Combinations for a large set of tools

[almahmoud]

xref: galaxyproject/tools-iuc#2773

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

---

List of tools this PR address and their requirements:

• 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
  cufflinks @2.2.1
  cummeRbund @2.8.2

• toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3
  cufflinks @2.2.1
  cummeRbund @2.8.2

• toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.1
  cufflinks @2.2.1
  cummeRbund @2.8.2

• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.3.5.0
  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
  Galaxy-ML @0.7.12

• 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
  htseq @0.6.1
  numpy @1.7.1
  samtools @0.1.19
  pysam @0.7.7

• 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
  R @2.15.0
  gtools @3.4.1

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

• toolshed.g2.bx.psu.edu/repos/devteam/bamleftalign/bamleftalign/0.0.2
  freebayes @freebayes-0.9.14_8a407cf5f4
  samtools @0.1.18

• toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/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/2.5.0.0
  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
  graphicsmagick @1.3.20
  meme @4.11.1

• toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/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/iuc/snpsift/snpSift_rmInfo/4.3+t.galaxy0
  snpsift @4.3.1t
  coreutils @8.25
  perl @5.26

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

• 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
  Galaxy-ML @0.7.12

• toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_bundlelinks/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/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
  macs2 @2.1.0
  numpy @1.7.1
  scipy @0.12.0
  R_3_0_1 @3.0.1
  gnu_awk @4.1.0

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

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

• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.0.0
  gnu_coreutils @8.22
  gnu_grep @2.14

• toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.4
  freebayes @0_9_20_b040236
  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
  duplex @0.5

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

• toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.1
  hisat @2.0
  hisat2 @2.0.0beta
  samtools @1.2

• toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.0
  hisat @2.0
  samtools @1.2

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.4
  sra-tools @2.10
  samtools @1.9

• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.5.0.0
  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
  Galaxy-ML @0.7.12

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

• toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.0.9
  mafft @7.221
  dunovo @2.0.9

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

• toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.0.6
  mafft @7.221
  dunovo @2.0.6

• toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_randsample/2.1.0.20151222.0
  macs2 @2.1.0.20151222
  numpy @1.7.1
  scipy @0.12.0

• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/1.136.0
  picard @1.136
  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
  Galaxy-ML @0.7.12

• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.24.0
  bedtools @2.24
  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
  gatk @1.4
  samtools @0.1.18

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.4
  sra-tools @2.10
  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
  R @3.0.3
  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
  bowtie2 @2.2.5
  tophat @2.1.0

• toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2
  bamtools @2.3.0_2d7685d2ae
  samtools @0.1.18

• toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1
  bamtools @2.3.0_2d7685d2ae
  samtools @0.1.18

• 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
  deepTools @2.2.3

• 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
  Galaxy-ML @0.7.12

• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0
  deeptools @3.0.2
  samtools @1.7

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

• toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.1.0
  R @3.0.3
  deseq2 @1.2.10
  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
  macs2 @2.1.0.20151222
  numpy @1.7.1
  scipy @0.12.0
  gnu_awk @4.1.0

• toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2
  cutadapt @1.8.3
  cutadapt @1.8

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

• toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.4.2
  python @3.6
  Galaxy-ML @0.7.12

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

• toolshed.g2.bx.psu.edu/repos/bgruening/keras_batch_models/keras_batch_models/0.4.2
  python @3.6
  Galaxy-ML @0.7.12

• toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/0.8.1
  mafft @7.221
  dunovo @0.8.1

• toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/2.0.8
  mafft @7.221
  dunovo @2.0.8

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

• toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6
  bowtie2 @2.2.6
  samtools @1.2

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

• toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2
  bowtie2 @2.2.6
  samtools @1.2

• toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20140616.0
  macs2 @2.1.0
  numpy @1.7.1
  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
  numpy @1.9
  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
  biopython @1.61
  numpy @1.7.1
  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
  Galaxy-ML @0.7.12

• toolshed.g2.bx.psu.edu/repos/tyty/structurefold/predict_pipeline/1.0
  rnastructure @5.7
  biopython @1.61
  numpy @1.7.1
  imaging @1.1.7
  matplotlib @1.2.1
  vienna_rna @2.1

• toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_randsample/2.1.0.20140616.0
  macs2 @2.1.0
  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
  bwa @0.7.10.039ea20639
  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
  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/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
  bowtie2 @2.2.5
  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
  Galaxy-ML @0.7.12

• 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
  freebayes @0.9.6_9608597d12e127c847ae03aa03440ab63992fedf
  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
  macs2 @2.1.0.20151222
  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
  macs2 @2.1.0
  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
  bwa @0.7.10.039ea20639
  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
  Galaxy-ML @0.7.12

• 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
  sra-tools @2.10
  samtools @1.9

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

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

• 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
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• toolshed.g2.bx.psu.edu/repos/iuc/duplex_family_size_distribution/fsd_beforevsafter/1.0.0
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• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.10.3
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• toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/freebayes-0.9.14
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• toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_train_test_split/sklearn_train_test_split/1.0.7.12
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• toolshed.g2.bx.psu.edu/repos/iuc/variant_analyzer/mut2read/1.0.0
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• toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3
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• toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4
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• toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy3
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• toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.3
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• toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.2
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• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.3.5.0
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• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.0.0
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• toolshed.g2.bx.psu.edu/repos/devteam/tophat_fusion_post/tophat_fusion_post/0.1
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• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/1.136.0
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CONVERTER_interval_to_bed_0
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bx-python @0.8.6

• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.3.6.0
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• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.3.6.0
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• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.3.0
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• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.0.0
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• toolshed.g2.bx.psu.edu/repos/sauria/hifive/hifive/0.1.0
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• toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0
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• toolshed.g2.bx.psu.edu/repos/boris/hetbox/hetbox/1.0
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• toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0
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• toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.3.6.0
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• toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0
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• toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2
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• toolshed.g2.bx.psu.edu/repos/boris/phylorelatives/phylorelatives/0.0.1
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• toolshed.g2.bx.psu.edu/repos/iuc/transit_resampling/transit_resampling/3.0.1+galaxy1
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• toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.7.12
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• toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgbroadcall/2.1.0.20151222.0
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• toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy1
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[mvdbeek]

As I said in galaxyproject/tools-iuc#2773 (comment) I think we should wait with mass-building containers until the current issues are addressed ... but I guess since we need to rebuild quite some container it isn't a big deal to merge them at this point.

But some of the dependencies listed here are not in Conda, so those dependencies need to be adapted to their names and versions in Conda, if they are available there.

Finally this is going to take too long on the CI system, each combination should be a PR. You can use planemo container_register to automate this. It'll also automatically skip those dependencies that are not available in conda.

[bgruening]

@almahmoud there are multiple things wrong here imho.

We never intended to build for all tools in your list a container. There are very old tools included, predating conda for example. We tried 4 years back to build also the old ones, but decided against this and make a clear cut. So if you plan to replicated usegalaxy.org this will not work - as many tools are just too old. A good indicator is R as a dependency, this should not be the case.

There are many tools included that are not https://github.com/galaxyproject/planemo-monitor/ and hence does not get a container. Maybe for a good reason? Again older stuff?

I think it would help if you can create such a list of all recent tools and if then something is failing we need to find out why planemo-monitor is not catching those tools - and fix planemo monitor.

[almahmoud]

@bgruening Definitely. So this list was just a quick extraction from the new dependency visualization tool that @jmchilton added to 20.01. I assumed it probably won't be merged with everything, but figured it'd be a good place to start and go down from here rather than trying to build a list ourselves from scratch, as that process has not taken off that well and seems like it would take too long.
I guess some questions on how to move forward:

• What is the cutoff for tools being "too old"? Or what can we do to filter this list to a reasonable one?
• We would like to replicate Main more or less, but understand that it won't be exactly the same because of all the manual things that have gone into it throughout the years. At a minimum, it would be great to at least be able to run the GTN workflows and have a user be able to use this without too much hassle transitioning.
• In terms of the tools, we are separately fixing individual tools for a select set of popular workflows, but it would also be great to have a (semi-)automated way of figuring out which (new) tools are missing containers. The UI component that John added is amazingly insightful but as long as it has unresolved containers on it that are not marked as deprecated or similar, but are also not expected to work (whether because they are too old or can't work in containers for any other reason), it undermines the idea behind it. ie, it would be great to learn how to filter the list to be representative of the tools that we are expecting to work in the end, so we can try to fix those and be set for the future as new tools are being added.

[bgruening]

We had a telco yesterday evening and discussed those points. @almahmoud is there anything missing? Can we close this PR?

[bgruening]

ping @almahmoud