: + name: "{{ galaxy_user_name }}" + uid: "{{ galaxy_user_id }}" + group: "{{ galaxy_user_group.name }}" + shell: /bin/bash + +galaxy_users_domain: repeatexplorer-elixir.cerit-sc.cz + +extra_certbot_domains: + - galaxy-re.grid.cesnet.cz + - galaxyelixir.vm.cesnet.cz + +#galaxy_commit_id: 72070dbd0a6d0f418d0b8f914825ea2b8e6a0a88 +galaxy_repo: https://github.com/CESNET/galaxy.git +galaxy_commit_id: release_25.0_regalaxy +galaxy_build_client: false + +galaxy_systemd_nofile_limit: 150000 + +# Postgresql DB backup using dump is not implemented in main branch (find the code in galaxy-re branch) +#postgresql_pg_dump_prefix: galaxy_db_backup +postgresql_backup_local_dir: "{{ galaxy_data_dir }}/backups/scripts" + +miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/conda" +miniconda_version: 23.5.2 # 23.5.0 # 4.12.0 +miniconda_channels: ['conda-forge', 'bioconda', 'iuc', 'r', 'anaconda', 'petrnovak', 'defaults'] +miniconda_base_env_packages: ['mamba'] + +pulsar: + user_name: galaxyelixir + nfs_home: brno11-elixir + nfs_prefix: pulsar-re + pbs_queue: galaxyre + pbs_gpu_queue: galaxy_gpu + +#Install pip docker package for ansible +pip_install_packages: + - docker + - python-ldap + +galaxy_config_files: + - src: files/galaxy/themes.yml + dest: "{{ galaxy_config.galaxy.themes_config_file }}" + - src: "files/{{ inventory_hostname }}/tpv_rules_local.yml" + dest: "{{ tpv_mutable_dir }}/tpv_rules_{{ inventory_hostname }}.yml" + - src: "{{ lookup('first_found', ['files/'+inventory_hostname+'/config/tool_conf.xml', 'files/galaxy/config/tool_conf.xml']) }}" + dest: "{{ galaxy_config_dir }}/tool_conf.xml" +# - src: files/galaxy/config/oidc_config.xml +# dest: "{{ galaxy_config_dir }}/oidc_config.xml" +# - src: "files/{{ inventory_hostname }}/all_tools.yml" +# dest: "{{ galaxy_config_dir }}/plugins/activities/all_tools.yml" + +galaxy_config_files_public: + - src: files/galaxy/config/sanitize_allowlist.txt + dest: "{{ galaxy_config.galaxy.sanitize_allowlist_file }}" + - src: templates/{{ inventory_hostname }}/static/welcome.html + dest: "{{ galaxy_mutable_config_dir }}/welcome.html" + - src: files/galaxy/static/usegalaxycz_straight.svg + dest: "{{ galaxy_server_dir }}/static/usegalaxycz_straight.svg" +# - src: files/galaxy/static/elixir_logo.png +# dest: "{{ galaxy_server_dir }}/static/elixir_logo.png" +# - src: files/galaxy/static/eu_msmt_eosc.svg +# dest: "{{ galaxy_server_dir }}/static/eu_msmt_eosc.svg" +# - src: files/galaxy/static/e-infra_logo.svg +# dest: "{{ galaxy_server_dir }}/static/e-infra_logo.svg" + - src: "files/{{ inventory_hostname }}/static/images/umbr_programs_icons/RE_header.png" + dest: "{{ galaxy_server_dir }}/static/images/umbr_programs_icons/RE_header.png" + - src: "files/{{ inventory_hostname }}/static/images/umbr_programs_icons/ELIXIR_CZECHREPUBLIC_white_background_small.png" + dest: "{{ galaxy_server_dir }}/static/images/umbr_programs_icons/ELIXIR_CZECHREPUBLIC_white_background_small.png" + - src: "files/{{ inventory_hostname }}/static/images/umbr_programs_icons/RE_logo.png" + dest: "{{ galaxy_server_dir }}/static/images/umbr_programs_icons/RE_logo.png" + +galaxy_config_templates: +# - src: templates/galaxy/config/reports.yml.j2 +# dest: "{{ galaxy_config.gravity.reports.config_file }}" +# - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/oidc_backends_config.xml.j2', 'templates/galaxy/config/oidc_backends_config.xml.j2']) }}" +# dest: "{{ galaxy_config_dir }}/oidc_backends_config.xml" + - src: "templates/{{ inventory_hostname }}/config/object_store_conf.xml.j2" + dest: "{{ galaxy_config.galaxy.object_store_config_file }}" + - src: "templates/{{ inventory_hostname }}/config/local_tool_conf.xml.j2" + dest: "{{ galaxy_config_dir }}/local_tool_conf.xml" + - src: templates/galaxy/config/tpv_rules_meta.yml.j2 + dest: "{{ tpv_mutable_dir }}/tpv_rules_meta.yml" + - src: "templates/galaxy/config/vault_conf.yml.j2" + dest: "{{ galaxy_config_dir }}/vault_conf.yml" + - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/auth_conf.xml.j2', 'templates/galaxy/config/auth_conf.xml.j2']) }}" + dest: "{{ galaxy_config.galaxy.auth_config_file }}" + - src: templates/galaxy/config/dependency_resolvers_conf.xml.j2 + dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}" + - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/file_source_templates.yml.j2', 'templates/galaxy/config/file_source_templates.yml.j2']) }}" + dest: "{{ galaxy_config_dir }}/file_source_templates.yml" + +galaxy_extra_dirs: + - "{{ galaxy_data_dir }}" + - "{{ tpv_config_dir }}" + - "{{ galaxy_config_dir }}/plugins/activities" + - "{{ galaxy_server_dir }}/static/images/umbr_programs_icons" + +rabbitmq_vhosts: + - pulsar # DEMON: used to be /pulsar and Pulsar config must be changed before (or right after) the change is deployed + - galaxy_internal + +tusd_instances: + - name: uploads + # user that tusd will run as + user: "{{ galaxy_user.name }}" + # group that tusd will run as + group: "{{ galaxy_user.group }}" + # args passed to tusd + args: + - -host=localhost + - "-port={{ galaxy_tusd_port }}" + - "-upload-dir={{ galaxy_tus_upload_store }}" + - "-hooks-http=https://{{ inventory_hostname }}{{ csnt_galaxy_url_prefix }}/api/upload/hooks" + - -hooks-http-forward-headers=X-Api-Key,Cookie + - -hooks-enabled-events pre-create + +flower_bind_interface: localhost +flower_port: 5555 +flower_user: "{{ galaxy_user.name }}" +flower_group: "{{ galaxy_user.group }}" + +# PROFTPD specific setup +proftpd_galaxy_auth: no +proftpd_create_ftp_upload_dir: yes +galaxy_ftp_upload_dir: "{{ galaxy_config.galaxy.ftp_upload_dir }}" +proftpd_display_connect: | + {{ galaxy_users_domain }} FTP server + + Unauthorized access is prohibited +proftpd_galaxy_modules: + - mod_ldap.c + - mod_tls.c +proftpd_global_options: + - AllowOverwrite: 'on' + - AllowStoreRestart: 'on' + - PassivePorts: '56000 60000' +proftpd_options: + - AuthOrder: mod_ldap.c + - UseIPv6: 'off' + - RequireValidShell: 'off' + - User: "{{ galaxy_user_name }}" + - Group: "{{ galaxy_user_group_name }}" + - Port: '990' + - Umask: '037 037' + - DefaultRoot: "{{ galaxy_ftp_upload_dir }}/%u@{{ galaxy_users_domain }}" + - CreateHome: 'on 700 NoRootPrivs' +proftpd_conf_ssl_certificate: /etc/letsencrypt/live/{{ inventory_hostname }}/cert.pem +proftpd_conf_ssl_certificate_key: /etc/letsencrypt/live/{{ inventory_hostname }}/privkey.pem +proftpd_conf_ssl_certificate_type: 'EC' +proftpd_tls_protocol: TLSv1.2 TLSv1.3 +proftpd_tls_options: EnableDiags NoSessionReuseRequired UseImplicitSSL +proftpd_use_mod_tls_shmcache: false diff --git a/host_vars/usegalaxy.cz/secret.yml b/host_vars/usegalaxy.cz/secret.yml index a76a3ff4..8ebebfba 100644 --- a/host_vars/usegalaxy.cz/secret.yml +++ b/host_vars/usegalaxy.cz/secret.yml @@ -1,213 +1,222 @@ $ANSIBLE_VAULT;1.1;AES256 -37373439383936643035356361336432383437616365653430623765313633663365396265393637 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f11e57b0..39ab1405 100644 --- a/host_vars/usegalaxy.cz/vars.yml +++ b/host_vars/usegalaxy.cz/vars.yml @@ -4,7 +4,8 @@ extra_certbot_domains: # where to put most of the data; we use RBD or NBD volumes rbd_mount_point: /rbd -galaxy_mutable_data_dir: "{{ rbd_mount_point }}/data" +rbd_data_dir: "{{ rbd_mount_point }}/data" +galaxy_mutable_data_dir: "{{ rbd_data_dir }}" galaxy_commit_id: release_25.0 galaxy_build_client: false diff --git a/hosts.yml b/hosts.yml index 61cb4bce..3971a1fc 100644 --- a/hosts.yml +++ b/hosts.yml @@ -8,6 +8,10 @@ galaxyservers: ansible_user: debian galaxy-qa2.galaxy.cloud.e-infra.cz: ansible_user: debian + galaxy-re.grid.cesnet.cz: + ansible_user: galaxy + repeatexplorer-elixir.cerit-sc.cz: + ansible_user: galaxy dbservers: children: galaxyservers @@ -18,6 +22,10 @@ production: ansible_user: galaxy-cz galaxy-umsa.grid.cesnet.cz: ansible_user: galaxy + galaxy-re.grid.cesnet.cz: + ansible_user: galaxy + repeatexplorer-elixir.cerit-sc.cz: + ansible_user: galaxy cloudservers: hosts: diff --git a/proftpd.yml b/proftpd.yml new file mode 100644 index 00000000..734f3347 --- /dev/null +++ b/proftpd.yml @@ -0,0 +1,34 @@ +--- +- hosts: galaxyservers + name: apt update, python, pip + become: true + become_user: root + pre_tasks: + - ansible.builtin.apt: + name: + - python3-pip + - python-is-python3 + update_cache: yes + when: ansible_os_family == 'Debian' + + - name: Install Dependencies + package: + name: ['acl', 'bzip2', 'git', 'make', 'tar', 'proftpd-mod-ldap'] + + roles: + - galaxyproject.proftpd + + post_tasks: + - name: Check if ProFTPd LDAP config exists + stat: + path: "templates/{{ inventory_hostname }}/config/proftpd_ldap.conf.j2" + register: proftpd_ldap_config + + - name: Configure ProFTPd LDAP option + template: + src: "templates/{{ inventory_hostname }}/config/proftpd_ldap.conf.j2" + dest: "{{ proftpd_config_include_dir }}/06_ldap.conf" + backup: yes + when: proftpd_ldap_config.stat.exists + notify: + - reload proftpd diff --git a/regalaxy_tools_install.yml b/regalaxy_tools_install.yml new file mode 100644 index 00000000..66ea90e7 --- /dev/null +++ b/regalaxy_tools_install.yml @@ -0,0 +1,29 @@ +--- +- hosts: galaxyservers + become: true + become_user: root + tasks: + ## Install required Galaxy tools + - name: Install required tools - create Ephemeris venv + ansible.builtin.shell: + cmd: python3 -m venv ~/ephemeris_venv + - name: Install required tools - install Ephemeris + ansible.builtin.shell: + cmd: source ~/ephemeris_venv/bin/activate && pip install ephemeris + - name: Install required tools - install Galaxy tools + ansible.builtin.shell: + cmd: ~/ephemeris_venv/bin/shed-tools install -g https://{{ inventory_hostname }}{{ csnt_galaxy_url_prefix }} -a {{ api_key }} -t {{ playbook_dir }}/files/{{ inventory_hostname }}/regalaxy_tool_list.yaml + when: "inventory_hostname in ['repeatexplorer-elixir.cerit-sc.cz', 'galaxy-re.grid.cesnet.cz']" + - name: Set-up pre-defined integrated_tool_panel config file on RE instance only + ansible.builtin.copy: + src: "{{ playbook_dir }}/files/{{ inventory_hostname }}/regalaxy_integrated_tool_panel.xml" + dest: "{{ galaxy_mutable_config_dir }}/integrated_tool_panel.xml" + owner: "{{ galaxy_user_name }}" + group: "{{ galaxy_user_group_name }}" + mode: '0644' + backup: true + when: "inventory_hostname in ['repeatexplorer-elixir.cerit-sc.cz', 'galaxy-re.grid.cesnet.cz']" + - name: Restart galaxy + become: true + become_user: root + ansible.builtin.command: galaxyctl restart diff --git a/roles/galaxyproject.proftpd/.github/workflows/lint.yml b/roles/galaxyproject.proftpd/.github/workflows/lint.yml new file mode 100644 index 00000000..a28475ec --- /dev/null +++ b/roles/galaxyproject.proftpd/.github/workflows/lint.yml @@ -0,0 +1,19 @@ +name: ansible-lint +on: [pull_request_target] +jobs: + ansible-lint: + name: ansible-lint + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + + - uses: actions/setup-python@v2 + with: + python-version: '3.x' + + - name: ansible-lint + uses: reviewdog/action-ansiblelint@v1 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + reporter: github-pr-review + filter_mode: nofilter diff --git a/roles/galaxyproject.proftpd/.github/workflows/release.yml b/roles/galaxyproject.proftpd/.github/workflows/release.yml new file mode 100644 index 00000000..66d74848 --- /dev/null +++ b/roles/galaxyproject.proftpd/.github/workflows/release.yml @@ -0,0 +1,32 @@ +--- +# This workflow requires a GALAXY_API_KEY secret present in the GitHub +# repository or organization. +# +# See: https://github.com/marketplace/actions/publish-ansible-role-to-galaxy +# See: https://github.com/ansible/galaxy/issues/46 + +name: Release + +'on': + push: + tags: + - '*' + +jobs: + release: + name: Release + runs-on: ubuntu-latest + steps: + - name: Check out the codebase. + uses: actions/checkout@v2 + + - name: Set up Python 3. + uses: actions/setup-python@v2 + with: + python-version: '3.x' + + - name: Install Ansible. + run: pip3 install ansible-core + + - name: Trigger a new import on Galaxy. + run: ansible-galaxy role import --api-key ${{ secrets.GALAXY_API_KEY }} $(echo ${{ github.repository }} | cut -d/ -f1) $(echo ${{ github.repository }} | cut -d/ -f2) --branch main diff --git a/roles/galaxyproject.proftpd/.travis.yml b/roles/galaxyproject.proftpd/.travis.yml new file mode 100644 index 00000000..36bbf620 --- /dev/null +++ b/roles/galaxyproject.proftpd/.travis.yml @@ -0,0 +1,29 @@ +--- +language: python +python: "2.7" + +# Use the new container infrastructure +sudo: false + +# Install ansible +addons: + apt: + packages: + - python-pip + +install: + # Install ansible + - pip install ansible + + # Check ansible version + - ansible --version + + # Create ansible.cfg with correct roles_path + - printf '[defaults]\nroles_path=../' >ansible.cfg + +script: + # Basic role syntax check + - ansible-playbook tests/test.yml -i tests/inventory --syntax-check + +notifications: + webhooks: https://galaxy.ansible.com/api/v1/notifications/ \ No newline at end of file diff --git a/roles/galaxyproject.proftpd/README.md b/roles/galaxyproject.proftpd/README.md new file mode 100644 index 00000000..a707a757 --- /dev/null +++ b/roles/galaxyproject.proftpd/README.md @@ -0,0 +1,192 @@ +proftpd +======= + +An [Ansible][ansible] role for installing and managing [proftpd][proftpd] servers. This role is designed to facilitate +the installation of ProFTPD for [Galaxy][galaxy] servers, and can configure ProFTPD to authenticate users against the +Galaxy PostgreSQL database. It can also configure TLS for FTPS (**note: NOT SFTP**). + +[ansible]: http://www.ansible.com/ +[proftpd]: http://www.proftpd.org/ +[galaxy]: http://galaxyproject.org/ + +Requirements +------------ + +This role installs ProFTPD from APT on Debian systems, EPEL on Enterprise Linux systems. Other systems and installation +methods are not supported. + +Role Variables +-------------- + +### Required variables ### + +**Variables required if `proftpd_galaxy_auth` is set**: + +- `proftpd_sql_db`: Database name to connect to for authentication info. Can include host information, see the [ProFTPD + SQLConnectInfo documentation for the "connection-info" parameter][proftpd-sql-connect-info] for details. +- `galaxy_user`: The name of the user running the Galaxy server. +- `galaxy_ftp_upload_dir`: Path to the Galaxy FTP upload directory, should match `ftp_upload_dir` in your Galaxy config. + - `proftpd_create_ftp_upload_dir` can be used to allow the role to create this with owner `galaxy_user` +- Additionally, you should set `User` and `Group` in `proftpd_options` to the user and group names of your Galaxy user. + +[proftpd-sql-connect-info]: http://www.proftpd.org/docs/contrib/mod_sql.html#SQLConnectInfo + +### Optional variables ### + +**Configuration** + +- `proftpd_options`: Set arbitrary options in the server config context of `proftpd.conf` (they will actually be set + in an included config file). This is a list of hashes (dictionaries) where keys are ProFTPD config options and values + are the option's value. Block tags such as `` are not supported. Options set in `proftpd_options` will + cause matching options in the base `proftpd.conf` file to be commented out. +- `proftpd_global_options`: Set arbitrary options in the `` context, same format as `proftpd_options`. Options + set in `proftpd_global_options` will ***NOT*** cause matching options in the base `proftpd.conf` file to be commented + out. + +**Enabling/disabling optional features** + +- `proftpd_galaxy_auth`: Attempt to authenticate users against a [Galaxy][galaxy] database. +- `proftpd_conf_ssl_certificate` and `proftpd_conf_ssl_certificate_key`: If set, enables TLS autoconfiguration. See + **FTP over SSL/TLS** below. + +**Display-on-connect message** + +- `proftpd_display_connect`: Message to display when users connect to the FTP server. This should be the message, not + the path to a file (this role will create the file and set [DisplayConnect][proftpd-display-connect] accordingly. +- `proftpd_display_connect_context` (default: `server`): If set to `global`, place the `ServerConnect` directive into a + `` block. If set to `server`, it is placed in the server context. + +[proftpd-display-connect]: http://www.proftpd.org/docs/directives/linked/config_ref_DisplayConnect.html + +**FTP over SSL/TLS** + +These variables control the use of TLS. If unset, TLS will not be enabled. See [mod_tls documentation][proftpd-mod-tls] +and Example Playbook for usage. + +- `proftpd_deploy_ssl`: Enable/disable copying local SSL keys to the remote host +- `proftpd_ssl_src_dir`: Where to copy SSL certificates from. +- `proftpd_conf_ssl_certificate`: Path on the remote host where the SSL certificate file should be placed. +- `proftpd_conf_ssl_certificate_type`: Type of the SSL certificate file, either RSA (default) or EC. +- `proftpd_conf_ssl_certificate_key`: Path on the remote host where the SSL private key file should be placed. +- `proftpd_conf_ssl_ca_certificate`: Path on the remote host where the SSL CA certificate chain should be placed. See + the [TLSCertificateChainFile][proftpd-tls-certificate-chain-file] documentation for the format of this file. +- `sslkeys`: A hash (dictionary) containing private keys. Keys are the filenames (without leading path elements) + matching `proftpd_conf_ssl_certificate_key`. + `proftpd_tls_protocol` (default: `TLSv1.1 TLSv1.2`): Set `TlSProtocol`. +- `proftpd_tls_cipher_suite` (default: + `EECDH+ECDSA+AESGCM:EECDH+aRSA+AESGCM:EECDH+ECDSA+SHA384:EECDH+ECDSA+SHA256:EECDH+aRSA+SHA384:EECDH+aRSA+SHA256:EECDH:EDH+aRSA:!RC4:!aNULL:!eNULL:!LOW:!3DES:!MD5:!EXP:!PSK:!SRP:!DSS`): + Set `TLSCipherSuite` +- `proftpd_tls_context` (default: `server`): If set to `global`, place TLS configuration directives that are + valid in the `` context into a `` block. If set to `server`, they are placed in the server context. +- `proftpd_use_mod_tls_shmcache`: (default: true): use TLSSessionCache, requires mod_tls_shmcache to be installed. +- `proftpd_tls_sesscache_path` (default: `/run/proftpd/sesscache`): Path to ProFTPD shm TLS session cache. +- `proftpd_tls_sesscache_timeout` (default: `300`): TLS session cache timeout (in seconds). +- `proftpd_tls_renegotiate`: (default: unset): TLS renegotation time (in seconds). +- `proftpd_tls_options`: (default: unset): Additional options for TLS, for example, `NoSessionReuseRequired`. + + +[proftpd-mod-tls]: http://www.proftpd.org/docs/contrib/mod_tls.html +[proftpd-tls-certificate-chain-file]: http://www.proftpd.org/docs/directives/linked/config_ref_TLSCertificateChainFile.html + +**Galaxy authentication options** + +These options are used if `proftpd_galaxy_auth` is set. + +- `proftpd_galaxy_options`: Additional options to set in the Galaxy authentication include file. Options set in + `proftpd_galaxy_options` will cause matching options in the base `proftpd.conf` file to be commented out. +- `proftpd_galaxy_default_options`: Default options set in the Galaxy authentication include file, you should only need + to explicitly set this if you need to remove items from the defaults. Matching options set in + `proftpd_galaxy_options` override the defaults. The defaults can be found in `defaults/main.yml`. +- `proftpd_sql_user` (default: the value of `galaxy_user`): Value of the `username` parameter to + [SQLConnectInfo][proftpd-sql-connect-info]. +- `proftpd_sql_password` (default: empty): Value of the `password` parameter to [SQLConnectInfo][proftpd-sql-connect-info]. +- `galaxy_user_uid` (default: looked up automatically): UID of the user running the Galaxy server. +- `galaxy_user_gid` (default: looked up automatically): GID of the user running the Galaxy server. +- `proftpd_galaxy_modules`: Default list of modules that will be loaded (uncommented in the base `proftpd.conf`) to + support Galaxy authentication, you should only need to explicitly set this if you need to change the default list. + The defaults can be found in `defaults/main.yml`. +- `proftpd_galaxy_auth_context` (default: `server`): If set to `global`, place Galaxy authentication directives + into a `` block. If set to `server`, they are placed in the server context. + +**Virtual servers/hosts** + +- `proftpd_virtualhosts`: Defines [ProFTPD virtual servers/hosts][proftpd-vhost]. If set, this should be a list where + each item is a hash (dict) with keys `id` (used in the vhost config file name), `address` (used in ``) and `options`, a list in the same format as `proftpd_options` below. Block tags such as `` are + not supported. + +It may be helpful to set `Port: 0` in `proftpd_options` to disable the server context when using virtual servers. + +[proftpd-vhost]: http://www.proftpd.org/docs/howto/Vhost.html + +Dependencies +------------ + +Although not a requirement, [geerlingguy.repo-epel][repo-epel] can be used to enable EPEL with Ansible. + +[repo-epel]: https://galaxy.ansible.com/geerlingguy/repo-epel/ + +Example Playbook +---------------- + +Install ProFTPD for Galaxy with TLS: + +```yaml +- name: Install and configure ProFTPD + hosts: ftpservers + remote_user: root + vars: + galaxy_user: galaxy + galaxy_ftp_upload: /srv/galaxy/ftp + proftpd_display_connect: | + example.org FTP server + + Unauthorized access is prohibited + proftpd_galaxy_auth: yes + proftpd_options: + - User: galaxy + - Group: galaxy + proftpd_sql_db: galaxy@/var/run/postgresql + proftpd_sql_user: galaxy + sslkeys: + 'snakeoil_privatekey.pem': | + -----BEGIN PRIVATE KEY----- + MIIE... + -----END PRIVATE KEY----- + proftpd_conf_ssl_certificate: snakeoil_cert.pem + proftpd_conf_ssl_certificate_key: snakeoil_privatekey.pem + proftpd_ssl_src_dir: files/ssl + + roles: + - galaxyproject.proftpd +``` + +If using virtual servers in conjunction with Galaxy authentication, [DefaultRoot][proftpd-default-root]'s `chroot(2)` +will fail when used inside of a ``. In this case, [mod_vroot][proftpd-mod-vroot] should be used (you may +find that it's already enabled for the server config context anyway). The following variables accomplish this: + +```yaml +proftpd_galaxy_auth_context: global +proftpd_galaxy_modules: + - mod_sql.c + - mod_sql_passwd.c + - mod_sql_postgres.c + - mod_vroot.c +proftpd_galaxy_options: + - VRootEngine: 'on' +``` + +[proftpd-default-root]: http://www.proftpd.org/docs/directives/linked/config_ref_DefaultRoot.html +[proftpd-mod-vroot]: http://www.castaglia.org/proftpd/modules/mod_vroot.html + +License +------- + +[Academic Free License ("AFL") v. 3.0][afl] + +[afl]: http://opensource.org/licenses/AFL-3.0 + +Author Information +------------------ + +[Nate Coraor](https://github.com/natefoo) diff --git a/roles/galaxyproject.proftpd/defaults/main.yml b/roles/galaxyproject.proftpd/defaults/main.yml new file mode 100644 index 00000000..3af4b141 --- /dev/null +++ b/roles/galaxyproject.proftpd/defaults/main.yml @@ -0,0 +1,34 @@ +--- +# defaults file for galaxyproject.proftpd + +proftpd_ssl_src_dir: files/ssl + +proftpd_galaxy_modules: + - mod_sql.c + - mod_sql_passwd.c + - mod_sql_postgres.c + +proftpd_galaxy_default_options: + - AuthOrder: mod_sql.c + - AuthPAM: 'off' + - Umask: '077' + - DefaultRoot: '~' + - CreateHome: on dirmode 700 + +proftpd_virtualhosts: [] + +proftpd_display_connect_context: 'server' +proftpd_tls_context: 'server' +proftpd_galaxy_auth_context: 'server' + +proftpd_tls_sesscache_timeout: 300 +proftpd_tls_renegotiate: null +proftpd_tls_options: null +proftpd_use_mod_tls_shmcache: true +proftpd_conf_ssl_certificate_type: 'RSA' + +proftpd_deploy_ssl: false + +proftpd_create_ftp_upload_dir: false + +__galaxy_user_name: "{{ galaxy_user.name | default(galaxy_user) }}" diff --git a/roles/galaxyproject.proftpd/handlers/main.yml b/roles/galaxyproject.proftpd/handlers/main.yml new file mode 100644 index 00000000..bb513597 --- /dev/null +++ b/roles/galaxyproject.proftpd/handlers/main.yml @@ -0,0 +1,12 @@ +--- +# handlers file for galaxyproject.proftpd + +- name: reload proftpd + service: + name: proftpd + state: reloaded + +- name: restart proftpd + service: + name: proftpd + state: restarted diff --git a/roles/galaxyproject.proftpd/meta/.galaxy_install_info b/roles/galaxyproject.proftpd/meta/.galaxy_install_info new file mode 100644 index 00000000..0b0d8daf --- /dev/null +++ b/roles/galaxyproject.proftpd/meta/.galaxy_install_info @@ -0,0 +1,2 @@ +install_date: 'Mon 19 May 2025 08:21:22 AM ' +version: 0.3.3 diff --git a/roles/galaxyproject.proftpd/meta/main.yml b/roles/galaxyproject.proftpd/meta/main.yml new file mode 100644 index 00000000..d03cfb8b --- /dev/null +++ b/roles/galaxyproject.proftpd/meta/main.yml @@ -0,0 +1,29 @@ +galaxy_info: + role_name: proftpd + namespace: galaxyproject + author: galaxyproject + description: Install and Configure ProFTPD (optionally, for Galaxy Servers). + company: The Galaxy Project + license: AFL v3.0 + min_ansible_version: 1.8 + platforms: + - name: Ubuntu + versions: + - trusty + - utopic + - vivid + - wily + - xenial + - yakkety + - name: Debian + versions: + - wheezy + - jessie + - stretch + - name: EL + versions: + - 7 + galaxy_tags: + - system + - ftp +dependencies: [] diff --git a/roles/galaxyproject.proftpd/tasks/debian.yml b/roles/galaxyproject.proftpd/tasks/debian.yml new file mode 100644 index 00000000..bea5370a --- /dev/null +++ b/roles/galaxyproject.proftpd/tasks/debian.yml @@ -0,0 +1,13 @@ +--- +# tasks file for galaxyproject.proftpd + +- name: Install ProFTPD (apt) + apt: + name: ['proftpd-basic', 'proftpd-mod-pgsql'] + +- name: Change Include + replace: + path: "{{ proftpd_config_file }}" + regexp: "Include {{ proftpd_config_dir }}/conf.d/$" + backup: yes + replace: "Include {{ proftpd_config_include_dir }}/*.conf" diff --git a/roles/galaxyproject.proftpd/tasks/galaxy_auth.yml b/roles/galaxyproject.proftpd/tasks/galaxy_auth.yml new file mode 100644 index 00000000..44e6a826 --- /dev/null +++ b/roles/galaxyproject.proftpd/tasks/galaxy_auth.yml @@ -0,0 +1,55 @@ +--- +# tasks file for galaxyproject.proftpd + +- name: Comment Galaxy proftpd.conf options + lineinfile: + name: "{{ proftpd_config_file }}" + regexp: '^(\s*{{ item | first }}\s.*)' + backrefs: yes + line: '#\1 # commented by Ansible' + backup: yes + with_flattened: + - "{{ proftpd_galaxy_default_options }}" + - "{{ proftpd_galaxy_options | default([]) }}" + notify: + - reload proftpd + +- name: Uncomment LoadModule directives for Galaxy + lineinfile: + name: "{{ proftpd_modules_config_file }}" + regexp: '^#\s*(LoadModule\s+{{ item }}.*)$' + backrefs: yes + line: '\1 # uncommented by Ansible' + backup: yes + with_items: "{{ proftpd_galaxy_modules }}" + notify: + - reload proftpd + +- name: Lookup Galaxy user UID + command: id -u {{ __galaxy_user_name }} + register: galaxy_user_uid_out + changed_when: no + when: galaxy_user_uid is undefined + +- name: Set Galaxy user UID fact + set_fact: + galaxy_user_uid: "{{ galaxy_user_uid_out.stdout }}" + when: galaxy_user_uid is undefined + +- name: Lookup Galaxy user GID + command: id -g {{ __galaxy_user_name }} + register: galaxy_user_gid_out + changed_when: no + when: galaxy_user_gid is undefined + +- name: Set Galaxy user GID fact + set_fact: + galaxy_user_gid: "{{ galaxy_user_gid_out.stdout }}" + when: galaxy_user_gid is undefined + +- name: Configure Galaxy authentication options + template: + src: galaxy_auth.conf.j2 + dest: "{{ proftpd_config_include_dir }}/10_galaxy_auth.conf" + notify: + - reload proftpd diff --git a/roles/galaxyproject.proftpd/tasks/main.yml b/roles/galaxyproject.proftpd/tasks/main.yml new file mode 100644 index 00000000..cdd9e3b5 --- /dev/null +++ b/roles/galaxyproject.proftpd/tasks/main.yml @@ -0,0 +1,85 @@ +--- +# tasks file for galaxyproject.proftpd + +- name: Set OS-specific variables + include_vars: "{{ ansible_os_family | lower }}.yml" + +- name: Include initial OS-specific tasks + include_tasks: "{{ ansible_os_family | lower}}.yml" + +- name: Comment base proftpd.conf options + lineinfile: + name: "{{ proftpd_config_file }}" + regexp: '^(\s*{{ item | first }}\s.*)' + backrefs: yes + line: '#\1 # commented by Ansible' + backup: yes + with_items: "{{ proftpd_options | default([]) }}" + notify: + - reload proftpd + +- name: Create base proftpd.conf options in include + template: + src: server.conf.j2 + dest: "{{ proftpd_config_include_dir }}/00_server.conf" + backup: yes + with_items: "{{ proftpd_options | default([]) }}" + notify: + - restart proftpd + +- name: Create DisplayConnect option in include if set + copy: + content: | + {% if proftpd_display_connect_context == 'global' %} + + {% endif -%} + DisplayConnect {{ proftpd_config_dir }}/proftpd_display_connect.txt + {% if proftpd_display_connect_context == 'global' %} + + {% endif -%} + dest: "{{ proftpd_config_include_dir }}/02_display_connect.conf" + when: proftpd_display_connect is defined + +- name: Copy DisplayConnect contents + copy: + content: "{{ proftpd_display_connect }}" + dest: "{{ proftpd_config_dir }}/proftpd_display_connect.txt" + when: proftpd_display_connect is defined + +- name: Create global config options in include + template: + src: global.conf.j2 + dest: "{{ proftpd_config_include_dir }}/03_global.conf" + backup: yes + when: proftpd_global_options is defined + notify: + - restart proftpd + +- name: Include tasks for TLS configuration + include_tasks: tls.yml + when: proftpd_conf_ssl_certificate is defined and proftpd_conf_ssl_certificate_key is defined + +- name: Include tasks for Galaxy authentication + include_tasks: galaxy_auth.yml + when: proftpd_galaxy_auth + +- name: Create VirtualHost configurations + template: + src: virtualhost.conf.j2 + dest: "{{ proftpd_config_include_dir }}/15_virtualhost_{{ item.id }}.conf" + backup: yes + with_items: "{{ proftpd_virtualhosts | default([]) }}" + +- name: Create parent ftp directory if needed + file: + path: "{{ galaxy_ftp_upload_dir }}" + owner: "{{ __galaxy_user_name }}" + mode: "0750" + state: directory + when: proftpd_create_ftp_upload_dir + +- name: Ensure ProFTPD is started and enabled + service: + name: proftpd + state: started + enabled: yes diff --git a/roles/galaxyproject.proftpd/tasks/redhat.yml b/roles/galaxyproject.proftpd/tasks/redhat.yml new file mode 100644 index 00000000..4ae0ece8 --- /dev/null +++ b/roles/galaxyproject.proftpd/tasks/redhat.yml @@ -0,0 +1,23 @@ +--- +# tasks file for galaxyproject.proftpd + +- name: Install ProFTPD (yum) + yum: + name: "{{ item }}" + with_items: + - proftpd + - proftpd-postgresql + - proftpd-utils + +- name: Add include statement to proftpd.conf + lineinfile: + name: "{{ proftpd_config_file }}" + insertafter: EOF + line: "Include {{ proftpd_config_include_dir }}/*.conf" + notify: + - reload proftpd + +- name: Create proftpd.conf include directory + file: + name: "{{ proftpd_config_include_dir }}" + state: directory diff --git a/roles/galaxyproject.proftpd/tasks/tls.yml b/roles/galaxyproject.proftpd/tasks/tls.yml new file mode 100644 index 00000000..d90e24d5 --- /dev/null +++ b/roles/galaxyproject.proftpd/tasks/tls.yml @@ -0,0 +1,45 @@ +--- +# tasks file for galaxyproject.proftpd + +- name: Configure TLS options + template: + src: tls.conf.j2 + dest: "{{ proftpd_config_include_dir }}/05_tls.conf" + backup: yes + notify: + - reload proftpd + +- name: Create TLS directories + file: + path: "{{ item | dirname }}" + state: directory + mode: 0755 + with_items: + - "{{ proftpd_conf_ssl_certificate | default('') }}" + - "{{ proftpd_conf_ssl_certificate_key | default('') }}" + when: proftpd_deploy_ssl + +- name: Install TLS CA certificate chain + copy: + src: "{{ proftpd_ssl_src_dir }}/{{ proftpd_conf_ssl_ca_certificate | basename }}" + dest: "{{ proftpd_conf_ssl_ca_certificate }}" + when: proftpd_deploy_ssl and proftpd_conf_ssl_ca_certificate is defined + notify: + - reload proftpd + +- name: Install TLS certificate + copy: + src: "{{ proftpd_ssl_src_dir }}/{{ proftpd_conf_ssl_certificate | basename }}" + dest: "{{ proftpd_conf_ssl_certificate }}" + when: proftpd_deploy_ssl + notify: + - reload proftpd + +- name: Install TLS private key + copy: + content: "{{ sslkeys[proftpd_conf_ssl_certificate_key | basename] }}" + dest: "{{ proftpd_conf_ssl_certificate_key }}" + mode: 0400 + when: proftpd_deploy_ssl + notify: + - reload proftpd diff --git a/roles/galaxyproject.proftpd/templates/galaxy_auth.conf.j2 b/roles/galaxyproject.proftpd/templates/galaxy_auth.conf.j2 new file mode 100644 index 00000000..f58daa12 --- /dev/null +++ b/roles/galaxyproject.proftpd/templates/galaxy_auth.conf.j2 @@ -0,0 +1,60 @@ +## +## This file is maintained by Ansible - CHANGES WILL BE OVERWRITTEN +## + +{% if proftpd_galaxy_auth_context == 'global' %} + +{% endif %} + +# Options from proftpd_galaxy_default_options +{% for pair in proftpd_galaxy_default_options -%} +{% for key in pair -%} +{{ key }} {{ pair[key] }} +{% endfor %} +{% endfor %} + +# Options from proftpd_galaxy_options +{% for pair in proftpd_galaxy_options | default([]) -%} +{% for key in pair -%} +{{ key }} {{ pair[key] }} +{% endfor %} +{% endfor %} + +# Allow users to overwrite and resume uploads +AllowOverwrite on +AllowStoreRestart on + +# Deny use of commands that allow modifying modification times and retrieving files + + DenyAll + + +# Basic module setup +SQLEngine on +SQLPasswordEngine on +SQLLogFile /var/log/proftpd/sql.log +SQLBackend postgres +SQLAuthenticate users + +# Database connection info +SQLConnectInfo {{ proftpd_sql_db }} {{ proftpd_sql_user | default(__galaxy_user_name) }} {{ proftpd_sql_password | default('') }} + +# Authenticate with PBKDF2, fall back to SHA1 +SQLAuthTypes PBKDF2 SHA1 +SQLPasswordPBKDF2 sql:/GetPBKDF2Params +SQLPasswordEncoding base64 + +# Set uid and gid of Galaxy user +SQLDefaultUID {{ galaxy_user_uid }} +SQLDefaultGID {{ galaxy_user_gid }} + +# Define named queries for user/salt lookups +SQLUserInfo custom:/LookupGalaxyUser +SQLPasswordUserSalt sql:/GetUserSalt +SQLNamedQuery GetPBKDF2Params SELECT "(CASE WHEN split_part(password, '$', 1) = 'PBKDF2' THEN UPPER(split_part(password, '$', 2)) ELSE 'SHA256' END), (CASE WHEN split_part(password, '$', 1) = 'PBKDF2' THEN split_part(password, '$', 3) ELSE '10000' END), 24 FROM galaxy_user WHERE email='%U'" +SQLNamedQuery GetUserSalt SELECT "(CASE WHEN split_part(password, '$', 1) = 'PBKDF2' THEN split_part(password, '$', 4) END) FROM galaxy_user WHERE email='%U'" +SQLNamedQuery LookupGalaxyUser SELECT "email, (CASE WHEN split_part(password, '$', 1) = 'PBKDF2' THEN split_part(password, '$', 5) ELSE encode(decode(password, 'hex'), 'base64') END),'{{ __galaxy_user_name }}','{{ __galaxy_user_name }}','{{ galaxy_ftp_upload_dir }}/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" + +{% if proftpd_galaxy_auth_context == 'global' %} + +{% endif %} diff --git a/roles/galaxyproject.proftpd/templates/global.conf.j2 b/roles/galaxyproject.proftpd/templates/global.conf.j2 new file mode 100644 index 00000000..c2b83c6e --- /dev/null +++ b/roles/galaxyproject.proftpd/templates/global.conf.j2 @@ -0,0 +1,11 @@ +## +## This file is maintained by Ansible - CHANGES WILL BE OVERWRITTEN +## + + +{% for pair in proftpd_global_options %} +{% for key in pair %} +{{ key }} {{ pair[key] }} +{% endfor %} +{% endfor %} + diff --git a/roles/galaxyproject.proftpd/templates/server.conf.j2 b/roles/galaxyproject.proftpd/templates/server.conf.j2 new file mode 100644 index 00000000..a7803826 --- /dev/null +++ b/roles/galaxyproject.proftpd/templates/server.conf.j2 @@ -0,0 +1,9 @@ +## +## This file is maintained by Ansible - CHANGES WILL BE OVERWRITTEN +## + +{% for pair in proftpd_options %} +{% for key in pair %} +{{ key }} {{ pair[key] }} +{% endfor %} +{% endfor %} diff --git a/roles/galaxyproject.proftpd/templates/tls.conf.j2 b/roles/galaxyproject.proftpd/templates/tls.conf.j2 new file mode 100644 index 00000000..238e3832 --- /dev/null +++ b/roles/galaxyproject.proftpd/templates/tls.conf.j2 @@ -0,0 +1,41 @@ +## +## This file is maintained by Ansible - CHANGES WILL BE OVERWRITTEN +## + +# Enable session reuse (must be in the server context) + +{% if proftpd_use_mod_tls_shmcache %} +LoadModule mod_tls_shmcache.c +TLSSessionCache shm:/file={{ proftpd_tls_sesscache_path }}&size=8388608 {{ proftpd_tls_sesscache_timeout }} +{% endif %} +{{ 'TLSRenegotiate ' ~ proftpd_tls_renegotiate if proftpd_tls_renegotiate else '' }} + +{% if proftpd_tls_context == 'global' %} + +{% endif %} + +# Enable TLS +LoadModule mod_tls.c +TLSEngine on +TLSLog {{ proftpd_log_dir | default('/var/log/proftpd') }}/tls.log + +# Limit allowed TLS protocols +TLSProtocol {{ proftpd_tls_protocol | default('TLSv1.1 TLSv1.2') }} + +# Require TLS +TLSRequired {{ proftpd_tls_required | default('on') }} + +{{ 'TLSOptions ' ~ proftpd_tls_options if proftpd_tls_options else '' }} + +# Limit TLS ciphers +TLSServerCipherPreference on +TLSCipherSuite {{ proftpd_tls_cipher_suite | default('EECDH+ECDSA+AESGCM:EECDH+aRSA+AESGCM:EECDH+ECDSA+SHA384:EECDH+ECDSA+SHA256:EECDH+aRSA+SHA384:EECDH+aRSA+SHA256:EECDH:EDH+aRSA:!RC4:!aNULL:!eNULL:!LOW:!3DES:!MD5:!EXP:!PSK:!SRP:!DSS') }} + +# Cert/Key +{{ 'TLSCertificateChainFile ' + proftpd_conf_ssl_ca_certificate if proftpd_conf_ssl_ca_certificate is defined else '' }} +TLS{{ proftpd_conf_ssl_certificate_type }}CertificateFile {{ proftpd_conf_ssl_certificate }} +TLS{{ proftpd_conf_ssl_certificate_type }}CertificateKeyFile {{ proftpd_conf_ssl_certificate_key }} + +{% if proftpd_tls_context == 'global' %} + +{% endif %} diff --git a/roles/galaxyproject.proftpd/templates/virtualhost.conf.j2 b/roles/galaxyproject.proftpd/templates/virtualhost.conf.j2 new file mode 100644 index 00000000..c0281fc2 --- /dev/null +++ b/roles/galaxyproject.proftpd/templates/virtualhost.conf.j2 @@ -0,0 +1,11 @@ +## +## This file is maintained by Ansible - CHANGES WILL BE OVERWRITTEN +## + + +{% for pair in item.options -%} +{% for key in pair -%} + {{ key }} {{ pair[key] }} +{% endfor %} +{% endfor %} + diff --git a/roles/galaxyproject.proftpd/tests/inventory b/roles/galaxyproject.proftpd/tests/inventory new file mode 100644 index 00000000..d18580b3 --- /dev/null +++ b/roles/galaxyproject.proftpd/tests/inventory @@ -0,0 +1 @@ +localhost \ No newline at end of file diff --git a/roles/galaxyproject.proftpd/tests/test.yml b/roles/galaxyproject.proftpd/tests/test.yml new file mode 100644 index 00000000..c8541711 --- /dev/null +++ b/roles/galaxyproject.proftpd/tests/test.yml @@ -0,0 +1,5 @@ +--- +- hosts: localhost + remote_user: root + roles: + - galaxyproject.proftpd \ No newline at end of file diff --git a/roles/galaxyproject.proftpd/vars/debian.yml b/roles/galaxyproject.proftpd/vars/debian.yml new file mode 100644 index 00000000..4d897722 --- /dev/null +++ b/roles/galaxyproject.proftpd/vars/debian.yml @@ -0,0 +1,7 @@ +--- + +proftpd_config_dir: /etc/proftpd +proftpd_config_file: "{{ proftpd_config_dir }}/proftpd.conf" +proftpd_modules_config_file: "{{ proftpd_config_dir }}/modules.conf" +proftpd_config_include_dir: "{{ proftpd_config_dir }}/conf.d" +proftpd_tls_sesscache_path: /run/proftpd_sesscache diff --git a/roles/galaxyproject.proftpd/vars/main.yml b/roles/galaxyproject.proftpd/vars/main.yml new file mode 100644 index 00000000..56eb2d45 --- /dev/null +++ b/roles/galaxyproject.proftpd/vars/main.yml @@ -0,0 +1,2 @@ +--- +# vars file for galaxyproject.proftpd diff --git a/roles/galaxyproject.proftpd/vars/redhat.yml b/roles/galaxyproject.proftpd/vars/redhat.yml new file mode 100644 index 00000000..04d54858 --- /dev/null +++ b/roles/galaxyproject.proftpd/vars/redhat.yml @@ -0,0 +1,7 @@ +--- + +proftpd_config_dir: /etc +proftpd_config_file: "{{ proftpd_config_dir }}/proftpd.conf" +proftpd_modules_config_file: "{{ proftpd_config_dir }}/proftpd.conf" +proftpd_config_include_dir: "{{ proftpd_config_dir }}/proftpd.conf.d" +proftpd_tls_sesscache_path: /run/proftpd/sesscache diff --git a/templates/galaxy-re.grid.cesnet.cz/config/auth_conf.xml.j2 b/templates/galaxy-re.grid.cesnet.cz/config/auth_conf.xml.j2 new file mode 100644 index 00000000..0f4afe43 --- /dev/null +++ b/templates/galaxy-re.grid.cesnet.cz/config/auth_conf.xml.j2 @@ -0,0 +1,146 @@ + + + + ldap + + + + + + Challenge + + + True + + + + + False + + + False + + + False + + + False + + + ldaps://perun.cesnet.cz:636 + + + + + OPT_X_TLS_REQUIRE_CERT=OPT_X_TLS_ALLOW + + + True + + + False + + + + + + + + + + + + + login;x-ns-einfra + dc=perun,dc=cesnet,dc=cz + + (&(objectclass=perunUser)(login;x-ns-einfra={username})) + perunGroupId={{ ldap_perun_group_id }},perunVoId={{ ldap_perun_vo_id }},dc=perun,dc=cesnet,dc=cz + + + + + + + perunUserId={{ ldap_perun_user_id }},ou=People,dc=perun,dc=cesnet,dc=cz + {{ ldap_user_password }} + + + + + + + {dn} + {password} + {username} + {username}@repeatexplorer-elixir.cerit-sc.cz + {gid} + + + + + + + + diff --git a/templates/galaxy-re.grid.cesnet.cz/config/local_tool_conf.xml.j2 b/templates/galaxy-re.grid.cesnet.cz/config/local_tool_conf.xml.j2 new file mode 100644 index 00000000..fa5dfdc9 --- /dev/null +++ b/templates/galaxy-re.grid.cesnet.cz/config/local_tool_conf.xml.j2 @@ -0,0 +1,8 @@ + + +
+
+ diff --git a/templates/galaxy-re.grid.cesnet.cz/config/object_store_conf.xml.j2 b/templates/galaxy-re.grid.cesnet.cz/config/object_store_conf.xml.j2 new file mode 100644 index 00000000..dc79aba6 --- /dev/null +++ b/templates/galaxy-re.grid.cesnet.cz/config/object_store_conf.xml.j2 @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + diff --git a/templates/galaxy-re.grid.cesnet.cz/config/proftpd_ldap.conf.j2 b/templates/galaxy-re.grid.cesnet.cz/config/proftpd_ldap.conf.j2 new file mode 100644 index 00000000..c7135ae7 --- /dev/null +++ b/templates/galaxy-re.grid.cesnet.cz/config/proftpd_ldap.conf.j2 @@ -0,0 +1,38 @@ +# +# Proftpd sample configuration for LDAP authentication. +# +# (This is not to be used if you prefer a PAM-based LDAP authentication) +# + +##DEMON: I put it here, because it should be somewhere if proftpd_galaxy_auth is not defined (i.e., used) +# Deny use of commands that allow modifying modification times and retrieving files + + DenyAll + + + +# Enable LDAP module +LoadModule mod_ldap.c + +# +# This is used for encrypted LDAPS connections +# +LDAPLog /var/log/proftpd/ldap.log +LDAPServer ldaps://perun.metacentrum.cz/??sub +LDAPBindDN "perunUserId={{ ldap_perun_user_id }},ou=People,dc=perun,dc=cesnet,dc=cz" "{{ ldap_user_password }}" +LDAPUsers "dc=perun,dc=cesnet,dc=cz" "(&(login=%v)(objectclass=perunUser)(memberof=perunGroupId={{ ldap_perun_group_id }},perunVoId={{ ldap_perun_vo_id }},dc=perun,dc=cesnet,dc=cz))" +LDAPSearchScope subtree +#set where to find attr +LDAPAttr uid login;x-ns-einfra +LDAPAttr uidNumber uidNumber;x-ns-cerit +#set uid to galaxyelixir and gid to meta +LDAPDefaultUID {{ galaxy_user_id }} +LDAPForceDefaultUID on +LDAPDefaultGID {{ galaxy_user_group_gid }} +LDAPForceDefaultGID on +#set homedir creation +LDAPGenerateHomedir on 700 +LDAPGenerateHomedirPrefix {{ galaxy_ftp_upload_dir }}/%u@{{ galaxy_users_domain }} +LDAPForceGeneratedHomedir on +LDAPGenerateHomedirPrefixNoUsername on + diff --git a/templates/galaxy-re.grid.cesnet.cz/static/welcome.html b/templates/galaxy-re.grid.cesnet.cz/static/welcome.html new file mode 100644 index 00000000..8bacb2a2 --- /dev/null +++ b/templates/galaxy-re.grid.cesnet.cz/static/welcome.html @@ -0,0 +1,118 @@ + + +

+

+

Developed and maintained by the Laboratory of Molecular Cytogenetics, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic

+

This RepeatExplorer Galaxy portal is a part of services provided by ELIXIR (European Research Infrastructure for Biological Information). Please acknowledge this fact in your publications by adding a statement: “Computational resources for RepeatExplorer analysis were provided by the ELIXIR-CZ project (LM2023055), part of the international ELIXIR infrastructure.”

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+

ELIXIR

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+
+

Contact information

+

If you need help, need to increase a data quota, or want to report a problem, please email the server administrator. If you encounter an error while running a tool, please report a bug using the bug icon in the dataset history.

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+

Resources

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REXdb

+

RepeatExplorer2, DANTE and DANTE_LTR tools use the REXdb database. REXdb is a comprehensive database of conserved protein domain sequences extracted from all types transposable elementa found in plants. More information about REXdb can be found in related publication or in REXdb repository.

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REXdb versions included in the server:

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    +
  • Viridiplantae 4.0 - The latest version, updated on 2024-11-06. This version covers additional sequences and lineages from non-angiosperm species including gymnosperms, ferns, and mosses
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  • Viridiplantae 3.0 - This version mainly covers domains extracted from elements of angiosperm species
    • +
  • Viridiplantae 2.2
    • +
  • Metazoa 3.0
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  • Metazoa 2.0
    • +
+
+

Common Use Cases of RepeatExplorer Server

+

The RepeatExplorer server provides a suite of tools designed for the comprehensive analysis of repetitive DNA sequences in genomic data. Here are the most common use cases for utilizing these tools:

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    +

  • Annotation of repeats directly from low coverage sequencing: It can be accomplished using the RepeatExplorer2 tool. This approach is ideal for initial exploration and annotation of repetitive sequences using low coverage data (refer to protocol 1 in the step-by-step protocols above).

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  • Comparative analysis of repeats in multiple species from low coverage sequencing reads: Use protocol 2 for analyzing repetitive DNA across different species.

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  • Tandem repeat annotation from low coverage sequencing: If your focus is primarily on tandem repeats, use the Tandem Repeat Analyzer tool (TAREAN). See protocol 3 in the step-by-step protocols for details.

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  • Chip-Seq experiments: The ChIP-seq Mapper tool identifies centromeric repeats from CENH3 ChIP-seq data without the need for a complete genome assembly, leveraging assembled contigs from repeat clusters as a reference for mapping reads and highlighting significantly enriched repeats (refer to protocol 4).

    • +

  • Annotation of full-Length LTR-retrotransposons in genome assemblies: For detailed annotation of LTR-retrotransposons within assembled genomes, use the DANTE + DANTE_LTR tools. (see https://github.com/kavonrtep/dante_ltr for details)

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  • Annotation of tandem repeats in genome assemblies: The TideCluster tools are designed for the annotation and analysis of tandem repeats within genome assemblies (see https://github.com/kavonrtep/TideCluster for more information).

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How to Cite

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Novak, P., Neumann, P., Macas, J. (2020) – Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols 15:3745–3776.

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Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29:792-793.

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Classification of repetitive elements using REXdb:

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Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) – Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA 10:1.

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The principle of repeat identification implemented in the RepeatExplorer:

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Novak, P., Neumann, P., Macas, J. (2010) - Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11:378.

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Using TAREAN for satellite repeat detection and characterization:

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Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) - TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acid Research 45:e111

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Novak, P., Hostakova, N., Neumann, P., Macas, J. (2024) – DANTE and DANTE_LTR: computational pipelines implementing lineage-centered annotation of LTR-retrotransposons in plant genomes. See our preprint on bioRxiv

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+

Terms of Use

+

RepeatExplorer is provided as free, public, Internet accessible service, in the hope that it will be useful, but WITHOUT ANY WARRANTY. Data transfer are encrypted, but data storage is not. If there are restrictions on the way your research data can be stored and used, please consult your local institutional review board or the project PI before uploading it to this Galaxy server. If you have protected data, large data storage requirements, or short deadlines you are encouraged to set up your own local Galaxy instance with RepeatExplorer Alternatively, you can install only RepeatExplorer and use its command line version. If you need help with RepeatExplorer or you want to report a problem, please email the server administrator.

\ No newline at end of file diff --git a/templates/galaxy/config/auth_conf.xml.j2 b/templates/galaxy/config/auth_conf.xml.j2 new file mode 100644 index 00000000..9a90ba93 --- /dev/null +++ b/templates/galaxy/config/auth_conf.xml.j2 @@ -0,0 +1,2 @@ + + diff --git a/templates/galaxy/config/dependency_resolvers_conf.xml.j2 b/templates/galaxy/config/dependency_resolvers_conf.xml.j2 new file mode 100644 index 00000000..29a93812 --- /dev/null +++ b/templates/galaxy/config/dependency_resolvers_conf.xml.j2 @@ -0,0 +1,2 @@ + + diff --git a/templates/galaxy/config/proftpd_ldap.conf.j2 b/templates/galaxy/config/proftpd_ldap.conf.j2 new file mode 100644 index 00000000..8a9620b4 --- /dev/null +++ b/templates/galaxy/config/proftpd_ldap.conf.j2 @@ -0,0 +1,9 @@ +# +# Proftpd sample configuration for LDAP authentication. +# +# (This is not to be used if you prefer a PAM-based LDAP authentication) +# + + + + diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index c5c3cdbb..cf4b994c 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -3,16 +3,21 @@ global: tools: default: + abstract: True cores: 1 - mem: cores * 4 + mem: "int(cores * 4)" env: + # Ensuring a consistent collation environment is good for reproducibility. + - name: LC_ALL + value: C - name: GALAXY_SLOTS - value: "{cores}" + value: "{int(cores)}" - name: GALAXY_MEMORY_MB value: "{int(mem)*1000}" context: walltime: 24 scratch: 50 + queue: "{{ pulsar.pbs_queue }}" scheduling: require: - pulsar @@ -45,6 +50,7 @@ tools: walltime: 24 scratch: 25 gpu_mem: 16 + queue: "{{ pulsar.pbs_gpu_queue }}" scheduling: require: - rosettafold @@ -55,7 +61,7 @@ tools: require: - singularity - .*testing.*: + testing.*: cores: 1 mem: 1 context: @@ -66,7 +72,7 @@ tools: # Only allow the tool to be executed if the user is an admin admin_users = app.config.admin_users # last line in block must evaluate to a value - which determines whether the TPV if conditional matches or not - not user or (user.email not in admin_users and user.email not in ['galaxy@cesnet.cz','galaxy@usegalaxy.cz']) + not user or (user.email not in admin_users and user.email not in ['galaxy@cesnet.cz','galaxy@usegalaxy.cz','galaxyelixir@repeatexplorer-elixir.cerit-sc.cz']) fail: Unauthorized. Only admins can execute this tool. - id: resource_params_defined @@ -85,6 +91,7 @@ tools: walltime: 24 scratch: 100 gpu_mem: 16 + queue: "{{ pulsar.pbs_gpu_queue }}" env: MPLCONFIGDIR: "$SCRATCHDIR" ALPHAFOLD_DB: "/scratch.ssd/galaxyeu/permanent/alphafold.db" @@ -102,40 +109,87 @@ tools: context: walltime: 48 - toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/.*: + .*/megahit/.*: cores: 16 mem: 256 context: walltime: 96 scratch: 100 + queue: elixircz + scheduling: + require: + - highmem - __SET_.*: + .*/fastq_groomer/.*: + cores: 1 + mem: 16 + + __DATA_FETCH__: inherits: local_running_tools __IMPORT_HISTORY__: - inherits: local_running_tools + inherits: local_running_tools + + __EXPORT_HISTORY__: + inherits: local_running_tools + + __SET_.*: + inherits: local_running_tools "Show .*": - inherits: local_running_tools + inherits: local_running_tools "Remove .*": - inherits: local_running_tools + inherits: local_running_tools cat1: - inherits: local_running_tools + inherits: local_running_tools .*/data_manager_.*: inherits: local_sing_running_tools + ebi_sra_main: + inherits: local_sing_running_tools + + sra_source: + inherits: local_sing_running_tools + + gff2bed1: + inherits: local_sing_running_tools + +# bed2gff1: +# inherits: local_sing_running_tools + + Extract_features1: + inherits: local_sing_running_tools + + export_remote: + inherits: local_sing_running_tools + + roles: training.*: max_cores: 4 - max_mem: max_cores * 4 # TODO check multiplier + max_mem: "int(max_cores * 3.8)" scheduling: require: - - pulsar - training + # DEMON: For testing purposes, set whatever you want here when needed + test.*: + scheduling: + require: + - test + + highmem: + mem: 512 + context: + queue: elixircz + scheduling: + require: + - highmem + + destinations: tpv_local: runner: local_runner @@ -157,8 +211,6 @@ destinations: singularity_enabled: true singularity_default_container_id: "/cvmfs/singularity.galaxyproject.org/all/python:3.8.3" env: - # Ensuring a consistent collation environment is good for reproducibility. - LC_ALL: C # The cache directory holds the docker containers that get converted SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/" # Singularity uses a temporary directory to build the squashfs filesystem @@ -166,15 +218,22 @@ destinations: scheduling: require: - local - prefer: - singularity - tpv_pulsar: + # DEMON: this is the common pulsar configuration + tpv_pulsar_common: + abstract: true runner: pulsar_tpv_runner - max_accepted_cores: 128 - max_accepted_mem: 512 + # DEMON: sum of cores in one VM (i.e., elmo5-*) + max_accepted_cores: 32 + # DEMON: sum of memory in one VM (i.e., elmo5-*) + max_accepted_mem: 185 + # DEMON: sum of GPUs in one VM (i.e., elmo5-*) max_accepted_gpus: 0 - max_cores: 16 + # DEMON: max number of cores one job will get + max_cores: 32 + # DEMON: max memory one job will get max_mem: 180 + # DEMON: max number of gpus one job will get max_gpus: 0 params: default_file_action: remote_rsync_transfer @@ -190,7 +249,27 @@ destinations: ssh_key: | {{ pulsar_ssh_key | indent(width=8,first=False) }} outputs_to_working_directory: false - submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_queue }} -N {{ pulsar.nfs_prefix }}_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N {{ pulsar.nfs_prefix }}_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + env: + TMPDIR: $SCRATCHDIR + TMP: $SCRATCHDIR + TEMP: $SCRATCHDIR + scheduling: + require: + - pulsar + # DEMON: this one uses conda dependences (no singularity) + tpv_pulsar_conda: + inherits: tpv_pulsar_common + scheduling: + require: + - conda + reject: + - singularity + # DEMON: this one uses singularity exclusively (consider it as a default configuration) + tpv_pulsar: + inherits: tpv_pulsar_common + runner: pulsar_tpv_runner + params: singularity_enabled: true singularity_volumes: "$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/cvmfs/data.galaxyproject.org:ro,$SCRATCHDIR:rw" singularity_default_container_id: "/cvmfs/singularity.galaxyproject.org/all/python:3.8.3" @@ -198,16 +277,13 @@ destinations: --env JAVA_OPTS="-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR" --env JAVA_TOOL_OPTIONS="-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR" env: - LC_ALL: C - TMPDIR: $SCRATCHDIR - TMP: $SCRATCHDIR - TEMP: $SCRATCHDIR SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/" SINGULARITY_TMPDIR: $SCRATCHDIR XDG_CACHE_HOME: $SCRATCHDIR scheduling: - require: - - pulsar + prefer: + - singularity + # DEMON: Some JAVA tools just ignore the traditional way of limiting the allowed memory tpv_pulsar_nasty_java: inherits: tpv_pulsar runner: pulsar_tpv_runner @@ -216,31 +292,49 @@ destinations: scheduling: require: - nasty-java + # DEMON: Pulsar for AlphaFold because of special configuration tpv_pulsar_alphafold: inherits: tpv_pulsar + runner: pulsar_tpv_runner max_accepted_gpus: 1 max_gpus: 1 - runner: pulsar_tpv_runner params: - singularity_run_extra_arguments: '--nv' + singularity_run_extra_arguments: '--nv --env SCRATCHDIR="$SCRATCHDIR" --env SCRATCH=$SCRATCHDIR' singularity_volumes: '$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,$SCRATCHDIR,$ALPHAFOLD_DB:/data/2.3:ro' - submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {{ pulsar.pbs_gpu_queue }} -N {{ pulsar.nfs_prefix }}_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N {{ pulsar.nfs_prefix }}_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" scheduling: require: - alphafold + # DEMON: Pulsar for TIAAS. It could schedule to a private small queue to ensure the participants of some course will not have to wait tpv_pulsar_training: inherits: tpv_pulsar runner: pulsar_tpv_runner scheduling: require: - training -# usegalaxy.cz specific: + # DEMON: For tools/users that need more memory for their jobs. Current approach is to add the user to highmem role for some time. Better approach would be to implement rescheduling for PBS over Pulsar runner + tpv_pulsar_highmem: + inherits: tpv_pulsar + runner: pulsar_tpv_runner + max_accepted_mem: 512 + max_mem: 512 + scheduling: + require: + - highmem + # DEMON: For testing purposes, set whatever you want here when needed + tpv_pulsar_test: + inherits: tpv_pulsar + runner: pulsar_tpv_runner + scheduling: + require: + - test +# DEMON: usegalaxy.cz specific destinations (unfortunately, because of inheritance they cannot be in placed in instance-specific TPV config file) tpv_pulsar_rosettafold: inherits: tpv_pulsar runner: pulsar_tpv_runner params: singularity_enabled: false - submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q galaxy_gpu@pbs-m1.metacentrum.cz -N pulsar_cz_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" + submit_native_specification: "-l select=1:ncpus={int(cores)}:mem={int(mem)}gb:scratch_local={int(scratch)}gb:ngpus={int(gpus)}:gpu_mem={int(gpu_mem)}gb -l walltime={int(walltime)}:00:00 -q {queue} -N pulsar_cz_j{job.id}__{tool.id if '/' not in tool.id else tool.id.split('/')[-2]+'_v'+tool.id.split('/')[-1]}__{user.username if user and hasattr(user, 'username') else 'anonymous'}" scheduling: require: - rosettafold diff --git a/templates/nginx/galaxy.j2 b/templates/nginx/galaxy.j2 index 2de0bb11..4cade006 100644 --- a/templates/nginx/galaxy.j2 +++ b/templates/nginx/galaxy.j2 @@ -1,12 +1,25 @@ +#DEMON: clearing user names of accidental blanks in postfix +map $remote_user $remote_user_clean { + "~(?[^ \t]+)" $name; +} + upstream galaxy { server {{ galaxy_config.gravity.gunicorn.bind }}; # Or if you serve galaxy at a path like http(s)://fqdn/galaxy # Remember to set galaxy_url_prefix in the galaxy.yml file. # server {{ galaxy_config.gravity.gunicorn.bind }}:/galaxy; + #DEMON: This hint actually didn't work back at time of setting this for RE Galaxy } server { +{% block root %} + {% if csnt_galaxy_url_prefix != '' %} + # main website serving as crossroad for registration and access to Galaxy + root /srv/welcome_page/welcome_page.clean; + {% endif %} +{% endblock root %} + # Listen on port 443 listen 443 ssl default_server; listen [::]:443 ssl default_server; @@ -24,10 +37,14 @@ server { proxy_read_timeout 600s; client_body_timeout 3600s; client_header_timeout 600s; +#DEMON: not sure if still need this. It used to be an optimization of data transfer from Pulsar to Galaxy for huge html_output_files (e.g., RepEx, TaReAn) but I can see, it's used only for TUS now +# proxy_request_buffering off; +# proxy_buffering off; +# proxy_http_version 1.1; # The most important location block, by default all requests are sent to gunicorn # If you serve galaxy at a path like /galaxy, change that below (and all other locations!) - location / { + location {{ csnt_galaxy_url_prefix }}/ { # Remove any forwarded headers that clients might have sent proxy_set_header X-Forwarded-For ""; proxy_set_header X-Forwarded-Proto ""; @@ -41,11 +58,24 @@ server { proxy_set_header Upgrade $http_upgrade; proxy_set_header Connection "upgrade"; + # DEMON: temp solution because of a bug + rewrite ^/galaxy/galaxy(.*)$ /galaxy$1 last; + # This is the backend to send the requests to proxy_pass http://galaxy; + + # Set up the error page directive for 403 errors + error_page 403 /warning.html; + error_page 502 /warning.html; } - location /api/upload/resumable_upload { + # Serve the warning page + location = /warning.html { + root /var/www/html; # Path to your warning page + internal; # Prevent direct access to this page + } + + location {{ csnt_galaxy_url_prefix }}/api/upload/resumable_upload { # Disable request and response buffering proxy_request_buffering off; proxy_buffering off; @@ -60,11 +90,18 @@ server { client_max_body_size 0; proxy_pass http://localhost:{{ galaxy_tusd_port }}/files; } + #DEMON: hopefully just a temporary hack, need to find out how to configure TUSd hook via ansible role + #DEMON: Not sure if we still need this + location /api/upload/hooks { + rewrite ^/api/upload/hooks(.*)$ {{ csnt_galaxy_url_prefix }}/api/upload/hooks$1 break; + proxy_pass https://{{ inventory_hostname }}; + } + # Static files can be more efficiently served by Nginx. Why send the # request to Gunicorn which should be spending its time doing more useful # things like serving Galaxy! - location /static { + location {{ csnt_galaxy_url_prefix }}/static { alias {{ galaxy_server_dir }}/static; expires 24h; } @@ -72,19 +109,19 @@ server { # In Galaxy instances started with run.sh, many config files are # automatically copied around. The welcome page is one of them. In # production, this step is skipped, so we will manually alias that. - location /static/welcome.html { + location {{ csnt_galaxy_url_prefix }}/static/welcome.html { alias {{ galaxy_mutable_config_dir }}/welcome.html; expires 24h; } # serve visualization and interactive environment plugin static content - location ~ ^/plugins/(?[^/]+?)/((?[^/_]*)_?)?(?[^/]*?)/static/(?.*?)$ { + location ~ ^{{ csnt_galaxy_url_prefix }}/plugins/(?[^/]+?)/((?[^/_]*)_?)?(?[^/]*?)/static/(?.*?)$ { alias {{ galaxy_server_dir }}/config/plugins/$plug_type/; try_files $vis_d/${vis_d}_${vis_name}/static/$static_file $vis_d/static/$static_file =404; } - location /robots.txt { + location {{ csnt_galaxy_url_prefix }}/robots.txt { alias {{ galaxy_server_dir }}/static/robots.txt; } @@ -95,6 +132,9 @@ server { location /_x_accel_redirect { internal; alias /; + # Add upstream response headers that would otherwise be omitted + add_header Access-Control-Allow-Origin $upstream_http_access_control_allow_origin; + add_header Access-Control-Allow-Methods $upstream_http_access_control_allow_methods; } # Support click-to-run in the GTN-in-Galaxy Webhook @@ -149,4 +189,11 @@ server { {% endif %} {% endblock tiaas %} +{% block rewrite %} + {% if csnt_galaxy_url_prefix != '' %} + # redirect /prefix -> /prefix/ + rewrite ^{{ csnt_galaxy_url_prefix }}$ {{ csnt_galaxy_url_prefix }}/ last; + {% endif %} +{% endblock rewrite %} + } diff --git a/templates/nginx/redirect-ssl.j2 b/templates/nginx/redirect-ssl.j2 index ff9d783b..2c592cb6 100644 --- a/templates/nginx/redirect-ssl.j2 +++ b/templates/nginx/redirect-ssl.j2 @@ -26,7 +26,7 @@ server { server_name "{{ host }}"; location /.well-known/acme-challenge/ { - root /srv/nginx/_well-known_root; + root {{ certbot_well_known_root }}; } location / { diff --git a/templates/repeatexplorer-elixir.cerit-sc.cz/config/auth_conf.xml.j2 b/templates/repeatexplorer-elixir.cerit-sc.cz/config/auth_conf.xml.j2 new file mode 100644 index 00000000..0f4afe43 --- /dev/null +++ b/templates/repeatexplorer-elixir.cerit-sc.cz/config/auth_conf.xml.j2 @@ -0,0 +1,146 @@ + + + + ldap + + + + + + Challenge + + + True + + + + + False + + + False + + + False + + + False + + + ldaps://perun.cesnet.cz:636 + + + + + OPT_X_TLS_REQUIRE_CERT=OPT_X_TLS_ALLOW + + + True + + + False + + + + + + + + + + + + + login;x-ns-einfra + dc=perun,dc=cesnet,dc=cz + + (&(objectclass=perunUser)(login;x-ns-einfra={username})) + perunGroupId={{ ldap_perun_group_id }},perunVoId={{ ldap_perun_vo_id }},dc=perun,dc=cesnet,dc=cz + + + + + + + perunUserId={{ ldap_perun_user_id }},ou=People,dc=perun,dc=cesnet,dc=cz + {{ ldap_user_password }} + + + + + + + {dn} + {password} + {username} + {username}@repeatexplorer-elixir.cerit-sc.cz + {gid} + + + + + + + + diff --git a/templates/repeatexplorer-elixir.cerit-sc.cz/config/local_tool_conf.xml.j2 b/templates/repeatexplorer-elixir.cerit-sc.cz/config/local_tool_conf.xml.j2 new file mode 100644 index 00000000..fa5dfdc9 --- /dev/null +++ b/templates/repeatexplorer-elixir.cerit-sc.cz/config/local_tool_conf.xml.j2 @@ -0,0 +1,8 @@ + + +
+
+ diff --git a/templates/repeatexplorer-elixir.cerit-sc.cz/config/object_store_conf.xml.j2 b/templates/repeatexplorer-elixir.cerit-sc.cz/config/object_store_conf.xml.j2 new file mode 100644 index 00000000..dc79aba6 --- /dev/null +++ b/templates/repeatexplorer-elixir.cerit-sc.cz/config/object_store_conf.xml.j2 @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + + + + + + diff --git a/templates/repeatexplorer-elixir.cerit-sc.cz/config/proftpd_ldap.conf.j2 b/templates/repeatexplorer-elixir.cerit-sc.cz/config/proftpd_ldap.conf.j2 new file mode 100644 index 00000000..c7135ae7 --- /dev/null +++ b/templates/repeatexplorer-elixir.cerit-sc.cz/config/proftpd_ldap.conf.j2 @@ -0,0 +1,38 @@ +# +# Proftpd sample configuration for LDAP authentication. +# +# (This is not to be used if you prefer a PAM-based LDAP authentication) +# + +##DEMON: I put it here, because it should be somewhere if proftpd_galaxy_auth is not defined (i.e., used) +# Deny use of commands that allow modifying modification times and retrieving files + + DenyAll + + + +# Enable LDAP module +LoadModule mod_ldap.c + +# +# This is used for encrypted LDAPS connections +# +LDAPLog /var/log/proftpd/ldap.log +LDAPServer ldaps://perun.metacentrum.cz/??sub +LDAPBindDN "perunUserId={{ ldap_perun_user_id }},ou=People,dc=perun,dc=cesnet,dc=cz" "{{ ldap_user_password }}" +LDAPUsers "dc=perun,dc=cesnet,dc=cz" "(&(login=%v)(objectclass=perunUser)(memberof=perunGroupId={{ ldap_perun_group_id }},perunVoId={{ ldap_perun_vo_id }},dc=perun,dc=cesnet,dc=cz))" +LDAPSearchScope subtree +#set where to find attr +LDAPAttr uid login;x-ns-einfra +LDAPAttr uidNumber uidNumber;x-ns-cerit +#set uid to galaxyelixir and gid to meta +LDAPDefaultUID {{ galaxy_user_id }} +LDAPForceDefaultUID on +LDAPDefaultGID {{ galaxy_user_group_gid }} +LDAPForceDefaultGID on +#set homedir creation +LDAPGenerateHomedir on 700 +LDAPGenerateHomedirPrefix {{ galaxy_ftp_upload_dir }}/%u@{{ galaxy_users_domain }} +LDAPForceGeneratedHomedir on +LDAPGenerateHomedirPrefixNoUsername on + diff --git a/templates/repeatexplorer-elixir.cerit-sc.cz/static/welcome.html b/templates/repeatexplorer-elixir.cerit-sc.cz/static/welcome.html new file mode 100644 index 00000000..090a489a --- /dev/null +++ b/templates/repeatexplorer-elixir.cerit-sc.cz/static/welcome.html @@ -0,0 +1,121 @@ + + +

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Developed and maintained by the Laboratory of Molecular Cytogenetics, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic

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This RepeatExplorer Galaxy portal is a part of services provided by ELIXIR (European Research Infrastructure for Biological Information). Please acknowledge this fact in your publications by adding a statement: “Computational resources for RepeatExplorer analysis were provided by the ELIXIR-CZ project (LM2023055), part of the international ELIXIR infrastructure.”

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ELIXIR

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12th Repeat Explorer Workshop, May 27–29, 2025

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Join us at the 12th Repeat Explorer Workshop, May 27–29, 2025, in České Budějovice, Czech Republic. The workshop will focus on “Repetitive DNA Annotation in Genome Assemblies” and will include theoretical sessions, hands-on training, and a mini-conference for presenting research on repeat analysis in plant and animal genomes. For more detailed information, please visit our workshop page: Workshop Details.

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Contact information

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If you need help, need to increase a data quota, or want to report a problem, please contact server administrator. If you encounter an error while running a tool, please report a bug using the bug icon in the dataset history.

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Resources

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REXdb

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RepeatExplorer2, DANTE and DANTE_LTR tools use the REXdb database. REXdb is a comprehensive database of conserved protein domain sequences extracted from all types transposable elementa found in plants. More information about REXdb can be found in related publication or in REXdb repository.

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REXdb versions included in the server:

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  • Viridiplantae 4.0 - The latest version, updated on 2024-11-06. This version covers additional sequences and lineages from non-angiosperm species including gymnosperms, ferns, and mosses
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  • Viridiplantae 3.0 - This version mainly covers domains extracted from elements of angiosperm species
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  • Viridiplantae 2.2
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  • Metazoa 3.0
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  • Metazoa 2.0
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Common Use Cases of RepeatExplorer Server

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The RepeatExplorer server provides a suite of tools designed for the comprehensive analysis of repetitive DNA sequences in genomic data. Here are the most common use cases for utilizing these tools:

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  • Annotation of repeats directly from low coverage sequencing: It can be accomplished using the RepeatExplorer2 tool. This approach is ideal for initial exploration and annotation of repetitive sequences using low coverage data (refer to protocol 1 in the step-by-step protocols above).

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  • Comparative analysis of repeats in multiple species from low coverage sequencing reads: Use protocol 2 for analyzing repetitive DNA across different species.

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  • Tandem repeat annotation from low coverage sequencing: If your focus is primarily on tandem repeats, use the Tandem Repeat Analyzer tool (TAREAN). See protocol 3 in the step-by-step protocols for details.

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  • Chip-Seq experiments: The ChIP-seq Mapper tool identifies centromeric repeats from CENH3 ChIP-seq data without the need for a complete genome assembly, leveraging assembled contigs from repeat clusters as a reference for mapping reads and highlighting significantly enriched repeats (refer to protocol 4).

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  • Annotation of full-Length LTR-retrotransposons in genome assemblies: For detailed annotation of LTR-retrotransposons within assembled genomes, use the DANTE + DANTE_LTR tools. (see https://github.com/kavonrtep/dante_ltr for details)

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  • Annotation of tandem repeats in genome assemblies: The TideCluster tools are designed for the annotation and analysis of tandem repeats within genome assemblies (see https://github.com/kavonrtep/TideCluster for more information).

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How to Cite

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Novak, P., Neumann, P., Macas, J. (2020) – Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols 15:3745–3776.

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Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29:792-793.

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Classification of repetitive elements using REXdb:

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Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) – Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA 10:1.

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The principle of repeat identification implemented in the RepeatExplorer:

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Novak, P., Neumann, P., Macas, J. (2010) - Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11:378.

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Using TAREAN for satellite repeat detection and characterization:

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Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) - TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acid Research 45:e111

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Novak, P., Hostakova, N., Neumann, P., Macas, J. (2024) – DANTE and DANTE_LTR: computational pipelines implementing lineage-centered annotation of LTR-retrotransposons in plant genomes. bioRxiv doi: https://doi.org/10.1101/2024.04.17.589915

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Terms of Use

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RepeatExplorer is provided as free, public, Internet accessible service, in the hope that it will be useful, but WITHOUT ANY WARRANTY. Data transfer are encrypted, but data storage is not. If there are restrictions on the way your research data can be stored and used, please consult your local institutional review board or the project PI before uploading it to this Galaxy server. If you have protected data, large data storage requirements, or short deadlines you are encouraged to set up your own local Galaxy instance with RepeatExplorer Alternatively, you can install only RepeatExplorer and use its command line version. If you need help with RepeatExplorer or you want to report a problem, please contact server administrator.

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