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Unresolved tool containers #2773

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afgane opened this issue Jan 6, 2020 · 1 comment
Closed

Unresolved tool containers #2773

afgane opened this issue Jan 6, 2020 · 1 comment

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@afgane
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afgane commented Jan 6, 2020

I was excited to try out the new dependency resolution UI in 20.01 but it also shined a light on just how many tools do not have a container to resolve to. Out of 1,660 tools available on the CVMFS, 570 do not resolve (34%). Admittedly, many are from non-IUC repos but I'm wondering what is the missing link and how can we increase the number of resolved containers?

Below is a list of currently unresolved containers. It would be helpful if those familiar with the tools could please edit the list to cross out the tools that are known not working or not necessary and ideally highlight the popular ones.

Further, could someone please detail the steps necessary to fix one of these tools? Sorry for a high-level question but I'm (still) not sure how the generic automated tool containerization pipeline works, especially when it comes to non-IUC repos.

Finally, I manually cross-searched a few tools listed in #2701, but didn't run into any overlap. I'm guessing the tools listed below will show up as missing tests only after a corresponding container has been created?

  • MAF_To_BED1
  • toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0
  • toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_extract_primers/1.0.0
  • toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_reheader/0.1.9
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_calc_freq/1.0.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_sfffiles/1.1.0
  • gff_filter_by_attribute
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfannotategenotypes/vcfannotategenotypes/0.0.3
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sort_seqs/1.25.0
  • CONVERTER_bed_to_bgzip_0
  • CONVERTER_vcf_to_vcf_bgzip_0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/1.126.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.24.0
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/0.0.3
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_seqs/1.20.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_draw_variants/1.1.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_oturep/1.23.0
  • CONVERTER_fasta_to_len
  • CONVERTER_vcf_to_tabix_0
  • toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatcompat/1.0.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_mantel/1.20.0
  • toolshed.g2.bx.psu.edu/repos/devteam/variant_select/gatk_variant_select/0.0.3
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_reorder/1.0.0
  • toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_make_phylip/1.1.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_single/1.20.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_rank_terms/1.0.0
  • toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_mergebedgraph/0.1.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otus/1.20.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.24.1
  • toolshed.g2.bx.psu.edu/repos/iuc/vegan_rarefaction/vegan_rarefaction/2.4-3
  • toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.7.6.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.24.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.24.1
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_tree_shared/1.26.0
  • toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.2
  • toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.1
  • MAF_To_Fasta1
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_offspring_heterozygosity/1.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/kraken/kraken/1.1.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_sum_gd_snp/1.0.0
  • toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.9
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_seqs/1.20.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.126.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_bin/1.21.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulabels/1.27.0
  • toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1
  • toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.0
  • toolshed.g2.bx.psu.edu/repos/devteam/count_gff_features/count_gff_features/0.2
  • toolshed.g2.bx.psu.edu/repos/devteam/count_gff_features/count_gff_features/0.1
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/0.0.3
  • toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_alignment/1.9.7.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_classic/1.88.0
  • CONVERTER_interval_to_bgzip_0
  • genomespace_push
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_design/1.20.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_multiintersectbed/0.1.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/1.126.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_groups/1.21.0
  • mousemine
  • toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.1
  • CONVERTER_interval_to_bed6_0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.126.0
  • toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0
  • Interval_Maf_Merged_Fasta2
  • toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/0.0.7
  • toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/0.0.6
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_filter_gd_snp/1.2.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_libshuff/1.20.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_otu/1.21.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/1.126.0
  • vcf_to_maf_customtrack1
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_screen_seqs/1.24.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_add_fst_column/1.1.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_find_intervals/1.0.0
  • CONVERTER_gff_to_interval_index_0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/1.136.0
  • toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.3
  • qual_stats_boxplot
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/0.0.3
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_phylo_diversity/1.21.0
  • toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_genomecoveragebed_histogram/0.1.0
  • hgv_linkToGProfile
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_coremicrobiome/1.27.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/1.126.0
  • toolshed.g2.bx.psu.edu/repos/devteam/microsats_alignment_level/microsats_align1/1.0.0
  • random_lines1
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_metastats/1.21.0
  • toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/1.9.7.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/1.136.0
  • Interval2Maf_pairwise1
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_prepare_population_structure/1.0.0
  • CONVERTER_vcf_to_bgzip_0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_reverse_seqs/1.20.0
  • toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatpurity/1.0.0
  • toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/fetchflank/1.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/1.126.0
  • Condense characters1
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_cluster_kegg/1.0.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_seqs/1.21.0
  • toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.9
  • gene2exon1
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_heatmap_sim/1.24.0
  • lped2pbedconvert
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_flows/1.23.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_make_gd_file/1.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/1.136.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_indicator/1.22.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_tree/1.21.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_filter_gd_snp/1.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/1.126.0
  • yeastmine
  • Filter1
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/1.126.0
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/0.0.3
  • toolshed.g2.bx.psu.edu/repos/nick/duplex/duplex/0.5
  • toolshed.g2.bx.psu.edu/repos/nick/duplex/duplex/0.3
  • toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2
  • ucsc_table_direct1
  • toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_covstats/0.1.9
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_tagbed/2.24.0
  • lped2fpedconvert
  • toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/sequence_content_trimmer/0.1
  • CONVERTER_gff_to_fli_0
  • toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/heteroprob/2.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/1.126.0
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/0.0.3
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_calc_freq/1.2.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_multiple_to_gd_genotype/1.0.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_nmds/1.20.0
  • MAF_filter
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_amova/1.20.0
  • toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_inbreeding_and_kinship/1.0.0
  • toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.1.6.0
  • wormbase
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_bin_seqs/1.21.0
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/0.0.3
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_uchime/1.23.0
  • modENCODEworm
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_select_snps/1.0.0
  • Grep1
  • toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1
  • toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.2
  • toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.3.0
  • CONVERTER_vcf_bgzip_to_tabix_0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sens_spec/1.20.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.24.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_weighted/1.26.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unifrac_unweighted/1.26.0
  • toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatellite/1.0.0
  • modENCODEfly
  • toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.2.01
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-mpa-report/1.1.0
  • toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-mpa-report/1.1.1
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_groups/1.25.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_new_oscar/1.0.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_specify/1.1.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/1.136.0
  • toolshed.g2.bx.psu.edu/repos/engineson/multiqc/multiqc/1.0.0.0
  • toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_split/1.28.0
  • flymine
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_normalize_shared/1.21.0
  • toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/PEsortedSAM2readprofile/1.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/sicer/peakcalling_sicer/0.0.2
  • Interval2Maf1
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/0.0.3
  • toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/0.0.3
  • toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_search/1.9.7.0
  • gff2bed1
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/0.0.3
  • maf_limit_size1
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_biom/1.26.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/1.126.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/1.136.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_dpmix/1.1.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_split_abund/1.20.0
  • toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.2
  • toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.1
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_phylogenetic_tree/1.0.0
  • CONVERTER_fastq_to_fqtoc0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddCommentsToBam/1.136.0
  • toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.1
  • toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_groups/1.24.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx/1.0.0
  • hgv_david
  • toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0
  • toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_convert/0.1.9
  • toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/1.136.0
  • toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_relabund/1.21.0
  • toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/0.0.3
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/0.0.4
  • toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.4.6.p5
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.136.0
  • toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0
  • hgv_beam
  • toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_delcall/0.1.9
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster_fragments/1.21.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_hcluster/1.20.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/1.136.0
  • toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.9
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_seqs/1.20.0
  • hgv_lps
  • toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1
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  • aggregate_scores_in_intervals2
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  • Summary_Statistics1
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  • Show beginning1
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  • ChangeCase
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  • gff_filter_by_feature_count
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  • tabular_to_dbnsfp
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  • __EXPORT_HISTORY__
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  • hgv_pass
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  • cat1
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  • CONVERTER_encodepeak_to_tabix_0
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  • Remove beginning1
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  • wiggle2simple1
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  • secure_hash_message_digest
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  • CONVERTER_fasta_to_tabular
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  • MAF_Limit_To_Species1
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  • CONVERTER_maf_to_fasta_0
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  • comp1
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  • wc_gnu
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  • IMPORT_HISTORY
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  • Cut1
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  • addValue
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  • pbed2ldindepconvert
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  • CONVERTER_len_to_linecount
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  • MAF_Thread_For_Species1
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  • Sff_extractor
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  • gtf_filter_by_attribute_values_list
  • eupathdb
  • bed2gff1
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  • Extract genomic DNA 1
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  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.24.0
  • MAF_To_Interval1
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_unique_seqs/1.21.0
  • toolshed.g2.bx.psu.edu/repos/iuc/vegan_diversity/vegan_diversity/2.4-3
  • CONVERTER_encodepeak_to_bgzip_0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_homova/1.20.0
  • Paste1
  • toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_masking/1.9.7.0
  • toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.8.24
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_find_intervals/1.1.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.126.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_tree/1.25.0
  • toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/0.0.6
  • toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.3.3
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chop_seqs/1.20.0
  • toolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/heatmap_1/1.0.0
  • toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_corr_axes/1.21.0
  • toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/GenotypeSTR/2.0.0
  • toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sffinfo/1.25.0
  • trimmer
  • hgv_ldtools
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_diversity_pi/1.1.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/1.136.0
  • toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_genomecoveragebed_bedgraph/0.1.0
  • toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0
  • toolshed.g2.bx.psu.edu/repos/iuc/vegan_fisher_alpha/vegan_fisher_alpha/2.4-3
  • toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_chimera_detection/1.9.7.0
  • toolshed.g2.bx.psu.edu/repos/devteam/kraken/kraken/1.1.2
  • toolshed.g2.bx.psu.edu/repos/iuc/cwpair2/cwpair2/1.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0
  • zebrafishmine
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_prepare_population_structure/1.2.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bed12tobed6/2.24.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_flows/1.27.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/1.126.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/1.126.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_trim_seqs/1.25.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/1.126.0
  • toolshed.g2.bx.psu.edu/repos/devteam/kraken_filter/kraken-filter/1.1.0
  • toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.0.6
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_gd_snp2vcf/1.1.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/1.126.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReplaceSamHeader/1.126.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_groups/1.25.0
  • toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_classify_seqs/1.22.0
  • join1
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_make_phylip/1.0.0
  • ebi_sra_main
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_average_fst/1.3.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_fastq_info/1.25.0
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/0.0.3
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_average_fst/1.1.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_single/1.21.0
  • toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.9
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_deunique_seqs/1.21.0
  • toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.0.0
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_seqs/1.20.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_shhh_seqs/1.24.0
  • toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_rarefaction_shared/1.27.0
  • DATA_FETCH
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_raxml/1.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/1.136.0
  • toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_coverage_distributions/1.0.0
  • MAF_Reverse_Complement_1
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_merge_files/1.20.0
  • CONVERTER_interval_to_tabix_0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_check/1.21.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.136.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_ccode/1.21.0
  • toolshed.g2.bx.psu.edu/repos/iuc/genetrack/genetrack/1.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotate/0.1
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/1.136.0
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_pathway_image/1.1.0
  • toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.1
  • toolshed.g2.bx.psu.edu/repos/devteam/cd_hit_dup/cd_hit_dup/0.0.1
  • hgv_gpass
  • intermine
  • Extract_features1
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_population_structure/1.0.0
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/0.0.3
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/1.126.0
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/1.136.0
  • toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/Profilegenerator/2.0.0
  • toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.0.6
  • genomespace_exporter
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/1.136.0
  • toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_sorting/1.9.7.0
  • maf_by_block_number1
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.24.0
  • toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.1
  • toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2
  • toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_specify/1.0.0
  • CONVERTER_picard_interval_list_to_bed6
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.24.0
  • genomespace_importer
  • toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.24.0
  • maf_stats1
  • toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar/1.126.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_single/1.21.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_shared/1.27.0
  • toolshed.g2.bx.psu.edu/repos/gregory-minevich/check_snpeff_candidates/check_snpeff_candidates/1.0.0
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otulabels/1.27.0
  • toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1
  • mergeCols1
  • toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.0
  • toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1
  • toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_group/1.20.0
  • master2pgSnp
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/0.0.3
  • toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/0.0.3
  • toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
  • CONVERTER_bed_to_gff_0
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mvdbeek commented Jan 7, 2020

A high-level view for building containers for Galaxy tools is this:
If it is a single package requirement in bioconda, the bioconda build process will publish a container.
If it is a single package requirement from conda-forge, or if multiple-package are required we use planemo-monitor against a list of known galaxy tool repos (any repo can be added to https://github.com/galaxyproject/planemo-monitor) to create PRs against https://github.com/BioContainers/multi-package-containers/, which in turn will build and publish those containers. This has some limitations, see below.

Some of the IUC tools listed here are not the latest version (at least bedtools), I don't think we have the resources to build and make sure containers work for old versions, at least at this point. Once things are smooth for all the latest versions we could consider running planemo-monitor against the tools on CVMFS.

A quick look at the converters suggests they don't have an annotated requirement, so that'd be a first step, that's a Galaxy issue. Once they do they will be built through planemo-monitor (https://github.com/galaxyproject/planemo-monitor/blob/master/repositories01.list#L1).

We also need to roll out a new planemo version that will build single-requirement containers and other improvements, but that's depending on galaxyproject/planemo#978,
which probably would build the rest of the IUC tools on your list that are at the latest version but that are not in #2701.

For non-IUC tools you could run planemo-monitor yourself (if you install planemo from master), but I think you should wait until we have a new planemo release, since the build process would probably result in many slightly broken containers right now (BioContainers/multi-package-containers#940 for some things that are still left to do).

almahmoud pushed a commit to almahmoud/multi-package-containers that referenced this issue Jan 7, 2020
Combinations for a large set of tools
5f9adcd 
xref: galaxyproject/tools-iuc#2773

List of tools this PR address and their requirements:
P.S.: Only extracted the tools having 2+ requirements. Let me know if I should add the single-requirement tool dependencies here too. Eg:

toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_otulabels/1.27.0 
mothur @1.33

toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1  
diamond @0.8.24

toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.0 
krona @2.6

-------------------------

toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.0.0  
gnu_coreutils @8.22
gnu_sed @4.2.2-sandbox

toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/1.136.0 
picard @1.136
R @3.1.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy0 
snpsift @4.3.1t
coreutils @8.25
perl @5.26

toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1 
snpsift @4.3.1t
coreutils @8.25
perl @5.26

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_stacking_ensemble_models/sklearn_stacking_ensemble_models/0.2.0  
python @3.6
Galaxy-ML @0.7.12

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.0.2  
R @3.0.3
deseq2 @1.2.10
diffbind @1.8.3

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_binlinks/0.69.8+galaxy1  
circos @0.69.8
python @2.7
bcbiogff @0.6.4
biopython @1.70
pybigwig @0.3.13
circos-tools @0.23

toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_resample/0.69.8+galaxy1  
circos @0.69.8
python @2.7
bcbiogff @0.6.4
biopython @1.70
pybigwig @0.3.13
circos-tools @0.23

toolshed.g2.bx.psu.edu/repos/iuc/variant_analyzer/read2mut/1.0.0  
python @2.7
matplotlib @1.4.0
pysam @0.15
xlsxwriter @1.1.0

toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/2.15  
bowtie @1.1.2
networkx @1.10
dunovo @2.15

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_numeric_clustering/sklearn_numeric_clustering/1.0.7.12 
python @3.6
Galaxy-ML @0.7.12

toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy1  
circos @0.69.8
python @2.7
bcbiogff @0.6.4
biopython @1.70
pybigwig @0.3.13
circos-tools @0.23

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/1.136.0 
picard @1.136
R @3.1.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.7.12 
python @3.6
Galaxy-ML @0.7.12

toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/1.0.1  
R @3.1.2
cummeRbund @2.8.2

toolshed.g2.bx.psu.edu/repos/tyty/structurefold/react_cal_pipeline/1.0  
biopython @1.61
numpy @1.7.1

toolshed.g2.bx.psu.edu/repos/iuc/duplex_family_size_distribution/fsd_regions/1.0.0  
python @2.7
matplotlib @1.4.0
pysam @0.15

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_refinepeak/2.1.0.20151222.0  
macs2 @2.1.0.20151222
numpy @1.7.1
scipy @0.12.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.0.0 
gnu_coreutils @8.22
gnu_sed @4.2.2-sandbox

toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.2  
bwa @0.7.12
samtools @1.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/iuc/vegan_diversity/vegan_diversity/0.0.2  
R @3.2.1
vegan @2.3-0

toolshed.g2.bx.psu.edu/repos/iuc/vegan_diversity/vegan_diversity/0.0.3  
R @3.2.1
vegan @2.3-0
r-vegan @2.3_0

toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/0.7.6 
bowtie2 @2.2.5
samtools @0.1.18
networkx @1.9
dunovo @0.7.6

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy0 
snpsift @4.3.1t
coreutils @8.25
perl @5.26

toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.1  
numpy @1.7.1
pyBamParser @0.0.1
pyBamTools @0.0.1

toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.2  
numpy @1.7.1
pyBamParser @0.0.1
pyBamTools @0.0.2

toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.7.2  
bzip2 @1.0.6
salmon @0.7.2

toolshed.g2.bx.psu.edu/repos/tyty/structurefold/get_read_pipeline/1.0 
biopython @1.61
numpy @1.7.1
samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.3  
bowtie2 @2.2.4
samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.4  
bowtie2 @2.2.4
samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1 
bwa @0.7.12
samtools @1.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgbroadcall/2.1.0.20140616.0  
macs2 @2.1.0
numpy @1.7.1
scipy @0.12.0
gnu_awk @4.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/devteam/best_regression_subsets/BestSubsetsRegression1/1.0.0 
numpy @1.7.1
rpy @1.0.3

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.9  
rpy @1.0.3
limma @3.25.3
biopython @1.65

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.2  
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toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3  
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toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.1  
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python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_data_preprocess/sklearn_data_preprocess/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/iuc/duplex_family_size_distribution/td/1.0.0 
python @2.7
matplotlib @1.4.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/iuc/charts/charts/1.0.1  
r-getopt @1.20.0
r-matrix @1.2-12

Count1  
coreutils @8.30
python @3.7

toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1  
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numpy @1.7.1
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/guru-ananda/karyotype_plot/karyotype_Plot_1/1.0.0  
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gtools @3.4.1

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toolshed.g2.bx.psu.edu/repos/devteam/bamleftalign/bamleftalign/0.0.2  
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toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy1 
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python @2.7
bcbiogff @0.6.4
biopython @1.70
pybigwig @0.3.13
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.1.0 
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toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_pairwise_metrics/sklearn_pairwise_metrics/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/0.69.8+galaxy1 
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python @2.7
bcbiogff @0.6.4
biopython @1.70
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toolshed.g2.bx.psu.edu/repos/iuc/variant_analyzer/mut2sscs/1.0.0  
python @2.7
matplotlib @1.4.0
pysam @0.15

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.1.0.20140616.0  
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python @2.7.10
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toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.0.0 
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toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.4  
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samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/iuc/transit_hmm/transit_hmm/3.0.1+galaxy1  
transit @3.0.1
python @3.7

toolshed.g2.bx.psu.edu/repos/nick/duplex/align_families/0.5 
mafft @7.221
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toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_estimator_attributes/sklearn_estimator_attributes/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.1  
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hisat2 @2.0.0beta
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toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.0  
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toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.4  
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python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.4.2  
python @3.6
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toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/1.136.0 
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toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.0.9 
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.3.5.0  
python @2.7.10
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toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.0.6 
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toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_randsample/2.1.0.20151222.0  
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toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/1.136.0 
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R @3.1.2

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_train_test_eval/sklearn_train_test_eval/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.24.0  
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samtools @1.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/devteam/print_reads/gatk_print_reads/0.0.2 
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samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.4  
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samtools @1.9

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/guerler/charts/charts/1.0.0  
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charts_r_packages @1.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0  
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toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1  
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.2.3.0  
python @2.7.10
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0  
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samtools @1.7

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.1.0  
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diffbind @1.8.3

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/2.1.0.20151222.0 
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numpy @1.7.1
scipy @0.12.0
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toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2  
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python @3.6
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toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.4.2  
python @3.6
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toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.0.0  
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gnu_sed @4.2.2-sandbox

toolshed.g2.bx.psu.edu/repos/bgruening/keras_batch_models/keras_batch_models/0.4.2  
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toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/0.8.1 
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toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.0.8 
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toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6  
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toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_regression_metrics/sklearn_regression_metrics/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2  
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toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20140616.0  
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scipy @0.12.0
R_3_0_1 @3.0.1
gnu_awk @4.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/scatterplot_rpy/1.0.3  
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rpy2 @2.8.5

toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.1  
gnu_awk @4.1.0
gb_taxonomy @8d245994d7

toolshed.g2.bx.psu.edu/repos/tyty/structurefold/iterative_map_pipeline/1.0  
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samtools @0.1.18
bowtie @0.12.7

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/0.7 
bowtie2 @2.2.5
samtools @0.1.18
networkx @1.9
dunovo @0.7.1

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_sample_generator/sklearn_sample_generator/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/tyty/structurefold/predict_pipeline/1.0  
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matplotlib @1.2.1
vienna_rna @2.1

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_randsample/2.1.0.20140616.0  
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numpy @1.7.1
scipy @0.12.0

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20140616.0  
macs2 @2.1.0
numpy @1.7.1
scipy @0.12.0

toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.1  
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samtools @1.1

toolshed.g2.bx.psu.edu/repos/nick/duplex/align_families/0.3 
mafft @7.221
duplex @0.3

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy1  
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python @2.7
bcbiogff @0.6.4
biopython @1.70
pybigwig @0.3.13
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toolshed.g2.bx.psu.edu/repos/iuc/duplex_family_size_distribution/fsd/1.0.0  
python @2.7
matplotlib @1.4.0

toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.0.1 
imagemagick @6.9.3
meme @4.11.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/2.0.8 
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samtools @0.1.18
networkx @1.10
dunovo @2.0.8

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.3  
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samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/0.7 
mafft @7.221
dunovo @0.7.1

toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.14  
mafft @7.221
dunovo @2.14

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.1.0.20151222.0  
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numpy @1.7.1
scipy @0.12.0
R @3.1.2
gnu_awk @4.1.0

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_filterdup/2.1.0.20140616.0 
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numpy @1.7.1
scipy @0.12.0

toolshed.g2.bx.psu.edu/repos/iuc/transit_tn5gaps/transit_tn5gaps/3.0.1+galaxy2  
transit @3.0.1
python @3.7

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.1  
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samtools @1.1

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.1+galaxy1  
transit @3.0.1
python @3.7

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_model_fit/sklearn_model_fit/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/2.14  
bowtie @1.1.2
networkx @1.10
dunovo @2.14

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4  
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samtools @1.9

toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1 
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samtools @1.2

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_clf_metrics/sklearn_clf_metrics/1.0.7.12 
python @3.6
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toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/2.0.12  
bowtie @1.1.2
networkx @1.10
dunovo @2.0.12

toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_dpmix/1.2.0 
gd_c_tools @0.1
matplotlib @1.2.1

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/1.136.0 
picard @1.136
R @3.1.2

toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration/gatk_table_recalibration/0.0.5 
gatk @1.4
samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/1.0.7.12 
python @3.6
Galaxy-ML @0.7.12

toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.4.2  
bwa @0.7.12
samtools @1.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0  
macs2 @2.1.0.20151222
numpy @1.7.1
scipy @0.12.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy1 
circos @0.69.8
python @2.7
bcbiogff @0.6.4
biopython @1.70
pybigwig @0.3.13
circos-tools @0.23

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.15  
mafft @7.221
dunovo @2.15

toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/2.0.9 
bowtie2 @2.2.5
samtools @0.1.18
networkx @1.10
dunovo @2.0.9

toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/2.0.6 
bowtie2 @2.2.5
samtools @0.1.18
networkx @1.11
dunovo @2.0.6

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_refinepeak/2.1.0.20140616.0  
macs2 @2.1.0
numpy @1.7.1
scipy @0.12.0

toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/0.8.1 
bowtie2 @2.2.5
samtools @0.1.18
networkx @1.9
dunovo @0.8.1

toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.0.12  
mafft @7.221
dunovo @2.0.12

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.2.2.0  
python @2.7.10
deepTools @2.2.2

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/1.0.7.12 
python @3.6
Galaxy-ML @0.7.12

toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.4.1  
freebayes @0_9_20_b040236
samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/iuc/vegan_fisher_alpha/vegan_fisher_alpha/0.0.2  
R @3.2.1
vegan @2.3-0

toolshed.g2.bx.psu.edu/repos/iuc/vegan_fisher_alpha/vegan_fisher_alpha/0.0.3  
R @3.2.1
vegan @2.3-0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_discriminant_classifier/sklearn_discriminant_classifier/1.0.7.12 
python @3.6
Galaxy-ML @0.7.12

toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.4  
r-getopt @1.20.0
r-gplots @2.17.0
r-rjson @0.2.15
bioconductor-deseq2 @1.10.1

toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy1 
snpeff @4.3.1t
python @3.6
biopython @1.70
python-magic @0.4.15
libmagic @5.32

toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy2 
snpeff @4.3.1t
python @3.6
biopython @1.70
python-magic @0.4.15
libmagic @5.32

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_tableviewer/0.69.8+galaxy1 
circos @0.69.8
python @2.7
bcbiogff @0.6.4
biopython @1.70
pybigwig @0.3.13
circos-tools @0.23

toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0  
snpsift @4.3.1t
coreutils @8.25
perl @5.26

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_filterdup/2.1.0.20151222.0 
macs2 @2.1.0.20151222
numpy @1.7.1
scipy @0.12.0

toolshed.g2.bx.psu.edu/repos/guru-ananda/rhmm/hmm_1/1.0.0 
R @2.15.0
RHmm @1.5.0

toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/2.0.6.1 
bowtie2 @2.2.5
samtools @0.1.18
networkx @1.11
dunovo @2.0.6

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/2.1.0.20140616.0 
macs2 @2.1.0
numpy @1.7.1
scipy @0.12.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/2.1.0.20151222.0 
macs2 @2.1.0.20151222
numpy @1.7.1
scipy @0.12.0

toolshed.g2.bx.psu.edu/repos/iuc/vegan_rarefaction/vegan_rarefaction/0.0.2  
R @3.2.1
vegan @2.3-0

toolshed.g2.bx.psu.edu/repos/iuc/vegan_rarefaction/vegan_rarefaction/0.0.3  
R @3.2.1
vegan @2.3-0

toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.7.12 
python @3.6
Galaxy-ML @0.7.12
plotly @3.1.1
graphviz @2.40.1
pydot @1.4.1

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/0.7.6 
mafft @7.221
dunovo @0.7.6

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_model_validation/sklearn_model_validation/1.0.7.12 
python @3.6
Galaxy-ML @0.7.12

toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_vcfCheck/4.3+t.galaxy0 
snpsift @4.3.1t
coreutils @8.25
perl @5.26

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7  
samtools @0.1.18
bowtie2 @2.1.0
tophat2 @2.0.9

toolshed.g2.bx.psu.edu/repos/nate/trinity_psc/trinity_psc/0.0.1 
bowtie @1.1.2
samtools @1.3
java @jre7
perl @5.18.4-threads
trinity @2.2.0

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9  
bowtie2 @2.2.5
tophat @2.0.14

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/0.4 
freebayes @0_9_20_b040236
samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy1 
circos @0.69.8
python @2.7
bcbiogff @0.6.4
biopython @1.70
pybigwig @0.3.13
circos-tools @0.23

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/iuc/duplex_family_size_distribution/fsd_beforevsafter/1.0.0  
python @2.7
matplotlib @1.4
biopython @1.71
pysam @0.15

toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.10.3  
sra-tools @2.10
samtools @1.9

toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/freebayes-0.9.14 
freebayes @freebayes-0.9.14_8a407cf5f4
samtools @0.1.18

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_train_test_split/sklearn_train_test_split/1.0.7.12 
python @3.6
Galaxy-ML @0.7.12

toolshed.g2.bx.psu.edu/repos/iuc/variant_analyzer/mut2read/1.0.0  
python @2.7
matplotlib @1.4.0
pysam @0.15

toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3  
hisat2 @2.0.3
hisat @2.0.3
samtools @1.2

toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4 
snpeff @4.3.1t
python @3.6
biopython @1.70
python-magic @0.4.15
libmagic @5.32

toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy3 
snpeff @4.3.1t
python @3.6
biopython @1.70
python-magic @0.4.15
libmagic @5.32

toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.3 
imagemagick @6.9.3
meme @4.11.0

toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.2 
imagemagick @6.9.3
meme @4.11.0

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.3.5.0  
python @2.7.10
deepTools @2.3.5

toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.0.0  
gnu_coreutils @8.22
perl @5.18.1
text_processing_perl_packages @1.0

toolshed.g2.bx.psu.edu/repos/devteam/tophat_fusion_post/tophat_fusion_post/0.1  
blast+ @2.2.28
bowtie @0.12.7
tophat2 @2.0.9

toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/1.136.0 
picard @1.136
R @3.1.2

CONVERTER_interval_to_bed_0 
python @2.7
bx-python @0.8.6

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.3.0  
python @2.7.10
deepTools @2.2.3

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.0.0  
python @2.7.10
deeptools @2.5.0

toolshed.g2.bx.psu.edu/repos/sauria/hifive/hifive/0.1.0 
hifive @1.5.3
mpi4py @2.0.0

toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0 
graphicsmagick @1.3.23
meme @4.12.0

toolshed.g2.bx.psu.edu/repos/boris/hetbox/hetbox/1.0  
R @2.15.0
rpy2 @2.2.6
numpy @1.7.1

toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0  
snpsift @4.3.1t
coreutils @8.25
perl @5.26

toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.3.6.0  
python @2.7.10
deepTools @2.3.6

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0  
macs2 @2.1.0.20151222
numpy @1.7.1
scipy @0.12.0
R @3.1.2

toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2 
libgd @2.2.3
circos @0.69.5
python @2.7
bcbiogff @0.6.4
biopython @1.70

toolshed.g2.bx.psu.edu/repos/boris/phylorelatives/phylorelatives/0.0.1  
R @2.15.0
rpy2 @2.2.6
dendropy @3.12.0
ape @3.0-8

toolshed.g2.bx.psu.edu/repos/iuc/transit_resampling/transit_resampling/3.0.1+galaxy1  
transit @3.0.1
python @3.7

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.7.12 
python @3.6
Galaxy-ML @0.7.12

toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgbroadcall/2.1.0.20151222.0  
macs2 @2.1.0.20151222
numpy @1.7.1
scipy @0.12.0
gnu_awk @4.1.0

toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy1  
circos @0.69.8
python @2.7
bcbiogff @0.6.4
biopython @1.70
pybigwig @0.3.13
circos-tools @0.23
@almahmoud almahmoud mentioned this issue Jan 7, 2020
Closed
@mvdbeek mvdbeek closed this as completed Apr 4, 2022
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