Unresolved tool containers

[afgane]

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
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
• toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/readdepth2seqdepth/1.0.0
• aggregate_scores_in_intervals2
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.136.0
• toolshed.g2.bx.psu.edu/repos/boris/getalleleseq/getalleleseq/0.0.1
• toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/0.0.3
• Summary_Statistics1
• toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.1
• toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2
• toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_degap_seqs/1.21.0
• toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-report/1.1.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_otu_hierarchy/1.20.0
• toolshed.g2.bx.psu.edu/repos/gregory-minevich/cloudmap_in_silico_complementation/in_silico_complementation/1.0.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_slayer/1.23.0
• Show beginning1
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.24.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_sum_gd_snp/1.1.0
• toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3
• toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc1+galaxy0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_discover_familial_relationships/1.0.0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/1.136.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_pca/1.0.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parsimony/1.20.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_filter_seqs/1.20.0
• toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.0
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.24.1
• ChangeCase
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/1.126.0
• gff_filter_by_feature_count
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_summary_tax/1.23.0
• tabular_to_dbnsfp
• toolshed.g2.bx.psu.edu/repos/iuc/repmatch_gff3/repmatch_gff3/1.0.2
• toolshed.g2.bx.psu.edu/repos/iuc/repmatch_gff3/repmatch_gff3/1.0.0
• CONVERTER_gff_to_bed_0
• toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806.1
• __EXPORT_HISTORY__
• pbed2lpedconvert
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• toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_sort/0.1.9
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.24.0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.0.0
• toolshed.g2.bx.psu.edu/repos/gregory-minevich/cloudmap_variant_discovery_mapping/cloudmap_variant_discovery_mapping/1.0.0
• toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0
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• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.0.0
• hgv_pass
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• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/1.136.0
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.24.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcoa/1.20.0
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• toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.2
• cat1
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• CONVERTER_encodepeak_to_tabix_0
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• Remove beginning1
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• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_extract_flanking_dna/1.0.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pcr_seqs/1.26.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_create_database/1.28.0
• toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_bamtobed/0.1.0
• wiggle2simple1
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• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_add_fst_column/1.2.0
• toolshed.g2.bx.psu.edu/repos/devteam/t_test_two_samples/t_test_two_samples/1.0.1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.0.0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.126.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_contigs/1.27.0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.0.0
• toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_average_fst/1.2.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_files/1.20.0
• toolshed.g2.bx.psu.edu/repos/gregory-minevich/snp_mapping_using_wgs/snp_mapping_using_wgs/1.0.0
• toolshed.g2.bx.psu.edu/repos/devteam/windowsplitter/winSplitter/1.0.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_phylogenetic_tree/1.1.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_count_groups/1.23.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_specify_restriction_enzymes/1.0.0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/1.126.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pairwise_seqs/1.20.0
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.24.0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/1.136.1
• toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_rare/1.20.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pre_cluster/1.24.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_pca/1.21.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_fastq/1.20.0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.0.0
• toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_header/0.1.9
• ratmine
• hbvar
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_prepare_population_structure/1.1.0
• ucsc_table_direct_archaea1
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_rabund/1.19.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_consensus_seqs/1.21.0
• toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/0.0.3
• upload1
• toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0
• toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2
• GeneBed_Maf_Fasta2
• createInterval
• toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_restore_attributes/1.1.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_perseus/1.24.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_seqs/1.21.0
• toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/0.0.2
• secure_hash_message_digest
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• toolshed.g2.bx.psu.edu/repos/devteam/vcfrandomsample/vcfrandomsample/0.0.3
• toolshed.g2.bx.psu.edu/repos/devteam/cummerbund_to_tabular/cummerbund_to_cuffdiff/1.0.1
• Convert characters1
• toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/1.0.0
• toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0
• toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.0.0
• toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_coveragebed_counts/0.1.0
• CONVERTER_fasta_to_tabular
• toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/space2underscore_readname/1.0.0
• MAF_Limit_To_Species1
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otulist/1.20.0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.0.0
• CONVERTER_maf_to_fasta_0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/1.136.0
• toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.6.13
• toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0
• comp1
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_chimera_pintail/1.21.0
• toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_remove_lineage/1.20.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_align_check/1.20.0
• toolshed.g2.bx.psu.edu/repos/nick/duplex/make_families/0.3
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_venn/1.24.0
• toolshed.g2.bx.psu.edu/repos/nick/duplex/make_families/0.5
• wc_gnu
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.24.0
• toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_shuffling/1.9.7.0
• toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/0.0.6
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.24.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_sharedseqs/1.21.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_seq_error/1.22.0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/1.126.0
• CONVERTER_wiggle_to_interval_0
• modmine
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_links/2.24.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_calc_freq/1.1.0
• CONVERTER_bed_to_tabix_0
• toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.9
• IMPORT_HISTORY
• toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.64
• toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65
• toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.63
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_clearcut/1.20.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cooccurrence/1.26.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_nucleotide_diversity_pi/1.0.0
• toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_assignment_of_optimal_breeding_pairs/1.0.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_restore_attributes/1.0.0
• Cut1
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.24.0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.126.0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/1.126.0
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.24.0
• toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1
• toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared/1.23.0
• toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/combineproballelecom/2.0.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_pathway_image/1.0.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_otus/1.20.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_sub_sample/1.23.0
• addValue
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_rank_terms/1.1.0
• toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/0.0.3
• toolshed.g2.bx.psu.edu/repos/iuc/resize_coordinate_window/resize_coordinate_window/1.0.1
• toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0
• toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/PEsortedSAM2readprofile/1.1.0
• pbed2ldindepconvert
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_list_otulabels/1.27.0
• CONVERTER_len_to_linecount
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.24.1
• toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.2
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/1.126.0
• MAF_Thread_For_Species1
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_dpmix/1.0.0
• toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_intersectbed_bam/0.1.0
• toolshed.g2.bx.psu.edu/repos/devteam/kraken_translate/kraken-translate/1.1.0
• Sff_extractor
• toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.9
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_get_lineage/1.21.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_offspring_heterozygosity_pedigree/1.0.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_collect_shared/1.24.0
• toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotator/0.1
• gtf_filter_by_attribute_values_list
• eupathdb
• bed2gff1
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_parse_list/1.19.0
• toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_evaluate_population_numbers/1.0.0
• toolshed.g2.bx.psu.edu/repos/gregory-minevich/ems_variant_density_mapping/ems_variant_density_mapping/1.0.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_make_shared_from_biom/1.25.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_cluster/1.28.0
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/mothur_anosim/1.20.0
• Extract genomic DNA 1
• toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/1.136.0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/1.126.0
• toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0
• toolshed.g2.bx.psu.edu/repos/devteam/table_annovar/table_annovar/0.1
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• CONVERTER_maf_to_interval_0
• CONVERTER_interval_to_bed12_0
• toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.1
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• toolshed.g2.bx.psu.edu/repos/devteam/mine/maximal_information_based_nonparametric_exploration/0.0.1
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• Show tail1
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• CONVERTER_interval_to_bedstrict_0
• toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_rebase/0.1.9
• toolshed.g2.bx.psu.edu/repos/jjohnson/mothur_toolsuite/tree_vector/1.0
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.24.0
• toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/1.126.0
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• CONVERTER_bed_to_fli_0
• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_reldistbed/2.24.0
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• MAF_To_Interval1
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• 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
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[mvdbeek]

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).