From ef3edd61dbf08d5dbd86e8ffcfbcb6f10cf687b0 Mon Sep 17 00:00:00 2001 From: github-actions Date: Thu, 9 May 2024 00:44:10 +0000 Subject: [PATCH] Automated deployment with updated cache 2024-05-09 --- counts.json | 1351 +++++++++-------- .../c/codoff:1.0.0--pyh7cba7a3_0.json | 76 + .../i/iseq:1.0.0--hdfd78af_0.json | 337 ++++ ...coring-matrices:0.2.0--py39hf95cd2a_0.json | 73 + .../s/sincei:0.3.1--pyhdfd78af_0.json | 246 +++ .../s/squigualiser:0.6.3--pyhca03a8a_0.json | 143 ++ .../t/tadrep:0.9.2--pyhdfd78af_0.json | 386 +++++ .../w/wgatools:0.1.0--h7c767d4_1.json | 37 + 8 files changed, 1987 insertions(+), 662 deletions(-) create mode 100644 quay.io/biocontainers/c/codoff:1.0.0--pyh7cba7a3_0.json create mode 100644 quay.io/biocontainers/i/iseq:1.0.0--hdfd78af_0.json create mode 100644 quay.io/biocontainers/s/scoring-matrices:0.2.0--py39hf95cd2a_0.json create mode 100644 quay.io/biocontainers/s/sincei:0.3.1--pyhdfd78af_0.json create mode 100644 quay.io/biocontainers/s/squigualiser:0.6.3--pyhca03a8a_0.json create mode 100644 quay.io/biocontainers/t/tadrep:0.9.2--pyhdfd78af_0.json create mode 100644 quay.io/biocontainers/w/wgatools:0.1.0--h7c767d4_1.json diff --git a/counts.json b/counts.json index 0df920a..5365a2e 100644 --- a/counts.json +++ b/counts.json @@ -2326,16 +2326,16 @@ "2csfastq_1csfastq": 1, "2ft": 2, "2ndscore": 1, - "2to3": 3620, - "2to3-3.10": 795, - "2to3-3.11": 263, + "2to3": 3625, + "2to3-3.10": 798, + "2to3-3.11": 264, "2to3-3.12": 173, "2to3-3.4": 6, "2to3-3.5": 103, "2to3-3.6": 342, "2to3-3.7": 383, "2to3-3.8": 574, - "2to3-3.9": 650, + "2to3-3.9": 651, "3EdgeTests": 1, "3_1_filter_mapQ_for_sam.pl": 1, "3seq": 1, @@ -2949,7 +2949,7 @@ "FEELnc_pipeline.sh": 1, "FEELnc_tpLevel2gnLevelClassification.R": 1, "FEELnc_tpLevel2gnLevelClassification.R.bak": 1, - "FET.pl": 43, + "FET.pl": 44, "FEW.pl": 6, "FFEval": 2, "FGAP": 1, @@ -4817,20 +4817,20 @@ "abawaca": 1, "abba-baba": 31, "abeona": 1, - "abi-dump": 21, - "abi-dump.2": 17, + "abi-dump": 22, + "abi-dump.2": 18, "abi-dump.2.10.0": 1, "abi-dump.2.10.8": 3, "abi-dump.2.10.9": 3, - "abi-dump.2.11.0": 9, + "abi-dump.2.11.0": 10, "abi-dump.2.9.6": 1, "abi-dump.3": 4, "abi-dump.3.0.0": 2, "abi-dump.3.0.3": 1, "abi-dump.3.1.0": 1, - "abi-load": 11, - "abi-load.2": 9, - "abi-load.2.11.0": 9, + "abi-load": 12, + "abi-load.2": 10, + "abi-load.2.11.0": 10, "abi-load.3": 2, "abi-load.3.0.0": 2, "abi2fq": 1, @@ -4895,7 +4895,7 @@ "abyss-tofastq": 17, "ac-diamond": 1, "accession_retrieve": 1, - "accn-at-a-time": 255, + "accn-at-a-time": 256, "accurate_bkp.py": 1, "acdc": 25, "acdc-filter-fasta-by-name.awk": 1, @@ -4997,7 +4997,7 @@ "addtit.pl": 2, "adf_checker.pl": 1, "adhocfilelist": 1, - "adig": 4482, + "adig": 4486, "adjustPeakFile.pl": 5, "adjustRedunGroupFile.pl": 5, "adjustScanRankerScoreByGroup": 2, @@ -5113,7 +5113,7 @@ "agrvate": 1, "agtsampleinforw.dll": 2, "ahmm-s": 1, - "ahost": 4482, + "ahost": 4486, "airr-tools": 5, "akita_data.py": 1, "akita_data_read.py": 1, @@ -5149,22 +5149,22 @@ "alifold.pl": 1, "align": 1, "align-bwa.smk": 1, - "align-cache": 17, - "align-cache.2": 15, + "align-cache": 18, + "align-cache.2": 16, "align-cache.2.10.8": 3, "align-cache.2.10.9": 3, - "align-cache.2.11.0": 9, + "align-cache.2.11.0": 10, "align-cache.3": 2, "align-cache.3.0.0": 2, - "align-columns": 198, + "align-columns": 199, "align-ema.smk": 1, "align-families.py": 1, - "align-info": 21, - "align-info.2": 17, + "align-info": 22, + "align-info.2": 18, "align-info.2.10.0": 1, "align-info.2.10.8": 3, "align-info.2.10.9": 3, - "align-info.2.11.0": 9, + "align-info.2.11.0": 10, "align-info.2.9.6": 1, "align-info.3": 4, "align-info.3.0.0": 2, @@ -5210,7 +5210,7 @@ "alignment-translate": 1, "alignment-workflow": 1, "alignmentProjector": 4, - "alignmentSieve": 10, + "alignmentSieve": 11, "alignment_handler": 1, "alignment_handler_multi": 1, "alignment_stator": 1, @@ -5279,7 +5279,7 @@ "amdgpu-arch": 1, "ame": 13, "amgr": 1, - "amino-acid-composition": 286, + "amino-acid-composition": 287, "aminoextract": 2, "amk_ccc": 2, "amk_fft2": 2, @@ -5709,15 +5709,15 @@ "arcasHLA": 1, "archer": 1, "architeuthis": 1, - "archive-ncbinlp": 10, - "archive-nihocc": 10, - "archive-nmcds": 10, - "archive-pmc": 10, - "archive-pubmed": 285, - "archive-taxonomy": 10, + "archive-ncbinlp": 11, + "archive-nihocc": 11, + "archive-nmcds": 11, + "archive-pmc": 11, + "archive-pubmed": 286, + "archive-taxonomy": 11, "archive_directory.py": 2, "archosv": 2, - "archspec": 6, + "archspec": 7, "arcs": 2, "arcs-make": 2, "are_there_primers": 1, @@ -5725,7 +5725,7 @@ "argnorm": 1, "argparse2tool": 1, "argparse2tool_check_path": 1, - "args2slice": 10, + "args2slice": 11, "args_oap": 1, "aria2c": 17, "ariba": 3, @@ -5767,8 +5767,8 @@ "arwen": 1, "as": 8, "asadmin": 29, - "ascli": 2, - "ascp": 2, + "ascli": 3, + "ascp": 3, "ascp_download.sh": 1, "ase": 3, "ase-build": 3, @@ -5777,7 +5777,7 @@ "ase-info": 3, "ase-run": 3, "aserver": 428, - "asession": 2, + "asession": 3, "asgal": 1, "asgal_BitVector.py": 1, "asgal_SplicingGraph.py": 1, @@ -5802,14 +5802,14 @@ "asn2ff": 1, "asn2gb": 2, "asn2idx": 1, - "asn2ref": 10, - "asn2xml": 199, + "asn2ref": 11, + "asn2xml": 200, "asndhuff": 1, "asntool": 1, "asp-cp": 87, "asp-ls": 87, "asp-ls.bak": 1, - "aspera-license": 2, + "aspera-license": 3, "asqcan": 1, "asscom2": 1, "assemble-complexSVs": 1, @@ -5905,7 +5905,7 @@ "autometa-taxonomy-majority-vote": 2, "autometa-unclustered-recruitment": 2, "autometa-update-databases": 2, - "autopoint": 5268, + "autopoint": 5270, "autoreconf.bak": 10, "autoscan.bak": 10, "autoupdate.bak": 10, @@ -5931,7 +5931,7 @@ "aws_completer": 6, "aws_zsh_completer.sh": 6, "awslimitchecker": 1, - "axel": 1, + "axel": 2, "axiome": 1, "axtAndBed": 1, "axtBest": 1, @@ -6012,12 +6012,12 @@ "baltic.py": 1, "bam": 1, "bam-extractor": 2, - "bam-load": 19, - "bam-load.2": 17, + "bam-load": 20, + "bam-load.2": 18, "bam-load.2.10.0": 1, "bam-load.2.10.8": 3, "bam-load.2.10.9": 3, - "bam-load.2.11.0": 9, + "bam-load.2.11.0": 10, "bam-load.2.9.6": 1, "bam-load.3": 2, "bam-load.3.0.0": 2, @@ -6085,10 +6085,10 @@ "bam2wig": 14, "bam2wig.py": 3, "bamAlignCleaner": 1, - "bamCompare": 10, - "bamCoverage": 10, + "bamCompare": 11, + "bamCoverage": 11, "bamFlags": 3, - "bamPEFragmentSize": 10, + "bamPEFragmentSize": 11, "bamToBed": 269, "bamToBw.pl": 3, "bamToFastq": 269, @@ -6498,7 +6498,7 @@ "beta_diversity.py": 4, "beta_diversity_through_plots.py": 1, "beta_significance.py": 1, - "between-two-genes": 286, + "between-two-genes": 287, "bf.sh": 1, "bfc": 1, "bfconvert": 1, @@ -6543,7 +6543,8 @@ "bigscape.py": 1, "bigsi": 1, "bigtools": 1, - "bigwigCompare": 10, + "bigwigAverage": 1, + "bigwigCompare": 11, "bigwigaverageoverbed": 1, "bigwiginfo": 1, "bigwigmerge": 1, @@ -6706,7 +6707,7 @@ "blast_check_pair.pl": 1, "blast_filter.pl": 1, "blast_format_unit_test": 5, - "blast_formatter": 318, + "blast_formatter": 319, "blast_names_mapping.tsv": 1, "blast_outfmt6_replace_trans_id_w_gene_symbol.pl": 1, "blast_report": 20, @@ -6721,12 +6722,12 @@ "blastbesties": 1, "blastcl3": 1, "blastclust": 30, - "blastdb_aliastool": 318, + "blastdb_aliastool": 319, "blastdb_convert": 20, "blastdb_format_unit_test": 5, "blastdb_path": 20, - "blastdbcheck": 318, - "blastdbcmd": 318, + "blastdbcheck": 319, + "blastdbcmd": 319, "blastdbcp": 52, "blastdiag_unit_test": 5, "blastengine_unit_test": 5, @@ -6734,13 +6735,13 @@ "blastfilter_unit_test": 5, "blasthits_unit_test": 5, "blastinput_unit_test": 5, - "blastn": 318, - "blastn_vdb": 33, + "blastn": 319, + "blastn_vdb": 34, "blastoptions_unit_test": 5, - "blastp": 318, + "blastp": 319, "blastpgp": 30, "blastsetup_unit_test": 5, - "blastx": 318, + "blastx": 319, "blastzWrapper": 1, "blat": 19, "blat2gbrowse.pl": 14, @@ -6763,8 +6764,8 @@ "blossom5": 1, "blossom_randGraph.py": 1, "blosum62.fas": 2, - "blst2gm": 10, - "blst2tkns": 198, + "blst2gm": 11, + "blst2tkns": 199, "bmaToLinks.pl": 1, "bmfilter": 4, "bmge": 1, @@ -6782,7 +6783,7 @@ "bogusness": 3, "bohra": 1, "boink": 1, - "bokeh": 62, + "bokeh": 63, "bold2utax.py": 1, "bold_identification": 1, "bolt": 2, @@ -6982,7 +6983,7 @@ "broad_utils.py": 1, "brockman_pipeline": 1, "brooklyn_plot": 1, - "brotli": 404, + "brotli": 407, "browse": 18, "bs_call": 2, "bs_seeker2-align.py": 1, @@ -7073,13 +7074,13 @@ "build_universe": 1, "builder.pl": 1, "bulk-counts": 4, - "bundle": 18, + "bundle": 19, "bundle_image": 29, "bundledoc": 1, "bundlelinks": 1, - "bundler": 18, + "bundler": 19, "bunwarpj": 4, - "bunzip2": 6570, + "bunzip2": 6575, "burden_test_vase": 1, "burst_linux_DB12": 1, "burst_linux_DB15": 1, @@ -7130,16 +7131,16 @@ "bxStats.py": 1, "bxcl_seqqc": 1, "bxtools": 1, - "bzcat": 6570, - "bzcmp": 6570, - "bzdiff": 6570, - "bzegrep": 6570, - "bzfgrep": 6570, - "bzgrep": 6570, - "bzip2": 6570, - "bzip2recover": 6570, - "bzless": 6570, - "bzmore": 6570, + "bzcat": 6575, + "bzcmp": 6575, + "bzdiff": 6575, + "bzegrep": 6575, + "bzfgrep": 6575, + "bzgrep": 6575, + "bzip2": 6575, + "bzip2recover": 6575, + "bzless": 6575, + "bzmore": 6575, "c++": 5, "c++filt": 8, "c-index-test": 8, @@ -7156,7 +7157,7 @@ "cPecanLibTests": 1, "cPecanModifyHmm": 1, "cPecanRealign": 1, - "c_rehash": 7719, + "c_rehash": 7726, "ca2ace.pl": 3, "ca2ctg": 2, "ca2mates": 2, @@ -7165,12 +7166,12 @@ "ca2ta": 2, "ca_ikki_v5.pl": 1, "cacert.pem": 57, - "cache-mgr": 21, - "cache-mgr.2": 17, + "cache-mgr": 22, + "cache-mgr.2": 18, "cache-mgr.2.10.0": 1, "cache-mgr.2.10.8": 3, "cache-mgr.2.10.9": 3, - "cache-mgr.2.11.0": 9, + "cache-mgr.2.11.0": 10, "cache-mgr.2.9.6": 1, "cache-mgr.3": 4, "cache-mgr.3.0.0": 2, @@ -7332,7 +7333,7 @@ "capnpc-c++": 52, "capnpc-capnp": 52, "capnpc-cython": 1, - "captoinfo": 7651, + "captoinfo": 7657, "captus_assembly": 1, "caqc.pl": 3, "caqc_help.ini": 3, @@ -7427,9 +7428,9 @@ "ccache-swig": 13, "cccheck": 15, "ccconfig": 56, - "ccextract": 11, - "ccextract.2": 9, - "ccextract.2.11.0": 9, + "ccextract": 12, + "ccextract.2": 10, + "ccextract.2.11.0": 10, "ccextract.3": 2, "ccextract.3.0.0": 2, "cchardetect": 1, @@ -7449,18 +7450,18 @@ "ccsmeth": 1, "cct": 39, "cctk": 1, - "cd-hit": 44, - "cd-hit-2d": 44, - "cd-hit-2d-para.pl": 44, - "cd-hit-454": 44, - "cd-hit-clstr_2_blm8.pl": 43, - "cd-hit-div": 44, - "cd-hit-div.pl": 44, + "cd-hit": 45, + "cd-hit-2d": 45, + "cd-hit-2d-para.pl": 45, + "cd-hit-454": 45, + "cd-hit-clstr_2_blm8.pl": 44, + "cd-hit-div": 45, + "cd-hit-div.pl": 45, "cd-hit-dup": 1, - "cd-hit-est": 45, - "cd-hit-est-2d": 44, + "cd-hit-est": 46, + "cd-hit-est-2d": 45, "cd-hit-lap": 1, - "cd-hit-para.pl": 44, + "cd-hit-para.pl": 45, "cda2dcm": 1, "cdbfasta": 12, "cdbg-ops": 1, @@ -7532,12 +7533,12 @@ "cfadmin": 29, "cfsan_snp_pipeline": 1, "cftp": 1, - "cg-load": 19, - "cg-load.2": 17, + "cg-load": 20, + "cg-load.2": 18, "cg-load.2.10.0": 1, "cg-load.2.10.8": 3, "cg-load.2.10.9": 3, - "cg-load.2.11.0": 9, + "cg-load.2.11.0": 10, "cg-load.2.9.6": 1, "cg-load.3": 2, "cg-load.3.0.0": 2, @@ -7765,10 +7766,10 @@ "circulocov": 1, "cirdna": 24, "cirtap": 1, - "cit2pmid": 10, + "cit2pmid": 11, "civicpy": 1, "cjk-gs-integrate": 1, - "cjpeg": 5731, + "cjpeg": 5734, "ckeygen": 1, "cksum": 82, "claMLST": 1, @@ -7870,11 +7871,11 @@ "cleanmap.awk": 1, "cleanme.pl": 1, "cleanpp.sh": 3, - "cleanup-blastdb-volumes.py": 247, + "cleanup-blastdb-volumes.py": 248, "cleanup-coverage.py": 2, "cleanup-stale-gcp-resources.py": 1, "cleanup.py": 1, - "clear": 7651, + "clear": 7657, "clearCNV": 1, "clearcut": 1, "cleric": 1, @@ -7925,29 +7926,29 @@ "clove": 1, "clp": 99, "clsify": 1, - "clstr2tree.pl": 44, - "clstr2txt.pl": 44, - "clstr2xml.pl": 44, - "clstr_cut.pl": 44, - "clstr_list.pl": 43, - "clstr_list_sort.pl": 43, - "clstr_merge.pl": 44, - "clstr_merge_noorder.pl": 44, - "clstr_quality_eval.pl": 44, - "clstr_quality_eval_by_link.pl": 44, - "clstr_reduce.pl": 44, - "clstr_renumber.pl": 44, - "clstr_rep.pl": 44, - "clstr_reps_faa_rev.pl": 44, - "clstr_rev.pl": 44, - "clstr_select.pl": 44, - "clstr_select_rep.pl": 44, - "clstr_size_histogram.pl": 44, - "clstr_size_stat.pl": 44, - "clstr_sort_by.pl": 44, - "clstr_sort_prot_by.pl": 44, - "clstr_sql_tbl.pl": 44, - "clstr_sql_tbl_sort.pl": 44, + "clstr2tree.pl": 45, + "clstr2txt.pl": 45, + "clstr2xml.pl": 45, + "clstr_cut.pl": 45, + "clstr_list.pl": 44, + "clstr_list_sort.pl": 44, + "clstr_merge.pl": 45, + "clstr_merge_noorder.pl": 45, + "clstr_quality_eval.pl": 45, + "clstr_quality_eval_by_link.pl": 45, + "clstr_reduce.pl": 45, + "clstr_renumber.pl": 45, + "clstr_rep.pl": 45, + "clstr_reps_faa_rev.pl": 45, + "clstr_rev.pl": 45, + "clstr_select.pl": 45, + "clstr_select_rep.pl": 45, + "clstr_size_histogram.pl": 45, + "clstr_size_stat.pl": 45, + "clstr_sort_by.pl": 45, + "clstr_sort_prot_by.pl": 45, + "clstr_sql_tbl.pl": 45, + "clstr_sql_tbl_sort.pl": 45, "clumpMaker": 3, "clumpify.sh": 30, "clust": 1, @@ -8069,6 +8070,7 @@ "codes_parser": 1, "codes_split_file": 1, "codingorf": 1, + "codoff": 1, "codon_freq_from_bicodons.py": 1, "codon_stuff.py": 1, "codon_stuff_threader.py": 1, @@ -8124,7 +8126,7 @@ "combine": 4, "combine-assembled-files.sh": 1, "combine-subexons": 1, - "combine-uid-lists": 10, + "combine-uid-lists": 11, "combineAndAnnotateReferences.pl": 1, "combineFile": 2, "combineFragandDBGraph_fastg.py": 1, @@ -8226,7 +8228,7 @@ "compileSpliceCands": 12, "compile_STARE_Linux.sh": 1, "compile_STARE_macOS.sh": 1, - "compile_et": 5764, + "compile_et": 5768, "compiled_table.py": 1, "compleasm": 1, "complementBed": 269, @@ -8253,9 +8255,9 @@ "compute-uniform-priors": 13, "computeCoverageStat": 3, "computeFlankingRegion.pl": 12, - "computeGCBias": 10, - "computeMatrix": 10, - "computeMatrixOperations": 10, + "computeGCBias": 11, + "computeMatrix": 11, + "computeMatrixOperations": 11, "computeOrderedMatrix": 1, "compute_CLmotif_scores.sh": 1, "compute_base_probs.pl": 5, @@ -8409,7 +8411,7 @@ "convert2bed-float128": 14, "convert2bed-megarow": 14, "convert2bed-typical": 14, - "convert2blastmask": 318, + "convert2blastmask": 319, "convert2snns": 2, "convertCoordinates.pl": 5, "convertFastaQualToFastQ.rb": 1, @@ -8525,7 +8527,7 @@ "core_diversity_analyses.py": 1, "core_methods.py": 1, "core_overlap_plot.py": 1, - "corelist": 1675, + "corelist": 1678, "corepack": 11, "coreprocess.pl": 3, "coresnpfilter": 1, @@ -8537,7 +8539,7 @@ "correct-frags": 3, "correct-olaps": 3, "correct.py": 2, - "correctGCBias": 10, + "correctGCBias": 11, "correctGaps": 3, "correctOverlaps": 6, "correctPacBio": 3, @@ -8629,7 +8631,7 @@ "cp2k_run": 1, "cp2k_shell.ssmp": 1, "cpack": 11, - "cpan": 1675, + "cpan": 1678, "cpancover": 6, "cpanm": 242, "cpat.py": 1, @@ -8822,7 +8824,7 @@ "csv2rdf": 32, "csv2tsv": 1, "csv2xlsx": 1, - "csv2xml": 198, + "csv2xml": 199, "csvExtractBorders": 1, "csvFrags2text": 1, "csv_to_tsv": 1, @@ -8868,8 +8870,8 @@ "curate_database.py": 1, "curate_universe": 1, "curesim": 2, - "curl": 5086, - "curl-config": 5880, + "curl": 5088, + "curl-config": 5884, "curlywhirly": 1, "curve_keygen": 68, "cusp": 24, @@ -9017,7 +9019,7 @@ "dataset_manager.py": 1, "datasets": 2, "datasets-cli": 2, - "datatool": 318, + "datatool": 319, "datavzrd": 2, "date": 82, "datma.py": 1, @@ -9227,7 +9229,7 @@ "deepsig": 1, "deepsignal_plant": 1, "deepsvr": 1, - "deeptools": 10, + "deeptools": 11, "defaults.cfg": 1, "defaults.py": 2, "defense-finder": 2, @@ -9254,7 +9256,7 @@ "deltaBS.pl": 1, "delta_filter_wrapper.py": 5, "delta_unit_test": 5, - "deltablast": 318, + "deltablast": 319, "deltapd": 1, "demes": 4, "demesdraw": 1, @@ -9305,7 +9307,7 @@ "depth_calc.py": 1, "depth_estim_from_vcf.sh": 1, "depythontex": 1, - "derb": 5793, + "derb": 5795, "derep_stuff.py": 1, "deripcal": 1, "derna": 1, @@ -9389,7 +9391,7 @@ "diff_iso_usage": 1, "diff_motif": 1, "diffacto": 1, - "difference-uid-lists": 10, + "difference-uid-lists": 11, "difference_from_first_TSS_script_mordor.r": 1, "difference_from_first_TSS_script_mordor_chrom_wide.r": 1, "differentialBindingAffinity_multipleSNPs": 1, @@ -9428,7 +9430,7 @@ "dirmngr-client": 2, "dirname": 82, "dirseq": 2, - "disambiguate-nucleotides": 198, + "disambiguate-nucleotides": 199, "disco": 17, "disco.cfg": 1, "disco_2.cfg": 1, @@ -9468,7 +9470,7 @@ "django-admin": 4, "django-admin.py": 3, "django-admin.pyc": 1, - "djpeg": 5731, + "djpeg": 5734, "dkfzbiasfilter.py": 1, "dkfzbiasfilter_summarize.py": 1, "dlcoal_to_dlcpar": 1, @@ -9539,7 +9541,7 @@ "docker_test_script": 1, "docking_py": 1, "docopt.py": 1, - "docutils": 78, + "docutils": 79, "dodge": 1, "dodgedists": 1, "doesitcache": 46, @@ -9579,15 +9581,15 @@ "download-db.sh": 9, "download-dfam.py": 1, "download-entities.pl": 2, - "download-ncbi-data": 271, + "download-ncbi-data": 272, "download-ncbi-genomes": 1, - "download-ncbi-software": 198, + "download-ncbi-software": 199, "download-ncbi-taxa.sh": 1, "download-ncbi-taxmaps": 1, "download-ncbi-taxonomy": 1, - "download-pmc": 10, - "download-pubmed": 285, - "download-sequence": 285, + "download-pmc": 11, + "download-pubmed": 286, + "download-sequence": 286, "download-spatypes.sh": 1, "download-srr-files": 3, "download-taxonomy.sh": 1, @@ -9687,7 +9689,7 @@ "drtext": 24, "drttest": 1, "drugbank": 1, - "ds2pme": 10, + "ds2pme": 11, "dsCompareCurves": 1, "dsComputeBEDDensity": 1, "dsComputeGCCoverage": 1, @@ -9824,7 +9826,7 @@ "dupre": 1, "dupsifter": 1, "dust": 13, - "dustmasker": 318, + "dustmasker": 319, "dv_call_variants.py": 1, "dv_make_examples.py": 1, "dv_postprocess_variants.py": 1, @@ -9913,7 +9915,7 @@ "ecodbtaxstat": 1, "ecofind": 1, "ecogrep": 1, - "ecommon.sh": 198, + "ecommon.sh": 199, "econtact": 88, "ecotag": 1, "ecotaxspecificity": 1, @@ -9949,9 +9951,9 @@ "edonr256-hash": 9, "edonr512-hash": 9, "eel": 1, - "efetch": 286, + "efetch": 287, "effectivet3": 1, - "efilter": 286, + "efilter": 287, "efishent": 1, "efn": 1, "efn2": 5, @@ -9967,7 +9969,7 @@ "eigenstrat_database_tools": 1, "eigenstrat_rename_snps": 1, "eigenstrat_snp_coverage": 1, - "einfo": 286, + "einfo": 287, "einsi": 97, "einverted": 24, "eject": 13, @@ -9996,7 +9998,7 @@ "elfedit": 8, "elgato_report.py": 1, "eliminateBadSuperReadsUsingList": 1, - "elink": 286, + "elink": 287, "elm2meme": 13, "elprep": 1, "elsize": 6, @@ -10031,8 +10033,8 @@ "enano": 1, "enasearch": 1, "enc": 1, - "enc2xs": 1675, - "encguess": 1675, + "enc2xs": 1678, + "encguess": 1678, "encode2var": 1, "encode_dir": 1, "encode_exclude_loci": 1, @@ -10064,7 +10066,7 @@ "enumall": 1, "enumerate_paths.py": 1, "env": 82, - "env-execute": 6814, + "env-execute": 6821, "env.yml": 1, "env_parallel": 99, "env_parallel.ash": 99, @@ -10081,7 +10083,7 @@ "environment.yml": 1, "envpath": 3, "envset.cmd": 1, - "envsubst": 5268, + "envsubst": 5270, "eoulsan.sh": 1, "epa-ng": 4, "epestfind": 24, @@ -10097,7 +10099,7 @@ "epimuller-define": 1, "epimuller-draw": 1, "epimuller-parse": 1, - "epost": 286, + "epost": 287, "eprimer3": 24, "eprimer32": 24, "eproxy": 88, @@ -10119,7 +10121,7 @@ "erase-pubmed": 1, "erase_annoying_sequences.py": 1, "erate-estimate": 3, - "erb": 29, + "erb": 30, "erds_pipeline": 1, "ericscript.pl": 1, "erne-bs5": 1, @@ -10132,11 +10134,11 @@ "errno": 3, "errorEstimate": 6, "error_corrected2frg": 1, - "esample": 271, + "esample": 272, "esbuild": 1, "esd2esi": 10, "esdcompat": 12, - "esearch": 286, + "esearch": 287, "esh": 1, "esimsa": 1, "esl-afetch": 163, @@ -10184,8 +10186,8 @@ "estimate-mer-threshold": 3, "estimate-metagene-profile-bayes-factors": 3, "estimate-orf-bayes-factors": 2, - "estimateReadFiltering": 10, - "estimateScaleFactor": 10, + "estimateReadFiltering": 11, + "estimateScaleFactor": 11, "estimateScalePerMotif.sh": 1, "estimateSelfSimilarity.pl": 1, "estimate_observation_richness.py": 1, @@ -10195,7 +10197,7 @@ "estscan": 1, "estwise": 3, "estwisedb": 3, - "esummary": 286, + "esummary": 287, "etandem": 24, "ete": 2, "ete3": 56, @@ -10250,7 +10252,7 @@ "excise_precursors.pl": 1, "excise_precursors_iterative_final.pl": 1, "excl_seqs": 2, - "exclude-uid-lists": 271, + "exclude-uid-lists": 272, "exclude_N": 1, "exclude_loci": 1, "exclude_loci_backup": 1, @@ -10276,7 +10278,7 @@ "expam": 1, "expam_limit": 1, "expand": 82, - "expand-current": 271, + "expand-current": 272, "expandCols": 269, "expand_fastq": 1, "expand_links.pl": 7, @@ -10445,7 +10447,7 @@ "ezez4makefile_v4.pl": 1, "ezez4qsub_vx1.pl": 1, "ezez_vx1.pl": 1, - "f2py": 2018, + "f2py": 2022, "f2py2": 135, "f2py2.7": 135, "f2py3": 1591, @@ -10486,7 +10488,7 @@ "fadvise": 1, "fahash": 1, "fai": 1, - "faidx": 117, + "faidx": 118, "faidx_dir": 1, "fairseq-eval-lm": 1, "fairseq-generate": 1, @@ -10710,20 +10712,20 @@ "fasten_trim": 1, "fasten_validate": 1, "faster_reps.py": 1, - "fasterq-dump": 21, - "fasterq-dump-orig": 19, + "fasterq-dump": 22, + "fasterq-dump-orig": 20, "fasterq-dump-orig.2.10.0": 1, "fasterq-dump-orig.2.10.8": 3, "fasterq-dump-orig.2.10.9": 3, - "fasterq-dump-orig.2.11.0": 9, + "fasterq-dump-orig.2.11.0": 10, "fasterq-dump-orig.3.0.0": 2, "fasterq-dump-orig.3.0.3": 1, "fasterq-dump-orig.3.1.0": 1, - "fasterq-dump.2": 17, + "fasterq-dump.2": 18, "fasterq-dump.2.10.0": 1, "fasterq-dump.2.10.8": 3, "fasterq-dump.2.10.9": 3, - "fasterq-dump.2.11.0": 9, + "fasterq-dump.2.11.0": 10, "fasterq-dump.2.9.6": 1, "fasterq-dump.3": 4, "fasterq-dump.3.0.0": 2, @@ -10751,20 +10753,20 @@ "fastq-clipper": 2, "fastq-count": 1, "fastq-dl": 2, - "fastq-dump": 21, - "fastq-dump-orig": 19, + "fastq-dump": 22, + "fastq-dump-orig": 20, "fastq-dump-orig.2.10.0": 1, "fastq-dump-orig.2.10.8": 3, "fastq-dump-orig.2.10.9": 3, - "fastq-dump-orig.2.11.0": 9, + "fastq-dump-orig.2.11.0": 10, "fastq-dump-orig.3.0.0": 2, "fastq-dump-orig.3.0.3": 1, "fastq-dump-orig.3.1.0": 1, - "fastq-dump.2": 17, + "fastq-dump.2": 18, "fastq-dump.2.10.0": 1, "fastq-dump.2.10.8": 3, "fastq-dump.2.10.9": 3, - "fastq-dump.2.11.0": 9, + "fastq-dump.2.11.0": 10, "fastq-dump.2.9.6": 1, "fastq-dump.3": 4, "fastq-dump.3.0.0": 2, @@ -10776,9 +10778,9 @@ "fastq-interleave": 11, "fastq-join": 3, "fastq-kmers": 2, - "fastq-load": 11, - "fastq-load.2": 9, - "fastq-load.2.11.0": 9, + "fastq-load": 12, + "fastq-load.2": 10, + "fastq-load.2.11.0": 10, "fastq-load.3": 2, "fastq-load.3.0.0": 2, "fastq-match": 2, @@ -10987,12 +10989,12 @@ "fermi2.pl": 2, "fetch": 4, "fetch-extras": 73, - "fetch-local": 10, - "fetch-nmcds": 10, - "fetch-pmc": 10, - "fetch-pubmed": 285, + "fetch-local": 11, + "fetch-nmcds": 11, + "fetch-pmc": 11, + "fetch-pubmed": 286, "fetch-tax.pl": 1, - "fetch-taxonomy": 10, + "fetch-taxonomy": 11, "fetchChromSizes": 5, "fetchEnaLibraryFastqs.sh": 1, "fetchFastq.sh": 1, @@ -11071,18 +11073,18 @@ "filter-alignments.py": 1, "filter-bam": 2, "filter-bam-by-ids": 3, - "filter-columns": 186, - "filter-genbank": 10, + "filter-columns": 187, + "filter-genbank": 11, "filter-gff": 1, "filter-nonunique-peptide-matches": 2, "filter-positions.pl": 1, "filter-ppx.pl": 14, - "filter-record": 10, + "filter-record": 11, "filter-sort": 1, "filter-stage-1.prl": 4, "filter-stage-2.prl": 4, "filter-stats.pl": 1, - "filter-stop-words": 286, + "filter-stop-words": 287, "filter-stoptags.py": 7, "filter-table": 12, "filter-variations": 2, @@ -11258,7 +11260,7 @@ "find-all-symbols": 2, "find-compounds.pl": 1, "find-duplicate-reads": 2, - "find-in-gene": 198, + "find-in-gene": 199, "find-knots.py": 7, "find-mango-assembly.sh": 1, "find-mango-home": 1, @@ -11467,7 +11469,7 @@ "font-awesome-to-png": 2, "font2c": 3, "fontinst": 1, - "fonttools": 378, + "fonttools": 381, "fop": 1, "forceOneClusterPerPairMem.py": 1, "forest.py": 1, @@ -11554,7 +11556,7 @@ "freec": 1, "freec2bed.pl": 1, "freec2circos.pl": 1, - "freetype-config": 5793, + "freetype-config": 5796, "freeze_graph": 25, "freq2group.pl": 5, "frequency.py": 1, @@ -11698,8 +11700,8 @@ "funr": 1, "funzip": 25, "fuse": 1, - "fuse-ranges": 198, - "fuse-segments": 186, + "fuse-ranges": 199, + "fuse-segments": 187, "fuse.sh": 30, "fusion-bloom": 1, "fusion-bloom.makefile": 1, @@ -11978,9 +11980,9 @@ "gb2fasta": 1, "gbSmallDNA2gff.pl": 14, "gbase": 2, - "gbf2fsa": 10, - "gbf2ref": 10, - "gbf2xml": 285, + "gbf2fsa": 11, + "gbf2ref": 11, + "gbf2xml": 286, "gbf2xml.bak": 1, "gbfalncut": 2, "gbfcut": 2, @@ -12077,9 +12079,9 @@ "gdaltindex": 36, "gdaltransform": 36, "gdalwarp": 36, - "gdbm_dump": 24, - "gdbm_load": 24, - "gdbmtool": 24, + "gdbm_dump": 25, + "gdbm_load": 25, + "gdbmtool": 25, "gdbus": 1650, "gdbus-codegen": 1648, "gdc-client": 1, @@ -12104,7 +12106,7 @@ "gecco": 1, "geckodriver": 2, "geecee": 24, - "gem": 29, + "gem": 30, "gem-indexer": 3, "gem-mapper": 3, "gem-retriever": 3, @@ -12134,20 +12136,20 @@ "genbank_to": 1, "genblastG": 1, "genbox": 1, - "genbrk": 5793, - "gencfu": 5793, + "genbrk": 5795, + "gencfu": 5795, "genclust": 1, - "gencnval": 5793, + "gencnval": 5795, "gencode_extract_relevant_gtf_exons.pl": 1, "gencode_singleton_unit_test": 5, "genconf": 1, "gencore": 1, "gencove": 1, "gendb": 13, - "gendict": 5793, + "gendict": 5795, "gendist": 10, "gene2protein.db3": 2, - "gene2range": 186, + "gene2range": 187, "gene2xml": 1, "geneAssociationZscore.py": 1, "geneBody_coverage.py": 3, @@ -12296,7 +12298,7 @@ "genotyphi.py": 1, "genpcz": 2, "genpept2gsi.pl": 2, - "genrb": 5793, + "genrb": 5795, "genreflex": 3, "genremdinputs.py": 6, "genrestr": 4, @@ -12495,8 +12497,8 @@ "get_sequence_type": 1, "get_sequences_for_meme.py": 1, "get_simple_cycs.py": 1, - "get_species_taxids.sh": 285, - "get_species_taxids.sh.bak": 280, + "get_species_taxids.sh": 286, + "get_species_taxids.sh.bak": 281, "get_standard_headers": 1, "get_stats_summary.pl": 1, "get_subontology_from.pl": 1, @@ -12566,9 +12568,9 @@ "getscu": 1, "getsize": 13, "getsnvfreq_by_interval": 1, - "gettext": 5268, - "gettext.sh": 5268, - "gettextize": 5268, + "gettext": 5270, + "gettext.sh": 5270, + "gettextize": 5270, "getuniqgenomealign": 1, "getuniqgenomealign_interval": 1, "getuniqgenomealign_sample_names": 1, @@ -12668,7 +12670,7 @@ "gi2taxid.sh": 30, "gid-taxid": 1, "gie": 39, - "gif2h5": 528, + "gif2h5": 530, "gif2hdf": 122, "gif2rgb": 735, "gif2tiff": 189, @@ -12741,11 +12743,11 @@ "glnexus_cli": 1, "glob_res.pl": 1, "global.json": 1, - "glpsol": 224, + "glpsol": 225, "glsearch36": 7, "gm": 2, - "gm2ranges": 10, - "gm2segs": 10, + "gm2ranges": 11, + "gm2segs": 11, "gmap": 13, "gmap.nosimd": 8, "gmap.sse42": 11, @@ -13074,7 +13076,7 @@ "gsnapl.sse42": 11, "gsnd": 104, "gsort": 5, - "gss-client": 5764, + "gss-client": 5768, "gss-server": 2, "gst-completion-helper": 1, "gst-device-monitor-1.0": 227, @@ -13295,39 +13297,39 @@ "h264dec": 9, "h264enc": 9, "h2load": 3929, - "h2ph": 1675, - "h2xs": 1675, + "h2ph": 1678, + "h2xs": 1678, "h4_ncdump": 122, "h4_ncgen": 122, "h4cc": 122, "h4redeploy": 122, - "h52gif": 528, - "h5c++": 528, - "h5cc": 533, - "h5clear": 512, - "h5copy": 528, - "h5debug": 528, - "h5delete": 71, - "h5diff": 528, - "h5dump": 530, - "h5fc": 515, - "h5format_convert": 512, - "h5fuse.sh": 41, - "h5import": 528, - "h5jam": 528, - "h5ls": 528, - "h5mkgrp": 528, + "h52gif": 530, + "h5c++": 530, + "h5cc": 535, + "h5clear": 514, + "h5copy": 530, + "h5debug": 530, + "h5delete": 72, + "h5diff": 530, + "h5dump": 532, + "h5fc": 517, + "h5format_convert": 514, + "h5fuse.sh": 42, + "h5import": 530, + "h5jam": 530, + "h5ls": 530, + "h5mkgrp": 530, "h5pcc": 3, "h5perf": 3, - "h5perf_serial": 528, + "h5perf_serial": 530, "h5pfc": 3, - "h5redeploy": 528, - "h5repack": 528, - "h5repart": 528, - "h5stat": 528, - "h5tools_test_utils": 21, - "h5unjam": 528, - "h5watch": 512, + "h5redeploy": 530, + "h5repack": 530, + "h5repart": 530, + "h5stat": 530, + "h5tools_test_utils": 22, + "h5unjam": 530, + "h5watch": 514, "hAMRoaster": 1, "h_num": 1, "haarz.x": 1, @@ -13510,9 +13512,9 @@ "hecatomb": 1, "hed": 1, "heinz": 1, - "helicos-load": 11, - "helicos-load.2": 9, - "helicos-load.2.11.0": 9, + "helicos-load": 12, + "helicos-load.2": 10, + "helicos-load.2.11.0": 10, "helicos-load.3": 2, "helicos-load.3.0.0": 2, "helixturnhelix": 24, @@ -13526,7 +13528,7 @@ "hexdump": 13, "hgGcPercent": 3, "hgvs-shell": 1, - "hgvs2spdi": 198, + "hgvs2spdi": 199, "hhalign": 4, "hhalign_omp": 4, "hhblits": 4, @@ -13838,21 +13840,21 @@ "humann_unpack_pathways": 1, "humid": 1, "hv-pipeline.py": 1, - "hwloc-annotate": 58, + "hwloc-annotate": 59, "hwloc-assembler": 2, "hwloc-assembler-remote": 2, - "hwloc-bind": 58, - "hwloc-calc": 58, - "hwloc-compress-dir": 58, - "hwloc-diff": 58, + "hwloc-bind": 59, + "hwloc-calc": 59, + "hwloc-compress-dir": 59, + "hwloc-diff": 59, "hwloc-distances": 2, - "hwloc-distrib": 58, - "hwloc-gather-cpuid": 56, - "hwloc-gather-topology": 58, - "hwloc-info": 58, - "hwloc-ls": 58, - "hwloc-patch": 58, - "hwloc-ps": 58, + "hwloc-distrib": 59, + "hwloc-gather-cpuid": 57, + "hwloc-gather-topology": 59, + "hwloc-info": 59, + "hwloc-ls": 59, + "hwloc-patch": 59, + "hwloc-ps": 59, "hyb_analyze": 1, "hyb_check": 1, "hyb_eval": 1, @@ -13918,10 +13920,10 @@ "icescreen": 1, "ichar": 1, "icon-font-to-png": 2, - "iconv": 5461, - "icu-config": 5793, - "icuexportdata": 2009, - "icuinfo": 5793, + "iconv": 5462, + "icu-config": 5795, + "icuexportdata": 2011, + "icuinfo": 5795, "id": 82, "idba": 10, "idba.o": 10, @@ -13951,20 +13953,20 @@ "idfetch": 1, "idiag-socket-details": 8, "idle": 332, - "idle3": 3289, - "idle3.10": 795, - "idle3.11": 263, + "idle3": 3294, + "idle3.10": 798, + "idle3.11": 264, "idle3.12": 173, "idle3.4": 6, "idle3.5": 103, "idle3.6": 342, "idle3.7": 383, "idle3.8": 574, - "idle3.9": 650, + "idle3.9": 651, "idlj": 117, "idmatrix.sh": 30, "idn": 30, - "idn2": 256, + "idn2": 258, "idpAssemble": 2, "idpQonvert": 2, "idpQuery": 2, @@ -14031,11 +14033,11 @@ "igor": 1, "igor-compute_pgen": 1, "igphyml": 1, - "igraph": 38, + "igraph": 39, "igraph_extract_clusters.R": 1, "igv_jasmine": 1, "igvtools": 5, - "igzip": 77, + "igzip": 78, "iit_dump": 11, "iit_get": 11, "iit_store": 11, @@ -14044,20 +14046,20 @@ "ilasm": 15, "illinkanalyzer": 13, "illumina-cleanup": 1, - "illumina-dump": 21, - "illumina-dump.2": 17, + "illumina-dump": 22, + "illumina-dump.2": 18, "illumina-dump.2.10.0": 1, "illumina-dump.2.10.8": 3, "illumina-dump.2.10.9": 3, - "illumina-dump.2.11.0": 9, + "illumina-dump.2.11.0": 10, "illumina-dump.2.9.6": 1, "illumina-dump.3": 4, "illumina-dump.3.0.0": 2, "illumina-dump.3.0.3": 1, "illumina-dump.3.1.0": 1, - "illumina-load": 11, - "illumina-load.2": 9, - "illumina-load.2.11.0": 9, + "illumina-load": 12, + "illumina-load.2": 10, + "illumina-load.2.11.0": 10, "illumina-load.3": 2, "illumina-load.3.0.0": 2, "illumina.py": 1, @@ -14168,12 +14170,12 @@ "infoalign": 24, "infoassembly": 24, "infobase": 24, - "infocmp": 7651, + "infocmp": 7657, "inforesidue": 24, "informant.py": 1, "infoseq": 24, - "infotocap": 7651, - "ini2xml": 10, + "infotocap": 7657, + "ini2xml": 11, "init_Trinotate_sqlite_db.pl": 1, "init_db.sh": 1, "initdb": 45, @@ -14231,7 +14233,7 @@ "installpackages.R": 1, "installvst": 15, "instance_events": 29, - "instmodsh": 1675, + "instmodsh": 1678, "int_seqs_to_char_strings.py": 58, "intake": 1, "intake-server": 1, @@ -14266,7 +14268,7 @@ "interprophet.rb": 1, "interproscan.sh": 1, "intersect": 5, - "intersect-uid-lists": 284, + "intersect-uid-lists": 285, "intersectBed": 269, "intersectFiles.py": 2, "intersectGenomicSets.py": 1, @@ -14341,7 +14343,7 @@ "iqtree": 26, "iqtree2": 15, "ir": 1, - "irb": 29, + "irb": 30, "irescue": 1, "irf": 1, "irida-sistr-results": 1, @@ -14371,6 +14373,7 @@ "isatab_validate": 1, "isatools": 1, "isect_mercator_alignment_gff": 1, + "iseq": 1, "isescan.py": 1, "isjobcomplete.sh": 1, "islandpath": 2, @@ -14543,7 +14546,7 @@ "jobTreeStatus": 2, "jobTreeTest_Dependencies.py": 1, "join": 82, - "join-into-groups-of": 286, + "join-into-groups-of": 287, "join-long-chromosomes": 3, "join.pl": 1, "join.pl.bak": 1, @@ -14567,8 +14570,8 @@ "jp.py": 100, "jpackage": 114, "jpeg2hdf": 122, - "jpegtran": 5731, - "jpgicc": 971, + "jpegtran": 5734, + "jpgicc": 974, "jpredapi": 1, "jps": 533, "jq": 300, @@ -14580,12 +14583,12 @@ "jsearch": 1, "jshell": 424, "json2gff": 1, - "json2xml": 198, + "json2xml": 199, "json_collect_data_source.py": 1, - "json_pp": 1675, - "json_xs": 344, + "json_pp": 1678, + "json_xs": 345, "jsondiff": 8, - "jsonl2xml": 10, + "jsonl2xml": 11, "jsonpatch": 8, "jsonpointer": 10, "jsonschema": 206, @@ -14637,17 +14640,17 @@ "jupyter-serverextension": 37, "jupyter-troubleshoot": 143, "jupyter-trust": 136, - "just-first-key": 10, + "just-first-key": 11, "just_blast_test.pl": 1, "jwebserver": 32, - "k5srvutil": 5764, + "k5srvutil": 5768, "k8": 159, "k8-Linux": 1, "k_means": 1, "k_means_coefficient": 1, "k_neighbors": 1, "k_neighbors_coefficient": 1, - "kadmin": 5764, + "kadmin": 5768, "kadmin.local": 2, "kadmind": 2, "kaiju": 4, @@ -14677,18 +14680,18 @@ "kanji-fontmap-creator": 1, "kapastats.sh": 29, "kaptive.py": 2, - "kar": 19, + "kar": 20, "kar+": 2, "kar+.3": 2, "kar+.3.0.0": 2, "kar+meta": 2, "kar+meta.3": 2, "kar+meta.3.0.0": 2, - "kar.2": 17, + "kar.2": 18, "kar.2.10.0": 1, "kar.2.10.8": 3, "kar.2.10.9": 3, - "kar.2.11.0": 9, + "kar.2.11.0": 10, "kar.2.9.6": 1, "kar.3": 2, "kar.3.0.0": 2, @@ -14730,18 +14733,18 @@ "kdb-index.3": 2, "kdb-index.3.0.0": 2, "kdb5_util": 2, - "kdbmeta": 21, - "kdbmeta.2": 17, + "kdbmeta": 22, + "kdbmeta.2": 18, "kdbmeta.2.10.0": 1, "kdbmeta.2.10.8": 3, "kdbmeta.2.10.9": 3, - "kdbmeta.2.11.0": 9, + "kdbmeta.2.11.0": 10, "kdbmeta.2.9.6": 1, "kdbmeta.3": 4, "kdbmeta.3.0.0": 2, "kdbmeta.3.0.3": 1, "kdbmeta.3.1.0": 1, - "kdestroy": 5764, + "kdestroy": 5768, "kea-config": 35, "keep-header": 1, "keep-ribo-periodic": 1, @@ -14751,16 +14754,16 @@ "keggcharter.py": 1, "keggpathway_map.py": 1, "keyFreq": 1, - "keyctl": 2394, + "keyctl": 2398, "keygen": 1, "keyring": 10, "keytool": 533, - "kget": 17, - "kget.2": 17, + "kget": 18, + "kget.2": 18, "kget.2.10.0": 1, "kget.2.10.8": 3, "kget.2.10.9": 3, - "kget.2.11.0": 9, + "kget.2.11.0": 10, "kget.2.9.6": 1, "kggseq": 1, "kggseq1.log": 1, @@ -14782,7 +14785,7 @@ "kinSimRiboswitch": 1, "king": 1, "kingfisher": 1, - "kinit": 5764, + "kinit": 5768, "kinship-read": 1, "kinshipDecompose": 1, "kinwalker": 48, @@ -14795,7 +14798,7 @@ "kitsch": 10, "kitsune": 1, "kleborate": 1, - "klist": 5764, + "klist": 5768, "kma": 18, "kma_index": 18, "kma_shm": 18, @@ -14880,7 +14883,7 @@ "kp1mer_to_kmer.py": 1, "kp2np.py": 1, "kpal": 2, - "kpasswd": 5764, + "kpasswd": 5768, "kpileup.py": 1, "kprop": 2, "kpropd": 2, @@ -14927,7 +14930,7 @@ "krakenuniq-report": 1, "krakenuniq-translate": 1, "krakmeopen": 1, - "krb5-config": 5764, + "krb5-config": 5768, "krb5-send-pr": 2, "krb5kdc": 2, "kreport2krona.py": 3, @@ -14943,9 +14946,9 @@ "kseq_split": 1, "ksnp": 1, "kssd": 1, - "ksu": 5764, + "ksu": 5768, "ksw": 1, - "kswitch": 5764, + "kswitch": 5768, "ktClassifyBLAST": 16, "ktClassifyHits": 12, "ktGetContigMagnitudes": 16, @@ -14976,12 +14979,12 @@ "ktserver": 2, "kttimedmgr": 2, "kttimedtest": 2, - "ktutil": 5764, + "ktutil": 5768, "ktutilmgr": 2, "ktutilserv": 2, "ktutiltest": 2, "kubectl": 1, - "kvno": 5764, + "kvno": 5768, "kwip": 2, "kwip-stats": 2, "l4p-tmpl": 32, @@ -15039,12 +15042,12 @@ "latexmk": 1, "latexpand": 1, "latexrevise": 1, - "latf-load": 19, - "latf-load.2": 17, + "latf-load": 20, + "latf-load.2": 18, "latf-load.2.10.0": 1, "latf-load.2.10.8": 3, "latf-load.2.10.9": 3, - "latf-load.2.11.0": 9, + "latf-load.2.11.0": 10, "latf-load.2.9.6": 1, "latf-load.3": 2, "latf-load.3.0.0": 2, @@ -15099,7 +15102,7 @@ "lefse_plot_features.py": 1, "lefse_plot_res.py": 1, "lefse_run.py": 1, - "legacy_blast.pl": 318, + "legacy_blast.pl": 319, "legsta": 1, "lemon-0.x-to-1.x.sh": 4, "lemur": 1, @@ -15133,8 +15136,8 @@ "libclair3.cpython-36m-x86_64-linux-gnu.so": 1, "libclair3.o": 1, "libclair3.so": 1, - "libdeflate-gunzip": 4093, - "libdeflate-gzip": 4093, + "libdeflate-gunzip": 4096, + "libdeflate-gzip": 4096, "libdrawgram.so": 5, "libdrawtree.so": 5, "libfile.pl": 1, @@ -15143,9 +15146,9 @@ "libiomp5md.dll": 1, "liblist.pl": 1, "liblist.pl.bak": 1, - "libnetcfg": 1675, - "libpng-config": 5845, - "libpng16-config": 5845, + "libnetcfg": 1678, + "libpng-config": 5848, + "libpng16-config": 5848, "libpypy-c.so": 1, "libpypy-c.so.debug": 1, "libpypy3-c.so.debug": 3, @@ -15201,7 +15204,7 @@ "link_ssv.py": 1, "linkage2allegro": 1, "linkhsp_unit_test": 5, - "linkicc": 971, + "linkicc": 974, "linknets": 2, "links2sql.pl": 7, "linksBed": 269, @@ -15413,7 +15416,7 @@ "longshot": 3, "longstitch": 1, "look": 13, - "loompy": 9, + "loompy": 10, "lorax": 1, "lordec-build-SR-graph": 2, "lordec-correct": 2, @@ -15467,8 +15470,8 @@ "lsmem": 13, "lsns": 13, "lss3": 29, - "lstopo": 58, - "lstopo-no-graphics": 58, + "lstopo": 59, + "lstopo-no-graphics": 59, "ltqnorm.pl": 1, "ltqnorm.pl.bak": 1, "ltr_finder": 3, @@ -15508,17 +15511,17 @@ "lz4_decompress": 2, "lz4c": 3498, "lz4cat": 3498, - "lzcat": 7477, - "lzcmp": 7477, - "lzdiff": 7477, - "lzegrep": 7477, - "lzfgrep": 7477, - "lzgrep": 7477, - "lzless": 7477, - "lzma": 7477, - "lzmadec": 7477, - "lzmainfo": 7477, - "lzmore": 7477, + "lzcat": 7483, + "lzcmp": 7483, + "lzdiff": 7483, + "lzegrep": 7483, + "lzfgrep": 7483, + "lzgrep": 7483, + "lzless": 7483, + "lzma": 7483, + "lzmadec": 7483, + "lzmainfo": 7483, + "lzmore": 7483, "lzop_build_offset_table.py": 58, "m-party": 1, "m-tx": 1, @@ -15659,7 +15662,7 @@ "mageckGSEA": 1, "magetab_insert_array.pl": 1, "magetab_insert_sub.pl": 1, - "magic": 19, + "magic": 20, "magic-sequence": 2, "magic-square": 2, "magicblast": 1, @@ -15800,7 +15803,7 @@ "make_mate_frg.pl": 1, "make_midpoint_matrix": 1, "make_mr_frg.pl": 1, - "make_multi_seq.pl": 44, + "make_multi_seq.pl": 45, "make_ndx": 4, "make_nr_pangenome_matrix.pl": 1, "make_otu_heatmap.py": 1, @@ -15829,12 +15832,12 @@ "makeagp2.awk": 1, "makeagp_full.awk": 1, "makeagp_full2.awk": 1, - "makeblastdb": 320, + "makeblastdb": 321, "makecert": 15, "makechimeras.sh": 30, "makeclusterdb": 4, "makecontaminatedgenomes.sh": 30, - "makeconv": 5793, + "makeconv": 5795, "makedtx": 1, "makefasta.awk": 1, "makegeo": 35, @@ -15843,13 +15846,13 @@ "makehmmerdb": 173, "makeidx.pl": 4, "makemat": 30, - "makembindex": 318, + "makembindex": 319, "makenucseq": 24, "makepBAM_genome.sh": 1, "makepBAM_transcriptome.sh": 1, "makeplot.pl": 3, "makepolymers.sh": 30, - "makeprofiledb": 318, + "makeprofiledb": 319, "makeprotseq": 24, "maker": 1, "maker2chado": 1, @@ -16180,11 +16183,11 @@ "mcxmap": 24, "mcxrand": 23, "mcxsubs": 24, - "md5cp": 17, - "md5cp.2": 15, + "md5cp": 18, + "md5cp.2": 16, "md5cp.2.10.8": 3, "md5cp.2.10.9": 3, - "md5cp.2.11.0": 9, + "md5cp.2.11.0": 10, "md5cp.3": 2, "md5cp.3.0.0": 2, "md5fa": 503, @@ -17032,24 +17035,24 @@ "mseqtools": 1, "msformatter": 1, "msfragger": 2, - "msgattrib": 5268, - "msgcat": 5268, - "msgcmp": 5268, - "msgcomm": 5268, - "msgconv": 5268, - "msgen": 5268, - "msgexec": 5268, + "msgattrib": 5270, + "msgcat": 5270, + "msgcmp": 5270, + "msgcomm": 5270, + "msgconv": 5270, + "msgen": 5270, + "msgexec": 5270, "msgf2pin": 1, "msgf_plus": 3, - "msgfilter": 5268, - "msgfmt": 5268, + "msgfilter": 5270, + "msgfmt": 5270, "msgfplus_search.rb": 1, - "msggrep": 5268, - "msginit": 5268, - "msgmerge": 5268, + "msggrep": 5270, + "msginit": 5270, + "msgmerge": 5270, "msgserv": 1, - "msgunfmt": 5268, - "msguniq": 5268, + "msgunfmt": 5270, + "msguniq": 5270, "msi": 1, "msi_cluster2reads": 1, "msi_clustr2map.pl": 1, @@ -17123,8 +17126,8 @@ "multi-bin-packing": 2, "multi-extract": 2, "multiBamCov": 269, - "multiBamSummary": 10, - "multiBigwigSummary": 10, + "multiBamSummary": 11, + "multiBigwigSummary": 11, "multiIntersectBed": 269, "multiSub": 1, "multi_length_hist.py": 1, @@ -17300,7 +17303,7 @@ "nasm": 1, "nasp": 1, "native2ascii": 112, - "natsort": 140, + "natsort": 141, "nb-classify": 1, "nb-train": 1, "nbmodel_stan2.py": 1, @@ -17339,9 +17342,9 @@ "ncrf_to_bed": 2, "ncrf_to_bed.py": 2, "ncurses5-config": 565, - "ncurses6-config": 6944, + "ncurses6-config": 6950, "ncursesw5-config": 703, - "ncursesw6-config": 6945, + "ncursesw6-config": 6951, "ndg_httpclient": 2, "ndisasm": 1, "ndmetis": 58, @@ -17431,7 +17434,7 @@ "nf-test": 1, "nfe-umbrella-slice": 6, "ngd": 9, - "ngettext": 5268, + "ngettext": 5270, "ngg_barabasi_albert": 2, "ngg_barbell": 2, "ngg_complete": 2, @@ -17441,9 +17444,9 @@ "ngg_newman_watts_strogatz": 2, "ngg_path": 2, "ngg_ring_lattice": 2, - "nghttp": 4432, - "nghttpd": 4432, - "nghttpx": 4432, + "nghttp": 4436, + "nghttpd": 4436, + "nghttpx": 4436, "ngless": 2, "ngless-wrapped": 1, "nglview": 2, @@ -17477,7 +17480,7 @@ "ngsngs": 1, "ngsplotdb.py": 5, "ngsutils": 1, - "nhance.sh": 10, + "nhance.sh": 11, "nhmmer": 173, "nhmmscan": 173, "nib-conform": 2, @@ -17584,7 +17587,7 @@ "normalize_multicov.pl": 1, "normalize_oneD.R": 1, "normalize_table.py": 1, - "normalizer": 450, + "normalizer": 451, "normandcorrectwrapper.sh": 1, "nose2": 1, "nose2-2.7": 1, @@ -17624,7 +17627,7 @@ "nproc": 82, "npth-config": 2, "npx": 15, - "nquire": 286, + "nquire": 287, "nquire.bak": 1, "nrForwardSplicedReads.pl": 1, "nr_ORFs_gff3.pl": 5, @@ -17683,7 +17686,7 @@ "nullarbor.pl": 1, "nulltype_module.py": 1, "numCI": 4, - "numba": 130, + "numba": 131, "number-lines": 1, "numfmt": 82, "numlines": 1, @@ -17966,11 +17969,11 @@ "openslide-quickhash1sum": 2, "openslide-show-properties": 2, "openslide-write-png": 2, - "openssl": 7719, + "openssl": 7726, "opentargets_validator": 1, - "opj_compress": 625, - "opj_decompress": 625, - "opj_dump": 625, + "opj_compress": 628, + "opj_decompress": 628, + "opj_dump": 628, "opl2ofm": 1, "opsin": 1, "opt": 6, @@ -18138,14 +18141,14 @@ "pacbio-correct": 2, "pacbio-correct.3": 2, "pacbio-correct.3.0.0": 2, - "pacbio-load": 11, - "pacbio-load.2": 9, - "pacbio-load.2.11.0": 9, + "pacbio-load": 12, + "pacbio-load.2": 10, + "pacbio-load.2.11.0": 10, "pacbio-load.3": 2, "pacbio-load.3.0.0": 2, - "pacbio-loadxml": 11, - "pacbio-loadxml.2": 9, - "pacbio-loadxml.2.11.0": 9, + "pacbio-loadxml": 12, + "pacbio-loadxml.2": 10, + "pacbio-loadxml.2.11.0": 10, "pacbio-loadxml.3": 2, "pacbio-loadxml.3.0.0": 2, "pacbio_post_process": 4, @@ -18458,14 +18461,14 @@ "pbt_plotting_example.py": 38, "pbt_plotting_example.pyc": 1, "pbtools-gather": 1, - "pbunzip2": 75, + "pbunzip2": 76, "pbutgcns": 3, "pbvalidate": 1, "pbvariantcaller": 1, "pbvariantcaller_dir": 1, "pbwt": 1, - "pbzcat": 75, - "pbzip2": 75, + "pbzcat": 76, + "pbzip2": 76, "pca": 1, "pca_anim_mc.pl": 2, "pcatoy": 1, @@ -18474,14 +18477,14 @@ "pcnt_bezier.lua": 1, "pcoaPlot.py": 2, "pcor": 1, - "pcre-config": 4929, + "pcre-config": 4930, "pcre2-config": 3688, "pcre2_jit_test": 3677, "pcre2grep": 3688, "pcre2posix_test": 113, "pcre2test": 3688, - "pcregrep": 4929, - "pcretest": 4929, + "pcregrep": 4930, + "pcretest": 4930, "pct2rgb.py": 4, "pctid_ani_sample": 1, "pcz_animate": 1, @@ -18679,7 +18682,7 @@ "perf": 1, "perfect-square": 2, "perform_controls.pl": 1, - "perl": 1675, + "perl": 1678, "perl-doc": 2, "perl-reversion": 9, "perl5.22.0": 54, @@ -18687,12 +18690,12 @@ "perl5.26.2": 369, "perl5.30.3": 5, "perl5.32.0": 64, - "perl5.32.1": 1183, - "perlbug": 1675, - "perldoc": 1675, - "perlivp": 1675, + "perl5.32.1": 1186, + "perlbug": 1678, + "perldoc": 1678, + "perlivp": 1678, "perltex": 1, - "perlthanks": 1675, + "perlthanks": 1678, "permuteGPAT++": 31, "permuteSmooth": 31, "permute_structure.pl": 1, @@ -18765,11 +18768,12 @@ "pgr-mdb": 1, "pgrep": 1, "pgt": 2, - "pgv-download-dataset": 1, - "pgv-mmseqs": 1, - "pgv-mummer": 1, - "pgv-pmauve": 1, - "pgv-simpleplot": 1, + "pgv-download-dataset": 2, + "pgv-gui": 1, + "pgv-mmseqs": 2, + "pgv-mummer": 2, + "pgv-pmauve": 2, + "pgv-simpleplot": 2, "ph5diff": 3, "phables": 1, "phame": 1, @@ -18832,7 +18836,7 @@ "phonopy-vasp-born": 1, "phonopy-vasp-efe": 1, "photo": 2, - "phrase-search": 284, + "phrase-search": 285, "phsolverserver": 3, "phy2nex": 1, "phykit": 1, @@ -19024,7 +19028,7 @@ "pickle_cat.py": 1, "pickorientation.awk": 1, "pickout": 1, - "piconv": 1675, + "piconv": 1678, "picopore": 1, "picopore-realtime": 1, "picopore-rename": 1, @@ -19032,7 +19036,7 @@ "picrust2_pipeline.py": 1, "pidof": 1, "pigeon": 1, - "pigz": 114, + "pigz": 116, "pilconvert.py": 23, "pildriver.py": 23, "pilercr": 7, @@ -19063,10 +19067,10 @@ "pints_caller": 1, "pints_normalizer": 1, "pints_visualizer": 1, - "pip": 3621, + "pip": 3626, "pip2": 1, "pip2.7": 1, - "pip3": 2546, + "pip3": 2551, "pipdeptree": 1, "pipelign": 1, "pipeline.py": 1, @@ -19217,13 +19221,13 @@ "pkfix-helper": 1, "pkg-config": 76, "pkg-config.bin": 76, - "pkgdata": 5793, + "pkgdata": 5795, "pkginfo": 10, "pkill": 1, "pktogf": 1, "pktype": 1, "pl2bat.pl": 3, - "pl2pm": 1675, + "pl2pm": 1678, "plaScope.sh": 1, "plac_runner.py": 60, "place_orient1.smk": 1, @@ -19272,29 +19276,29 @@ "plot.py": 2, "plotBfst.R": 17, "plotCorrGram.r": 5, - "plotCorrelation": 10, - "plotCoverage": 10, + "plotCorrelation": 11, + "plotCoverage": 11, "plotCoverageVsIdentity": 3, "plotDataStats.py": 1, - "plotEnrichment": 10, - "plotFingerprint": 10, + "plotEnrichment": 11, + "plotFingerprint": 11, "plotFunctions.py": 1, "plotHapLrt.R": 17, "plotHaplotypes.R": 17, "plotHaps": 31, - "plotHeatmap": 10, + "plotHeatmap": 11, "plotMappingSummary.R": 1, - "plotPCA": 10, + "plotPCA": 11, "plotPMD": 1, "plotPfst.R": 17, - "plotProfile": 10, + "plotProfile": 11, "plotProfile.R": 1, "plotSegments.R": 1, "plotSmoothed.R": 17, "plotUnknownResults.R": 1, "plotWCfst.R": 17, "plotXPEHH.R": 17, - "plot_2d.pl": 44, + "plot_2d.pl": 45, "plot_3Dpie.R": 3, "plot_RC_vs_GC.R": 1, "plot_aggregate_cut_matrix.R": 1, @@ -19317,7 +19321,7 @@ "plot_histogram.r": 1, "plot_histogram.r.bak": 1, "plot_isoform_usage": 1, - "plot_len1.pl": 44, + "plot_len1.pl": 45, "plot_marey.R": 1, "plot_matrix_heatmap.sh": 1, "plot_orf_density": 2, @@ -19386,11 +19390,11 @@ "pm4ngs-rnaseq-demo": 1, "pm4ngs-server": 1, "pm_which": 2, - "pma2apa": 10, - "pma2pme": 10, + "pma2apa": 11, + "pma2pme": 11, "pmap": 1, - "pmc2bioc": 10, - "pmc2info": 10, + "pmc2bioc": 11, + "pmc2info": 11, "pmd": 1, "pmdtools": 1, "pmemd_mdrun": 1, @@ -19416,21 +19420,21 @@ "pmxmutate": 1, "pn2pdf": 1, "pneumo-typer": 1, - "png-fix-itxt": 5845, + "png-fix-itxt": 5848, "pngcp": 89, - "pngfix": 5845, + "pngfix": 5848, "pngtogd": 232, "pngtogd2": 232, "pnps-gen": 1, "poa": 17, "pocheck": 1, "poclcc": 3, - "pod2html": 1675, - "pod2man": 1675, - "pod2text": 1675, - "pod2usage": 1675, + "pod2html": 1678, + "pod2man": 1678, + "pod2text": 1678, + "pod2usage": 1678, "pod_cover": 12, - "podchecker": 1675, + "podchecker": 1678, "podselect": 437, "poetry": 6, "pointwise_datasets_concatenator.py": 1, @@ -19560,20 +19564,20 @@ "predictProductivity": 1, "predict_num_reads": 1, "predicthaplo": 1, - "prefetch": 21, - "prefetch-orig": 19, + "prefetch": 22, + "prefetch-orig": 20, "prefetch-orig.2.10.0": 1, "prefetch-orig.2.10.8": 3, "prefetch-orig.2.10.9": 3, - "prefetch-orig.2.11.0": 9, + "prefetch-orig.2.11.0": 10, "prefetch-orig.3.0.0": 2, "prefetch-orig.3.0.3": 1, "prefetch-orig.3.1.0": 1, - "prefetch.2": 17, + "prefetch.2": 18, "prefetch.2.10.0": 1, "prefetch.2.10.8": 3, "prefetch.2.10.9": 3, - "prefetch.2.11.0": 9, + "prefetch.2.11.0": 10, "prefetch.2.9.6": 1, "prefetch.3": 4, "prefetch.3.0.0": 2, @@ -19656,7 +19660,7 @@ "prinseq-graphs-noPCA.pl": 3, "prinseq-graphs.pl": 3, "prinseq-lite.pl": 3, - "print-columns": 198, + "print-columns": 199, "print.pl": 1, "printIcounts": 1, "printScaff": 2, @@ -19749,7 +19753,7 @@ "project.sh.orig": 1, "projectAndStrip": 4, "projectFeatures": 3, - "project_tree_builder": 318, + "project_tree_builder": 319, "projinfo": 38, "projsync": 35, "prokka": 23, @@ -19893,7 +19897,7 @@ "protxml_to_table.rb": 1, "prov-compare": 9, "prov-convert": 9, - "prove": 1675, + "prove": 1678, "provean": 1, "provean.sh": 1, "provis": 1, @@ -19937,10 +19941,10 @@ "psiCalculator.py": 1, "psiPerGene.py": 1, "psibl2seq_unit_test": 5, - "psiblast": 318, + "psiblast": 319, "psiblast_iteration_unit_test": 5, "psiblast_unit_test": 5, - "psicc": 971, + "psicc": 974, "psiclass": 1, "psiphi": 24, "psite": 3, @@ -19992,9 +19996,9 @@ "pt2to3": 73, "ptGAUL.sh": 1, "ptangle": 1, - "ptar": 1675, - "ptardiff": 1675, - "ptargrep": 1675, + "ptar": 1678, + "ptardiff": 1678, + "ptargrep": 1678, "ptdump": 73, "ptest": 1, "ptex": 1, @@ -20143,7 +20147,7 @@ "pyami_sendmail": 29, "pyaml": 1, "pyatac": 1, - "pybabel": 45, + "pybabel": 46, "pybam.py": 1, "pybarrnap": 1, "pybed2GTF.py": 1, @@ -20170,23 +20174,23 @@ "pydamage": 1, "pydemult": 1, "pydicom": 1, - "pydoc": 3620, - "pydoc3": 3289, - "pydoc3.10": 795, - "pydoc3.11": 263, + "pydoc": 3625, + "pydoc3": 3294, + "pydoc3.10": 798, + "pydoc3.11": 264, "pydoc3.12": 173, "pydoc3.4": 6, "pydoc3.5": 103, "pydoc3.6": 342, "pydoc3.7": 383, "pydoc3.8": 574, - "pydoc3.9": 650, + "pydoc3.9": 651, "pydownsampler": 1, "pyega3": 1, "pyemojify": 1, "pyensembl": 8, "pyfasta": 7, - "pyfastx": 14, + "pyfastx": 15, "pyfba": 1, "pyfiglet": 8, "pyfish": 1, @@ -20195,12 +20199,12 @@ "pyflyte-execute": 1, "pyflyte-fast-execute": 1, 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"python3.10-config": 798, + "python3.11": 264, + "python3.11-config": 264, "python3.12": 173, "python3.12-config": 173, "python3.4": 6, @@ -20336,8 +20340,8 @@ "python3.7m-config": 383, "python3.8": 574, "python3.8-config": 574, - "python3.9": 650, - "python3.9-config": 650, + "python3.9": 651, + "python3.9-config": 651, "pythonsh": 2, "pythontex": 1, "pytleap": 6, @@ -20520,7 +20524,7 @@ "quorum": 4, "quorum_create_database": 4, "quorum_error_correct_reads": 4, - "quote-grouped-elements": 10, + "quote-grouped-elements": 11, "qv_to_bqv.py": 58, "qvality": 1, "qvalue": 13, @@ -20544,7 +20548,7 @@ "raau": 1, "rabbitqcplus": 1, "rabix": 1, - "racc": 15, + "racc": 16, "racc2y": 7, "raccoon": 1, "racon": 27, @@ -20579,7 +20583,7 @@ "ragtag_update_gff.py": 1, "rainbow": 3, "raiss": 1, - "rake": 29, + "rake": 30, "ramen": 13, "rampler": 26, "randRemoveBackground.pl": 5, @@ -20671,26 +20675,26 @@ "rbox": 3, "rbpbench": 1, "rbrms": 1, - "rbs": 8, + "rbs": 9, "rbt": 1, "rc_gnu.py": 1, "rc_s.py": 1, "rcc": 244, "rcc-qt4": 3, - "rcexplain": 21, - "rcexplain.2": 17, + "rcexplain": 22, + "rcexplain.2": 18, "rcexplain.2.10.0": 1, "rcexplain.2.10.8": 3, "rcexplain.2.10.9": 3, - "rcexplain.2.11.0": 9, + "rcexplain.2.11.0": 10, "rcexplain.2.9.6": 1, "rcexplain.3": 4, "rcexplain.3.0.0": 2, "rcexplain.3.0.3": 1, "rcexplain.3.1.0": 1, "rcf": 1, - "rchive": 285, - "rchive.Linux": 285, + "rchive": 286, + "rchive.Linux": 286, "rchive.go": 14, "rcl": 1, "rcl-dot-resmap.pl": 1, @@ -20701,27 +20705,27 @@ "rcldo.pl": 1, "rcopy": 19, "rcorrector": 2, - "rdbg": 8, + "rdbg": 9, "rdf2dot": 32, "rdfgraphisomorphism": 32, "rdfpipe": 32, "rdfs2dot": 32, - "rdjpgcom": 5731, + "rdjpgcom": 5734, "rdkit2fps": 1, "rdma_client": 19, "rdma_server": 19, "rdma_xclient": 19, "rdma_xserver": 19, - "rdoc": 29, + "rdoc": 30, "rdp_classifier": 3, "re-PCR": 1, "read-cov-plot": 2, "read-extractor": 1, - "read-filter-redact": 17, - "read-filter-redact.2": 15, + "read-filter-redact": 18, + "read-filter-redact.2": 16, "read-filter-redact.2.10.8": 3, "read-filter-redact.2.10.9": 3, - "read-filter-redact.2.11.0": 9, + "read-filter-redact.2.11.0": 10, "read-filter-redact.3": 2, "read-filter-redact.3.0.0": 2, "read-group-stats": 2, @@ -20798,7 +20802,7 @@ "recgraph": 1, "reciprocal_blast_local": 1, "reciprocal_blast_local.py": 1, - "recode-sr-latin": 5268, + "recode-sr-latin": 5270, "recode_dir": 1, "recode_dir_legacy": 1, "recoder": 24, @@ -20844,7 +20848,7 @@ "ref-variation.3": 2, "ref-variation.3.0.3": 1, "ref-variation.3.1.0": 1, - "ref2pmid": 10, + "ref2pmid": 11, "refFinder": 1, "ref_map.pl": 1, "ref_seqs_from_bam": 1, @@ -20880,7 +20884,7 @@ "refresh-versioned": 1, "refseq-download": 1, "refseq-extract": 1, - "refseq-nm-cds": 10, + "refseq-nm-cds": 11, "refseq_masher": 1, "refseqget": 24, "refseqsplit.py": 2, @@ -21094,7 +21098,7 @@ "renumberRMFiles.pl": 3, "renumber_structure": 1, "reorder": 1, - "reorder-columns": 286, + "reorder-columns": 287, "reorder-fasta": 3, "reorder.smk": 1, "reorient_sequences_by_id.py": 2, @@ -21160,7 +21164,7 @@ "rescue_fusion.py": 1, "reseq": 1, "reseq-prepare-names.py": 1, - "reset": 7651, + "reset": 7657, "resetFragLibrary": 2, "reset_array.pl": 1, "reset_experiment.pl": 1, @@ -21251,7 +21255,7 @@ "rhea-binning.R": 1, "rhea-normalize.R": 1, "rhocall": 1, - "ri": 29, + "ri": 30, "ribo": 1, "ribocount": 1, "ribocutter": 1, @@ -21421,9 +21425,9 @@ "rpkmforgenes.py": 1, "rppr": 17, "rps_unit_test": 5, - "rpsblast": 327, - "rpsbproc": 246, - "rpstblastn": 318, + "rpsblast": 328, + "rpsbproc": 247, + "rpstblastn": 319, "rqcfilter.sh": 30, "rqcfilter2.sh": 29, "rqw": 1, @@ -21470,16 +21474,26 @@ "rsidx": 1, "rsq": 1, "rsrq": 1, + "rst2html": 1, "rst2html.py": 184, + "rst2html4": 1, "rst2html4.py": 176, + "rst2html5": 1, "rst2html5.py": 181, + "rst2latex": 1, "rst2latex.py": 184, + "rst2man": 1, "rst2man.py": 184, + "rst2odt": 1, "rst2odt.py": 184, "rst2odt_prepstyles.py": 184, + "rst2pseudoxml": 1, "rst2pseudoxml.py": 184, + "rst2s5": 1, "rst2s5.py": 184, + "rst2xetex": 1, "rst2xetex.py": 184, + "rst2xml": 1, "rst2xml.py": 184, "rstpep2html.py": 184, "rstream": 19, @@ -21494,7 +21508,7 @@ "rtk2": 1, "rubibtex": 1, "rubikrotation": 1, - "ruby": 29, + "ruby": 30, "rucs": 1, "rumakeindex": 1, "run-HLA": 1, @@ -21513,7 +21527,7 @@ "run-htseq-workflow": 1, "run-mummer1": 44, "run-mummer3": 44, - "run-ncbi-converter": 285, + "run-ncbi-converter": 286, "run-ncbi-converter.bak": 1, "run-ntedit": 1, "run-roh.pl": 156, @@ -21716,7 +21730,7 @@ "run_vote.py": 1, "run_voteSpecies.py": 1, "run_vsclust_app.R": 1, - "run_with_lock": 308, + "run_with_lock": 309, "run_workflows.py": 1, "run_x_platform_fuzz_corpus": 37, "runabyss.py": 1, @@ -21806,20 +21820,20 @@ "sak": 2, "salmon": 12, "salty": 1, - "sam-dump": 21, - "sam-dump-orig": 19, + "sam-dump": 22, + "sam-dump-orig": 20, "sam-dump-orig.2.10.0": 1, "sam-dump-orig.2.10.8": 3, "sam-dump-orig.2.10.9": 3, - "sam-dump-orig.2.11.0": 9, + "sam-dump-orig.2.11.0": 10, "sam-dump-orig.3.0.0": 2, "sam-dump-orig.3.0.3": 1, "sam-dump-orig.3.1.0": 1, - "sam-dump.2": 17, + "sam-dump.2": 18, "sam-dump.2.10.0": 1, "sam-dump.2.10.8": 3, "sam-dump.2.10.9": 3, - "sam-dump.2.11.0": 9, + "sam-dump.2.11.0": 10, "sam-dump.2.9.6": 1, "sam-dump.3": 4, "sam-dump.3.0.0": 2, @@ -21976,7 +21990,15 @@ "sc3-sc3-validate.R": 1, "sc3-sc3.R": 1, "scBAMStats": 1, + "scBulkCoverage": 1, + "scClusterCells": 1, + "scCombineCounts": 1, + "scCountQC": 1, + "scCountReads": 1, "scExecute": 1, + "scFilterBarcodes": 1, + "scFilterStats": 1, + "scJSD": 1, "scReadCounts": 1, "scTE": 1, "scTEATAC": 1, @@ -22016,7 +22038,7 @@ "scancel-range": 1, "scancel_range.py": 1, "scandeps.pl": 2, - "scanpy": 40, + "scanpy": 41, "scanpy-cli": 1, "scanpy-filter-cells": 1, "scanpy-filter-genes": 1, @@ -22088,7 +22110,7 @@ "scitokens-test": 1, "scitokens-test-access": 1, "scitokens-verify": 1, - "sclient": 5764, + "sclient": 5768, "sclust_summary.sh": 1, "scluster": 3, "scmap-cli-post-install-tests.bats": 1, @@ -22107,7 +22129,7 @@ "scn-post-install-tests.sh": 1, "scn-predict.R": 1, "scn-train-model.R": 1, - "scn2xml": 10, + "scn2xml": 11, "scoary": 3, "scoary_GUI": 3, "scompare": 6, @@ -22226,7 +22248,7 @@ "segalign": 1, "segalign_repeat_masker": 1, "segemehl.x": 1, - "segmasker": 318, + "segmasker": 319, "segment-cnv": 1, "segment.py": 1, "segmentFst": 31, @@ -22281,6 +22303,7 @@ "selectreads": 1, "selectsites": 1, "selene_sdk": 1, + "selenium-manager": 1, "selscan": 1, "sem": 99, "send2trash": 20, @@ -22446,20 +22469,20 @@ "sexp-conv": 30, "sfdp": 198, "sfetch": 4, - "sff-dump": 21, - "sff-dump.2": 17, + "sff-dump": 22, + "sff-dump.2": 18, "sff-dump.2.10.0": 1, "sff-dump.2.10.8": 3, "sff-dump.2.10.9": 3, - "sff-dump.2.11.0": 9, + "sff-dump.2.11.0": 10, "sff-dump.2.9.6": 1, "sff-dump.3": 4, "sff-dump.3.0.0": 2, "sff-dump.3.0.3": 1, "sff-dump.3.1.0": 1, - "sff-load": 11, - "sff-load.2": 9, - "sff-load.2.11.0": 9, + "sff-load": 12, + "sff-load.2": 10, + "sff-load.2.11.0": 10, "sff-load.3": 2, "sff-load.3.0.0": 2, "sff2fastq": 1, @@ -22506,7 +22529,7 @@ "sharq.3": 2, "sharq.3.0.0": 2, "shasta": 1, - "shasum": 1675, + "shasum": 1678, "shed-tools": 2, "shell_utils.py": 1, "shiboken2": 2, @@ -22601,7 +22624,7 @@ "sim-cover2": 2, "sim-shotgun": 2, "sim4db": 3, - "sim_client": 5764, + "sim_client": 5768, "sim_reads": 10, "sim_reads.o": 10, "sim_reads_tran": 10, @@ -22659,6 +22682,7 @@ "simulator": 8, "simwalk2": 1, "sina": 1, + "sincei": 1, "sindex": 4, "single_cov": 1, "single_cov2": 1, @@ -22713,7 +22737,7 @@ "sketchy": 1, "skewer": 1, "skg_convert.py": 2, - "skip-if-file-exists": 255, + "skip-if-file-exists": 256, "skip_psl_self.awk": 2, "skip_psl_self_ss.awk": 2, "skip_selfmatches.py": 1, @@ -22836,8 +22860,8 @@ "snp-pileup": 2, "snp-pileup-quickbam": 1, "snp-sites": 13, - "snp2hgvs": 198, - "snp2tbl": 198, + "snp2hgvs": 199, + "snp2tbl": 199, "snpEff": 23, "snpEffAnnotate.py": 3, "snp_diversity.py": 1, @@ -22910,9 +22934,9 @@ "sort-last-maf": 1, "sort-snos": 2, "sort-snos.pl": 2, - "sort-table": 198, - "sort-uniq-count": 286, - "sort-uniq-count-rank": 286, + "sort-table": 199, + "sort-uniq-count": 287, + "sort-uniq-count-rank": 287, "sort2": 2, "sortBed": 269, "sortByRefAndCor.pl": 1, @@ -22989,7 +23013,7 @@ "sparsetable_unittest": 1, "spatypes.txt": 1, "spdi2prod": 12, - "spdi2tbl": 198, + "spdi2tbl": 199, "specialk": 1, "spectra-cluster-cli": 1, "spectral_clustering": 1, @@ -23005,13 +23029,13 @@ "spectrast_updateiRTs.py": 1, "speedtest.py": 1, "sphae": 1, - "sphinx-apidoc": 39, - "sphinx-autogen": 39, - "sphinx-build": 39, - "sphinx-quickstart": 39, + "sphinx-apidoc": 40, + "sphinx-autogen": 40, + "sphinx-build": 40, + "sphinx-quickstart": 40, "spine.pl": 1, "spinner.py": 1, - "splain": 1675, + "splain": 1678, "splash": 1, "splice_site_summary.pl": 1, "spliceai": 1, @@ -23020,7 +23044,7 @@ "splinter.pl": 1, "splinter_scaffolds.pl": 1, "split": 82, - "split-at-intron": 198, + "split-at-intron": 199, "split-bed12-blocks": 3, "split-coverages.py": 1, "split-fasta": 1, @@ -23149,7 +23173,7 @@ "sqlformat": 9, "sqlite.pl": 1, "sqlite3": 2709, - "sqlite3_analyzer": 7061, + "sqlite3_analyzer": 7066, "sqlitebrowser": 1, "sqlmetal": 15, "sqlsharp": 15, @@ -23160,26 +23184,27 @@ "squeakr": 1, "squeegee": 1, "squid": 1, + "squigualiser": 1, "squigulator": 1, "squire": 1, "squizz": 5, "sra-info": 1, "sra-info.3": 1, "sra-info.3.1.0": 1, - "sra-pileup": 21, - "sra-pileup-orig": 19, + "sra-pileup": 22, + "sra-pileup-orig": 20, "sra-pileup-orig.2.10.0": 1, "sra-pileup-orig.2.10.8": 3, "sra-pileup-orig.2.10.9": 3, - "sra-pileup-orig.2.11.0": 9, + "sra-pileup-orig.2.11.0": 10, "sra-pileup-orig.3.0.0": 2, "sra-pileup-orig.3.0.3": 1, "sra-pileup-orig.3.1.0": 1, - "sra-pileup.2": 17, + "sra-pileup.2": 18, "sra-pileup.2.10.0": 1, "sra-pileup.2.10.8": 3, "sra-pileup.2.10.9": 3, - "sra-pileup.2.11.0": 9, + "sra-pileup.2.11.0": 10, "sra-pileup.2.9.6": 1, "sra-pileup.3": 4, "sra-pileup.3.0.0": 2, @@ -23189,28 +23214,28 @@ "sra-search.3": 2, "sra-search.3.0.3": 1, "sra-search.3.1.0": 1, - "sra-sort": 19, - "sra-sort-cg": 17, - "sra-sort-cg.2": 15, + "sra-sort": 20, + "sra-sort-cg": 18, + "sra-sort-cg.2": 16, "sra-sort-cg.2.10.8": 3, "sra-sort-cg.2.10.9": 3, - "sra-sort-cg.2.11.0": 9, + "sra-sort-cg.2.11.0": 10, "sra-sort-cg.3": 2, "sra-sort-cg.3.0.0": 2, - "sra-sort.2": 17, + "sra-sort.2": 18, "sra-sort.2.10.0": 1, "sra-sort.2.10.8": 3, "sra-sort.2.10.9": 3, - "sra-sort.2.11.0": 9, + "sra-sort.2.11.0": 10, "sra-sort.2.9.6": 1, "sra-sort.3": 2, "sra-sort.3.0.0": 2, - "sra-stat": 21, - "sra-stat.2": 17, + "sra-stat": 22, + "sra-stat.2": 18, "sra-stat.2.10.0": 1, "sra-stat.2.10.8": 3, "sra-stat.2.10.9": 3, - "sra-stat.2.11.0": 9, + "sra-stat.2.11.0": 10, "sra-stat.2.9.6": 1, "sra-stat.3": 4, "sra-stat.3.0.0": 2, @@ -23222,40 +23247,40 @@ "sracat": 2, "sraconvert": 1, "srahunter": 1, - "srapath": 21, - "srapath-orig": 19, + "srapath": 22, + "srapath-orig": 20, "srapath-orig.2.10.0": 1, "srapath-orig.2.10.8": 3, "srapath-orig.2.10.9": 3, - "srapath-orig.2.11.0": 9, + "srapath-orig.2.11.0": 10, "srapath-orig.3.0.0": 2, "srapath-orig.3.0.3": 1, "srapath-orig.3.1.0": 1, - "srapath.2": 17, + "srapath.2": 18, "srapath.2.10.0": 1, "srapath.2.10.8": 3, "srapath.2.10.9": 3, - "srapath.2.11.0": 9, + "srapath.2.11.0": 10, "srapath.2.9.6": 1, "srapath.3": 4, "srapath.3.0.0": 2, "srapath.3.0.3": 1, "srapath.3.1.0": 1, - "sratools": 20, - "sratools.2": 16, + "sratools": 21, + "sratools.2": 17, "sratools.2.10.0": 1, "sratools.2.10.8": 3, "sratools.2.10.9": 3, - "sratools.2.11.0": 9, + "sratools.2.11.0": 10, "sratools.3": 4, "sratools.3.0.0": 2, "sratools.3.0.3": 1, "sratools.3.1.0": 1, "srcredact": 1, "sreformat": 5, - "srf-load": 11, - "srf-load.2": 9, - "srf-load.2.11.0": 9, + "srf-load": 12, + "srf-load.2": 10, + "srf-load.2.11.0": 10, "srf-load.3": 2, "srf-load.3.0.0": 2, "srf2fasta": 2, @@ -23476,15 +23501,15 @@ "strainscan_build": 1, "stranger": 1, "stream": 76, - "stream-local": 10, - "stream-pubmed": 284, + "stream-local": 11, + "stream-pubmed": 285, "stream_atac": 1, "stream_run_test": 1, "streamer_1d": 22, "streamlit": 6, "streamlit.cmd": 6, "streamsam.sh": 30, - "streamzip": 1247, + "streamzip": 1250, "streme": 6, "streme_xml_to_html": 6, "stress-ng": 1, @@ -23749,8 +23774,8 @@ "tableproxy64": 1, "tableschema": 1, "tablet": 1, - "tabs": 7651, - "tabulate": 126, + "tabs": 7657, + "tabulate": 127, "tabulate.py": 1, "tabulator": 1, "tabutils": 1, @@ -23764,6 +23789,7 @@ "tadbit": 1, "tadpipe.sh": 30, "tadpole.sh": 30, + "tadrep": 1, "tadtool": 1, "tadwrapper.sh": 30, "taeper": 1, @@ -23905,20 +23931,20 @@ "tba": 1, "tbl2asn": 29, "tbl2asn-test": 12, - "tbl2prod": 186, - "tbl2xml": 198, - "tblastn": 318, - "tblastn_vdb": 33, - "tblastx": 318, + "tbl2prod": 187, + "tbl2xml": 199, + "tblastn": 319, + "tblastn_vdb": 34, + "tblastx": 319, "tblite": 1, "tbox-scan": 1, "tbpore": 1, "tbtamr": 1, "tbvcfreport": 1, "tcdemux": 1, - "tclsh": 7298, + "tclsh": 7303, "tclsh8.5": 473, - "tclsh8.6": 7061, + "tclsh8.6": 7066, "tcode": 24, "tcsh": 3, "td_bignet": 2, @@ -23955,23 +23981,23 @@ "test-download": 2, "test-download.3": 2, "test-download.3.0.0": 2, - "test-edirect": 255, - "test-eutils": 284, + "test-edirect": 256, + "test-eutils": 285, "test-gzip": 1, "test-merStream": 5, - "test-pmc-index": 10, - "test-pubmed-index": 284, + "test-pmc-index": 11, + "test-pubmed-index": 285, "test-read-write-cursor": 2, "test-read-write-cursor.3": 2, "test-read-write-cursor.3.0.0": 2, "test-seqCache": 5, "test-seqStream": 5, - "test-sra": 21, - "test-sra.2": 17, + "test-sra": 22, + "test-sra.2": 18, "test-sra.2.10.0": 1, "test-sra.2.10.8": 3, "test-sra.2.10.9": 3, - "test-sra.2.11.0": 9, + "test-sra.2.11.0": 10, "test-sra.2.9.6": 1, "test-sra.3": 4, "test-sra.3.0.0": 2, @@ -24011,7 +24037,7 @@ "test_install.bak": 1, "test_miso": 1, "test_musicc.py": 2, - "test_pcre": 79, + "test_pcre": 80, "test_proton.bam": 1, "test_proton.bam.bai": 1, "test_regexp": 1, @@ -24114,7 +24140,7 @@ "thumbpdf": 1, "tiara": 2, "tiara-test": 2, - "tic": 7651, + "tic": 7657, "tiddit": 1, "tides": 1, "tidk": 1, @@ -24129,16 +24155,16 @@ "tiff2rgba": 5293, "tiffcmp": 5293, "tiffcomment": 18, - "tiffcp": 5484, + "tiffcp": 5487, "tiffcrop": 5293, "tiffdither": 5293, - "tiffdump": 5484, + "tiffdump": 5487, "tifffile": 21, - "tiffinfo": 5484, + "tiffinfo": 5487, "tiffmedian": 5293, - "tiffset": 5484, - "tiffsplit": 5484, - "tificc": 971, + "tiffset": 5487, + "tiffsplit": 5487, + "tificc": 974, "tigStore": 3, "tiger-hash": 11, "tigge_check": 1, @@ -24192,7 +24218,7 @@ "titan-gc-prepare.py": 1, "titan.py": 1, "titration": 2, - "tjbench": 358, + "tjbench": 361, "tkconch": 1, "tkpp": 1, "tksm": 1, @@ -24223,14 +24249,14 @@ "to_upper_case.pl.bak": 1, "toco": 75, "toco_from_protos": 75, - "toe": 7651, + "toe": 7657, "tohnsw": 1, "toil": 3, "toil-cwl-runner": 3, "toil-wdl-runner": 2, "tolkein": 1, "tombo": 2, - "toml2xml": 10, + "toml2xml": 11, "tomlq": 289, "tomsimilarity": 1, "tomtom": 13, @@ -24273,8 +24299,8 @@ "tpp_hostname": 2, "tpp_models.pl": 2, "tpptray.bat": 2, - "tput": 7651, - "tqdm": 335, + "tput": 7657, + "tqdm": 336, "tr": 82, "trace_comment": 2, "trace_comments": 2, @@ -24344,7 +24370,7 @@ "transform_gfa.py": 1, "transformers-cli": 2, "transformseq": 13, - "transicc": 971, + "transicc": 974, "transit": 1, "transition_counter": 1, "transl": 1, @@ -24360,8 +24386,8 @@ "translate_reduced_reads.pl": 1, "translatorx": 1, "translatorx_vLocal.pl": 1, - "transmute": 284, - "transmute.Linux": 198, + "transmute": 285, + "transmute.Linux": 199, "transposcope": 1, "transpose.pl": 1, "transpose.pl.bak": 1, @@ -24496,7 +24522,7 @@ "tryptic.py": 1, "ts": 3, "tsebra.py": 3, - "tset": 7651, + "tset": 7657, "tskit": 6, "tsort": 82, "tsp": 2, @@ -24531,7 +24557,7 @@ "tth-hash": 11, "ttree": 66, "tts": 5, - "ttx": 378, + "ttx": 381, "tty": 82, "turbocor": 1, "tutorial_eqtlbma.R": 1, @@ -24560,7 +24586,7 @@ "typeHLA.sh": 1, "type_constellations.py": 2, "typeoutfileinfo": 1, - "typeprof": 8, + "typeprof": 9, "typer": 1, "tzselect": 42, "uLTRA": 1, @@ -24646,7 +24672,7 @@ "uniprot_sprot_to_sqlite3.py": 2, "uniprot_support.py": 1, "uniq": 83, - "uniq-table": 186, + "uniq-table": 187, "uniqLine.pl": 1, "uniqPolishes": 3, "uniqscan": 1, @@ -24673,14 +24699,14 @@ "unix2mac": 1, "unlink": 82, "unlz4": 3498, - "unlzma": 7477, + "unlzma": 7483, "unmapped2anchors.py": 1, "unmerge": 1, "unmerge-paired-reads.sh": 2, "unnaf": 1, "unpack200": 421, "unpickle.py": 1, - "unpigz": 114, + "unpigz": 116, "unquip": 1, "unshare": 13, "unsquashfs": 3, @@ -24690,7 +24716,7 @@ "unstarch-typical": 14, "untangle": 2, "unweight_fasta.py": 1, - "unxz": 7702, + "unxz": 7708, "unzip": 32, "unzip.sh": 29, "unziphdf5": 1, @@ -24698,7 +24724,7 @@ "unzipont": 1, "unzipont_dir": 1, "unzipsfx": 25, - "unzstd": 5156, + "unzstd": 5160, "update-blastdb.py": 2, "update-serotypefinder-db": 1, "update-sort-bed-migrate-candidates": 14, @@ -24718,8 +24744,8 @@ "updateDeltaClr": 2, "updateLibSizes": 2, "update_alias.py": 1, - "update_blastdb.pl": 318, - "update_blastdb.pl.bak": 289, + "update_blastdb.pl": 319, + "update_blastdb.pl.bak": 290, "update_database": 1, "update_info.py": 3, "update_selected_column9_values.py": 2, @@ -24769,9 +24795,9 @@ "utmpdump": 13, "utrgff2gbrowse.pl": 14, "utrrnaseq": 12, - "uuclient": 5764, - "uuid": 36, - "uuid-config": 36, + "uuclient": 5768, + "uuid": 37, + "uuid-config": 37, "uuidgen": 13, "uuidparse": 13, "uuserver": 2, @@ -24797,7 +24823,7 @@ "vafator2decifer": 1, "valet.py": 1, "validate": 4, - "validate-docstrings": 1, + "validate-docstrings": 2, "validate-fasta-database": 1, "validateDB.pl": 1, "validateSNP.py": 1, @@ -24975,13 +25001,13 @@ "vcfVariantSummaryLite": 1, "vcf_allele_freq.py": 3, "vcf_assembly_checker": 1, - "vcf_filter.py": 86, + "vcf_filter.py": 87, "vcf_group_multiline.py": 3, "vcf_iit": 11, - "vcf_melt": 86, + "vcf_melt": 87, "vcf_modify_header.py": 3, "vcf_paste.py": 3, - "vcf_sample_filter.py": 83, + "vcf_sample_filter.py": 84, "vcf_strip_extra_headers": 31, "vcf_to_fa": 1, "vcf_to_matrix": 1, @@ -25097,67 +25123,67 @@ "vcfwave": 3, "vcontact2": 1, "vcontact2_gene2genome": 1, - "vdb-config": 21, - "vdb-config.2": 17, + "vdb-config": 22, + "vdb-config.2": 18, "vdb-config.2.10.0": 1, "vdb-config.2.10.8": 3, "vdb-config.2.10.9": 3, - "vdb-config.2.11.0": 9, + "vdb-config.2.11.0": 10, "vdb-config.2.9.6": 1, "vdb-config.3": 4, "vdb-config.3.0.0": 2, "vdb-config.3.0.3": 1, "vdb-config.3.1.0": 1, - "vdb-copy": 19, - "vdb-copy.2": 17, + "vdb-copy": 20, + "vdb-copy.2": 18, "vdb-copy.2.10.0": 1, "vdb-copy.2.10.8": 3, "vdb-copy.2.10.9": 3, - "vdb-copy.2.11.0": 9, + "vdb-copy.2.11.0": 10, "vdb-copy.2.9.6": 1, "vdb-copy.3": 2, "vdb-copy.3.0.0": 2, - "vdb-decrypt": 21, - "vdb-decrypt.2": 17, + "vdb-decrypt": 22, + "vdb-decrypt.2": 18, "vdb-decrypt.2.10.0": 1, "vdb-decrypt.2.10.8": 3, "vdb-decrypt.2.10.9": 3, - "vdb-decrypt.2.11.0": 9, + "vdb-decrypt.2.11.0": 10, "vdb-decrypt.2.9.6": 1, "vdb-decrypt.3": 4, "vdb-decrypt.3.0.0": 2, "vdb-decrypt.3.0.3": 1, "vdb-decrypt.3.1.0": 1, - "vdb-diff": 17, - "vdb-diff.2": 15, + "vdb-diff": 18, + "vdb-diff.2": 16, "vdb-diff.2.10.8": 3, "vdb-diff.2.10.9": 3, - "vdb-diff.2.11.0": 9, + "vdb-diff.2.11.0": 10, "vdb-diff.3": 2, "vdb-diff.3.0.0": 2, - "vdb-dump": 21, + "vdb-dump": 22, "vdb-dump-orig.2.10.8": 3, "vdb-dump-orig.2.10.9": 3, - "vdb-dump-orig.2.11.0": 9, + "vdb-dump-orig.2.11.0": 10, "vdb-dump-orig.3.0.0": 2, "vdb-dump-orig.3.0.3": 1, "vdb-dump-orig.3.1.0": 1, - "vdb-dump.2": 17, + "vdb-dump.2": 18, "vdb-dump.2.10.0": 1, "vdb-dump.2.10.8": 3, "vdb-dump.2.10.9": 3, - "vdb-dump.2.11.0": 9, + "vdb-dump.2.11.0": 10, "vdb-dump.2.9.6": 1, "vdb-dump.3": 4, "vdb-dump.3.0.0": 2, "vdb-dump.3.0.3": 1, "vdb-dump.3.1.0": 1, - "vdb-encrypt": 21, - "vdb-encrypt.2": 17, + "vdb-encrypt": 22, + "vdb-encrypt.2": 18, "vdb-encrypt.2.10.0": 1, "vdb-encrypt.2.10.8": 3, "vdb-encrypt.2.10.9": 3, - "vdb-encrypt.2.11.0": 9, + "vdb-encrypt.2.11.0": 10, "vdb-encrypt.2.9.6": 1, "vdb-encrypt.3": 4, "vdb-encrypt.3.0.0": 2, @@ -25166,42 +25192,42 @@ "vdb-get": 2, "vdb-get.3": 2, "vdb-get.3.0.0": 2, - "vdb-lock": 19, - "vdb-lock.2": 17, + "vdb-lock": 20, + "vdb-lock.2": 18, "vdb-lock.2.10.0": 1, "vdb-lock.2.10.8": 3, "vdb-lock.2.10.9": 3, - "vdb-lock.2.11.0": 9, + "vdb-lock.2.11.0": 10, "vdb-lock.2.9.6": 1, "vdb-lock.3": 2, "vdb-lock.3.0.0": 2, - "vdb-passwd": 19, - "vdb-passwd.2": 17, + "vdb-passwd": 20, + "vdb-passwd.2": 18, "vdb-passwd.2.10.0": 1, "vdb-passwd.2.10.8": 3, "vdb-passwd.2.10.9": 3, - "vdb-passwd.2.11.0": 9, + "vdb-passwd.2.11.0": 10, "vdb-passwd.2.9.6": 1, "vdb-passwd.3": 2, "vdb-passwd.3.0.0": 2, "vdb-sql": 2, "vdb-sql.3": 2, "vdb-sql.3.0.0": 2, - "vdb-unlock": 19, - "vdb-unlock.2": 17, + "vdb-unlock": 20, + "vdb-unlock.2": 18, "vdb-unlock.2.10.0": 1, "vdb-unlock.2.10.8": 3, "vdb-unlock.2.10.9": 3, - "vdb-unlock.2.11.0": 9, + "vdb-unlock.2.11.0": 10, "vdb-unlock.2.9.6": 1, "vdb-unlock.3": 2, "vdb-unlock.3.0.0": 2, - "vdb-validate": 21, - "vdb-validate.2": 17, + "vdb-validate": 22, + "vdb-validate.2": 18, "vdb-validate.2.10.0": 1, "vdb-validate.2.10.8": 3, "vdb-validate.2.10.9": 3, - "vdb-validate.2.11.0": 9, + "vdb-validate.2.11.0": 10, "vdb-validate.2.9.6": 1, "vdb-validate.3": 4, "vdb-validate.3.0.0": 2, @@ -25443,8 +25469,9 @@ "wftopfa": 3, "wg-blimp": 1, "wgMLST": 1, + "wgatools": 1, "wgdi": 1, - "wget": 414, + "wget": 416, "wgetdir": 1, "wgmlst": 1, "wgs2ncbi": 1, @@ -25453,7 +25480,7 @@ "wham": 1, "whamg": 1, "whatshap": 14, - "wheel": 3620, + "wheel": 3625, "wheezy.template": 2, "whereis": 13, "which": 1, @@ -25490,15 +25517,15 @@ "window-acgt": 2, "windowBed": 269, "windowMaker": 269, - "windowmasker": 318, - "windowmasker_2.2.22_adapter.py": 318, + "windowmasker": 319, + "windowmasker_2.2.22_adapter.py": 319, "winextract": 1, "winnowmap": 3, "wiq.py": 1, "wisestork": 1, - "wish": 7298, + "wish": 7303, "wish8.5": 473, - "wish8.6": 7061, + "wish8.6": 7066, "wkhtmltoimage": 2, "wkhtmltopdf": 2, "wlmscpfs": 1, @@ -25508,7 +25535,7 @@ "woltka": 1, "womtool": 4, "wopl2ofm": 1, - "word-at-a-time": 286, + "word-at-a-time": 287, "word-square": 2, "word_enrich.pl": 1, "wordcloud_cli": 1, @@ -25547,7 +25574,7 @@ "write_strain_fasta.py": 1, "writedb_entry": 1, "writedb_unit_test": 5, - "wrjpgcom": 5731, + "wrjpgcom": 5734, "ws": 2, "wsdl": 15, "wsdl2": 15, @@ -25613,7 +25640,7 @@ "x86_64-conda-linux-gnu-gfortran": 3326, "x86_64-conda-linux-gnu-gfortran.bin": 575, "x86_64-conda-linux-gnu-gprof": 3362, - "x86_64-conda-linux-gnu-ld": 5448, + "x86_64-conda-linux-gnu-ld": 5453, "x86_64-conda-linux-gnu-ld.bfd": 3362, "x86_64-conda-linux-gnu-ld.gold": 3362, "x86_64-conda-linux-gnu-nm": 3362, @@ -25649,7 +25676,7 @@ "x86_64-conda_cos6-linux-gnu-gfortran": 4095, "x86_64-conda_cos6-linux-gnu-gfortran.bin": 1344, "x86_64-conda_cos6-linux-gnu-gprof": 4129, - "x86_64-conda_cos6-linux-gnu-ld": 6282, + "x86_64-conda_cos6-linux-gnu-ld": 6287, "x86_64-conda_cos6-linux-gnu-ld.bfd": 4129, "x86_64-conda_cos6-linux-gnu-ld.gold": 4129, "x86_64-conda_cos6-linux-gnu-nm": 4129, @@ -25688,7 +25715,7 @@ "xgboost": 27, "xgboost.dll": 1, "xgboost.lib": 1, - "xgettext": 5268, + "xgettext": 5270, "xgui": 2, "xhmm": 1, "xinteract": 2, @@ -25702,23 +25729,23 @@ "xmfa2maf": 4, "xmfa2maf.pl": 1, "xml": 1, - "xml2-config": 5360, + "xml2-config": 5362, "xml2-config.bak": 34, "xml2dcm": 1, "xml2dsr": 1, - "xml2fsa": 198, - "xml2json": 198, - "xml2tbl": 271, + "xml2fsa": 199, + "xml2json": 199, + "xml2tbl": 272, "xml_grep": 64, "xml_merge": 64, "xml_pp": 64, "xml_spellcheck": 64, "xml_split": 64, "xml_to_bas.pl": 3, - "xmlcatalog": 5360, + "xmlcatalog": 5362, "xmlget": 20, "xmlindent": 1, - "xmllint": 5360, + "xmllint": 5362, "xmlpatterns": 242, "xmlpatterns-qt4": 3, "xmlpatternsvalidator": 242, @@ -25759,7 +25786,7 @@ "xsltproc_lite": 7, "xstreme": 2, "xstreme_html_to_tsv": 2, - "xsubpp": 1675, + "xsubpp": 1678, "xsv": 1, "xtandem": 3, "xtb": 1, @@ -25767,8 +25794,8 @@ "xtea_hg19": 1, "xtea_long": 1, "xtermcolor": 2, - "xtract": 286, - "xtract.Linux": 198, + "xtract": 287, + "xtract.Linux": 199, "xtract.go": 15, "xtract.pl": 1, "xtractcol": 1, @@ -25781,16 +25808,16 @@ "xxhsum": 31, "xy-plot": 88, "xyalign": 1, - "xz": 7702, - "xzcat": 7477, - "xzcmp": 7477, - "xzdec": 7477, - "xzdiff": 7477, - "xzegrep": 7477, - "xzfgrep": 7477, - "xzgrep": 7477, - "xzless": 7477, - "xzmore": 7477, + "xz": 7708, + "xzcat": 7483, + "xzcmp": 7483, + "xzdec": 7483, + "xzdiff": 7483, + "xzegrep": 7483, + "xzfgrep": 7483, + "xzgrep": 7483, + "xzless": 7483, + "xzmore": 7483, "y2racc": 7, "yacc": 4, "yacht": 1, @@ -25801,7 +25828,7 @@ "yak": 2, "yaml2gff.1.4.pl": 14, "yaml2obj": 4, - "yaml2xml": 10, + "yaml2xml": 11, "yamllint": 1, "yamlpp5-events": 4, "yamlpp5-highlight": 4, @@ -25851,7 +25878,7 @@ "zipHomerResults.pl": 5, "zipcloak": 2, "zipcmp": 90, - "zipdetails": 1675, + "zipdetails": 1678, "zipgrep": 25, "zipinfo": 25, "zipmerge": 90, @@ -25876,10 +25903,10 @@ "zrun": 3, "zsh": 3, "zsh-5.8": 3, - "zstd": 5156, - "zstdcat": 5156, - "zstdgrep": 4954, - "zstdless": 4954, - "zstdmt": 5156, + "zstd": 5160, + "zstdcat": 5160, + "zstdgrep": 4958, + "zstdless": 4958, + "zstdmt": 5160, "ztr_dump": 2 } \ No newline at end of file diff --git a/quay.io/biocontainers/c/codoff:1.0.0--pyh7cba7a3_0.json b/quay.io/biocontainers/c/codoff:1.0.0--pyh7cba7a3_0.json new file mode 100644 index 0000000..e416577 --- /dev/null +++ b/quay.io/biocontainers/c/codoff:1.0.0--pyh7cba7a3_0.json @@ -0,0 +1,76 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.10": "/usr/local/bin/2to3-3.10", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "clear": "/usr/local/bin/clear", + "codoff": "/usr/local/bin/codoff", + "f2py": "/usr/local/bin/f2py", + "idle3": "/usr/local/bin/idle3", + "idle3.10": "/usr/local/bin/idle3.10", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "openssl": "/usr/local/bin/openssl", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.10": "/usr/local/bin/pydoc3.10", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.10": "/usr/local/bin/python3.10", + "python3.10-config": "/usr/local/bin/python3.10-config", + "reset": "/usr/local/bin/reset", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tset": "/usr/local/bin/tset", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/i/iseq:1.0.0--hdfd78af_0.json b/quay.io/biocontainers/i/iseq:1.0.0--hdfd78af_0.json new file mode 100644 index 0000000..e2c48e6 --- /dev/null +++ b/quay.io/biocontainers/i/iseq:1.0.0--hdfd78af_0.json @@ -0,0 +1,337 @@ +{ + "abi-dump": "/usr/local/bin/abi-dump", + "abi-dump.2": "/usr/local/bin/abi-dump.2", + "abi-dump.2.11.0": "/usr/local/bin/abi-dump.2.11.0", + "abi-load": "/usr/local/bin/abi-load", + "abi-load.2": "/usr/local/bin/abi-load.2", + "abi-load.2.11.0": "/usr/local/bin/abi-load.2.11.0", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "align-cache": "/usr/local/bin/align-cache", + "align-cache.2": "/usr/local/bin/align-cache.2", + "align-cache.2.11.0": "/usr/local/bin/align-cache.2.11.0", + "align-info": "/usr/local/bin/align-info", + "align-info.2": "/usr/local/bin/align-info.2", + "align-info.2.11.0": "/usr/local/bin/align-info.2.11.0", + "ascli": "/usr/local/bin/ascli", + "ascp": "/usr/local/bin/ascp", + "asession": "/usr/local/bin/asession", + "aspera-license": "/usr/local/bin/aspera-license", + "autopoint": "/usr/local/bin/autopoint", + "axel": "/usr/local/bin/axel", + "bam-load": "/usr/local/bin/bam-load", + "bam-load.2": "/usr/local/bin/bam-load.2", + "bam-load.2.11.0": "/usr/local/bin/bam-load.2.11.0", + "bundle": "/usr/local/bin/bundle", + "bundler": "/usr/local/bin/bundler", + "c_rehash": "/usr/local/bin/c_rehash", + "cache-mgr": "/usr/local/bin/cache-mgr", + "cache-mgr.2": "/usr/local/bin/cache-mgr.2", + "cache-mgr.2.11.0": "/usr/local/bin/cache-mgr.2.11.0", + "captoinfo": "/usr/local/bin/captoinfo", + "ccextract": "/usr/local/bin/ccextract", + "ccextract.2": "/usr/local/bin/ccextract.2", + "ccextract.2.11.0": "/usr/local/bin/ccextract.2.11.0", + "cg-load": "/usr/local/bin/cg-load", + "cg-load.2": "/usr/local/bin/cg-load.2", + "cg-load.2.11.0": "/usr/local/bin/cg-load.2.11.0", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "corelist": "/usr/local/bin/corelist", + "cpan": "/usr/local/bin/cpan", + "curl": "/usr/local/bin/curl", + "curl-config": "/usr/local/bin/curl-config", + "derb": "/usr/local/bin/derb", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "envsubst": "/usr/local/bin/envsubst", + "erb": "/usr/local/bin/erb", + "fasterq-dump": "/usr/local/bin/fasterq-dump", + "fasterq-dump-orig": "/usr/local/bin/fasterq-dump-orig", + "fasterq-dump-orig.2.11.0": "/usr/local/bin/fasterq-dump-orig.2.11.0", + "fasterq-dump.2": "/usr/local/bin/fasterq-dump.2", + "fasterq-dump.2.11.0": "/usr/local/bin/fasterq-dump.2.11.0", + "fastq-dump": "/usr/local/bin/fastq-dump", + "fastq-dump-orig": "/usr/local/bin/fastq-dump-orig", + "fastq-dump-orig.2.11.0": "/usr/local/bin/fastq-dump-orig.2.11.0", + "fastq-dump.2": "/usr/local/bin/fastq-dump.2", + "fastq-dump.2.11.0": "/usr/local/bin/fastq-dump.2.11.0", + "fastq-load": "/usr/local/bin/fastq-load", + "fastq-load.2": "/usr/local/bin/fastq-load.2", + "fastq-load.2.11.0": "/usr/local/bin/fastq-load.2.11.0", + "gdbm_dump": "/usr/local/bin/gdbm_dump", + "gdbm_load": "/usr/local/bin/gdbm_load", + "gdbmtool": "/usr/local/bin/gdbmtool", + "gem": "/usr/local/bin/gem", + "genbrk": "/usr/local/bin/genbrk", + "gencfu": "/usr/local/bin/gencfu", + "gencnval": "/usr/local/bin/gencnval", + "gendict": "/usr/local/bin/gendict", + "genrb": "/usr/local/bin/genrb", + "gettext": "/usr/local/bin/gettext", + "gettext.sh": "/usr/local/bin/gettext.sh", + "gettextize": "/usr/local/bin/gettextize", + "gif2h5": "/usr/local/bin/gif2h5", + "gss-client": "/usr/local/bin/gss-client", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "h52gif": "/usr/local/bin/h52gif", + "h5c++": "/usr/local/bin/h5c++", + "h5cc": "/usr/local/bin/h5cc", + "h5clear": "/usr/local/bin/h5clear", + "h5copy": "/usr/local/bin/h5copy", + "h5debug": "/usr/local/bin/h5debug", + "h5diff": "/usr/local/bin/h5diff", + "h5dump": "/usr/local/bin/h5dump", + "h5fc": "/usr/local/bin/h5fc", + "h5format_convert": "/usr/local/bin/h5format_convert", + "h5import": "/usr/local/bin/h5import", + "h5jam": "/usr/local/bin/h5jam", + "h5ls": "/usr/local/bin/h5ls", + "h5mkgrp": "/usr/local/bin/h5mkgrp", + "h5perf_serial": "/usr/local/bin/h5perf_serial", + "h5redeploy": "/usr/local/bin/h5redeploy", + "h5repack": "/usr/local/bin/h5repack", + "h5repart": "/usr/local/bin/h5repart", + "h5stat": "/usr/local/bin/h5stat", + "h5unjam": "/usr/local/bin/h5unjam", + "h5watch": "/usr/local/bin/h5watch", + "helicos-load": "/usr/local/bin/helicos-load", + "helicos-load.2": "/usr/local/bin/helicos-load.2", + "helicos-load.2.11.0": "/usr/local/bin/helicos-load.2.11.0", + "iconv": "/usr/local/bin/iconv", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "idn2": "/usr/local/bin/idn2", + "illumina-dump": "/usr/local/bin/illumina-dump", + "illumina-dump.2": "/usr/local/bin/illumina-dump.2", + "illumina-dump.2.11.0": "/usr/local/bin/illumina-dump.2.11.0", + "illumina-load": "/usr/local/bin/illumina-load", + "illumina-load.2": "/usr/local/bin/illumina-load.2", + "illumina-load.2.11.0": "/usr/local/bin/illumina-load.2.11.0", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "instmodsh": "/usr/local/bin/instmodsh", + "irb": "/usr/local/bin/irb", + "iseq": "/usr/local/bin/iseq", + "json_pp": "/usr/local/bin/json_pp", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kar": "/usr/local/bin/kar", + "kar.2": "/usr/local/bin/kar.2", + "kar.2.11.0": "/usr/local/bin/kar.2.11.0", + "kdbmeta": "/usr/local/bin/kdbmeta", + "kdbmeta.2": "/usr/local/bin/kdbmeta.2", + "kdbmeta.2.11.0": "/usr/local/bin/kdbmeta.2.11.0", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kget": "/usr/local/bin/kget", + "kget.2": "/usr/local/bin/kget.2", + "kget.2.11.0": "/usr/local/bin/kget.2.11.0", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "latf-load": "/usr/local/bin/latf-load", + "latf-load.2": "/usr/local/bin/latf-load.2", + "latf-load.2.11.0": "/usr/local/bin/latf-load.2.11.0", + "libnetcfg": "/usr/local/bin/libnetcfg", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "magic": "/usr/local/bin/magic", + "makeconv": "/usr/local/bin/makeconv", + "md5cp": "/usr/local/bin/md5cp", + "md5cp.2": "/usr/local/bin/md5cp.2", + "md5cp.2.11.0": "/usr/local/bin/md5cp.2.11.0", + "msgattrib": "/usr/local/bin/msgattrib", + "msgcat": "/usr/local/bin/msgcat", + "msgcmp": "/usr/local/bin/msgcmp", + "msgcomm": "/usr/local/bin/msgcomm", + "msgconv": "/usr/local/bin/msgconv", + "msgen": "/usr/local/bin/msgen", + "msgexec": "/usr/local/bin/msgexec", + "msgfilter": "/usr/local/bin/msgfilter", + "msgfmt": "/usr/local/bin/msgfmt", + "msggrep": "/usr/local/bin/msggrep", + "msginit": "/usr/local/bin/msginit", + "msgmerge": "/usr/local/bin/msgmerge", + "msgunfmt": "/usr/local/bin/msgunfmt", + "msguniq": "/usr/local/bin/msguniq", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "ngettext": "/usr/local/bin/ngettext", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "openssl": "/usr/local/bin/openssl", + "pacbio-load": "/usr/local/bin/pacbio-load", + "pacbio-load.2": "/usr/local/bin/pacbio-load.2", + "pacbio-load.2.11.0": "/usr/local/bin/pacbio-load.2.11.0", + "pacbio-loadxml": "/usr/local/bin/pacbio-loadxml", + "pacbio-loadxml.2": "/usr/local/bin/pacbio-loadxml.2", + "pacbio-loadxml.2.11.0": "/usr/local/bin/pacbio-loadxml.2.11.0", + "perl": "/usr/local/bin/perl", + "perl5.32.1": "/usr/local/bin/perl5.32.1", + "perlbug": "/usr/local/bin/perlbug", + "perldoc": "/usr/local/bin/perldoc", + "perlivp": "/usr/local/bin/perlivp", + "perlthanks": "/usr/local/bin/perlthanks", + "piconv": "/usr/local/bin/piconv", + "pigz": "/usr/local/bin/pigz", + "pkgdata": "/usr/local/bin/pkgdata", + "pl2pm": "/usr/local/bin/pl2pm", + "pod2html": "/usr/local/bin/pod2html", + "pod2man": "/usr/local/bin/pod2man", + "pod2text": "/usr/local/bin/pod2text", + "pod2usage": "/usr/local/bin/pod2usage", + "podchecker": "/usr/local/bin/podchecker", + "prefetch": "/usr/local/bin/prefetch", + "prefetch-orig": "/usr/local/bin/prefetch-orig", + "prefetch-orig.2.11.0": "/usr/local/bin/prefetch-orig.2.11.0", + "prefetch.2": "/usr/local/bin/prefetch.2", + "prefetch.2.11.0": "/usr/local/bin/prefetch.2.11.0", + "prove": "/usr/local/bin/prove", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "racc": "/usr/local/bin/racc", + "rake": "/usr/local/bin/rake", + "rbs": "/usr/local/bin/rbs", + "rcexplain": "/usr/local/bin/rcexplain", + "rcexplain.2": "/usr/local/bin/rcexplain.2", + "rcexplain.2.11.0": "/usr/local/bin/rcexplain.2.11.0", + "rdbg": "/usr/local/bin/rdbg", + "rdoc": "/usr/local/bin/rdoc", + "read-filter-redact": "/usr/local/bin/read-filter-redact", + "read-filter-redact.2": "/usr/local/bin/read-filter-redact.2", + "read-filter-redact.2.11.0": "/usr/local/bin/read-filter-redact.2.11.0", + "recode-sr-latin": "/usr/local/bin/recode-sr-latin", + "reset": "/usr/local/bin/reset", + "ri": "/usr/local/bin/ri", + "ruby": "/usr/local/bin/ruby", + "sam-dump": "/usr/local/bin/sam-dump", + "sam-dump-orig": "/usr/local/bin/sam-dump-orig", + "sam-dump-orig.2.11.0": "/usr/local/bin/sam-dump-orig.2.11.0", + "sam-dump.2": "/usr/local/bin/sam-dump.2", + "sam-dump.2.11.0": "/usr/local/bin/sam-dump.2.11.0", + "sclient": "/usr/local/bin/sclient", + "sff-dump": "/usr/local/bin/sff-dump", + "sff-dump.2": "/usr/local/bin/sff-dump.2", + "sff-dump.2.11.0": "/usr/local/bin/sff-dump.2.11.0", + "sff-load": "/usr/local/bin/sff-load", + "sff-load.2": "/usr/local/bin/sff-load.2", + "sff-load.2.11.0": "/usr/local/bin/sff-load.2.11.0", + "shasum": "/usr/local/bin/shasum", + "sim_client": "/usr/local/bin/sim_client", + "splain": "/usr/local/bin/splain", + "sra-pileup": "/usr/local/bin/sra-pileup", + "sra-pileup-orig": "/usr/local/bin/sra-pileup-orig", + "sra-pileup-orig.2.11.0": "/usr/local/bin/sra-pileup-orig.2.11.0", + "sra-pileup.2": "/usr/local/bin/sra-pileup.2", + "sra-pileup.2.11.0": "/usr/local/bin/sra-pileup.2.11.0", + "sra-sort": "/usr/local/bin/sra-sort", + "sra-sort-cg": "/usr/local/bin/sra-sort-cg", + "sra-sort-cg.2": "/usr/local/bin/sra-sort-cg.2", + "sra-sort-cg.2.11.0": "/usr/local/bin/sra-sort-cg.2.11.0", + "sra-sort.2": "/usr/local/bin/sra-sort.2", + "sra-sort.2.11.0": "/usr/local/bin/sra-sort.2.11.0", + "sra-stat": "/usr/local/bin/sra-stat", + "sra-stat.2": "/usr/local/bin/sra-stat.2", + "sra-stat.2.11.0": "/usr/local/bin/sra-stat.2.11.0", + "srapath": "/usr/local/bin/srapath", + "srapath-orig": "/usr/local/bin/srapath-orig", + "srapath-orig.2.11.0": "/usr/local/bin/srapath-orig.2.11.0", + "srapath.2": "/usr/local/bin/srapath.2", + "srapath.2.11.0": "/usr/local/bin/srapath.2.11.0", + "sratools": "/usr/local/bin/sratools", + "sratools.2": "/usr/local/bin/sratools.2", + "sratools.2.11.0": "/usr/local/bin/sratools.2.11.0", + "srf-load": "/usr/local/bin/srf-load", + "srf-load.2": "/usr/local/bin/srf-load.2", + "srf-load.2.11.0": "/usr/local/bin/srf-load.2.11.0", + "streamzip": "/usr/local/bin/streamzip", + "tabs": "/usr/local/bin/tabs", + "test-sra": "/usr/local/bin/test-sra", + "test-sra.2": "/usr/local/bin/test-sra.2", + "test-sra.2.11.0": "/usr/local/bin/test-sra.2.11.0", + "tic": "/usr/local/bin/tic", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tset": "/usr/local/bin/tset", + "typeprof": "/usr/local/bin/typeprof", + "unlzma": "/usr/local/bin/unlzma", + "unpigz": "/usr/local/bin/unpigz", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "uuid": "/usr/local/bin/uuid", + "uuid-config": "/usr/local/bin/uuid-config", + "vdb-config": "/usr/local/bin/vdb-config", + "vdb-config.2": "/usr/local/bin/vdb-config.2", + "vdb-config.2.11.0": "/usr/local/bin/vdb-config.2.11.0", + "vdb-copy": "/usr/local/bin/vdb-copy", + "vdb-copy.2": "/usr/local/bin/vdb-copy.2", + "vdb-copy.2.11.0": "/usr/local/bin/vdb-copy.2.11.0", + "vdb-decrypt": "/usr/local/bin/vdb-decrypt", + "vdb-decrypt.2": "/usr/local/bin/vdb-decrypt.2", + "vdb-decrypt.2.11.0": "/usr/local/bin/vdb-decrypt.2.11.0", + "vdb-diff": "/usr/local/bin/vdb-diff", + "vdb-diff.2": "/usr/local/bin/vdb-diff.2", + "vdb-diff.2.11.0": "/usr/local/bin/vdb-diff.2.11.0", + "vdb-dump": "/usr/local/bin/vdb-dump", + "vdb-dump-orig.2.11.0": "/usr/local/bin/vdb-dump-orig.2.11.0", + "vdb-dump.2": "/usr/local/bin/vdb-dump.2", + "vdb-dump.2.11.0": "/usr/local/bin/vdb-dump.2.11.0", + "vdb-encrypt": "/usr/local/bin/vdb-encrypt", + "vdb-encrypt.2": "/usr/local/bin/vdb-encrypt.2", + "vdb-encrypt.2.11.0": "/usr/local/bin/vdb-encrypt.2.11.0", + "vdb-lock": "/usr/local/bin/vdb-lock", + "vdb-lock.2": "/usr/local/bin/vdb-lock.2", + "vdb-lock.2.11.0": "/usr/local/bin/vdb-lock.2.11.0", + "vdb-passwd": "/usr/local/bin/vdb-passwd", + "vdb-passwd.2": "/usr/local/bin/vdb-passwd.2", + "vdb-passwd.2.11.0": "/usr/local/bin/vdb-passwd.2.11.0", + "vdb-unlock": "/usr/local/bin/vdb-unlock", + "vdb-unlock.2": "/usr/local/bin/vdb-unlock.2", + "vdb-unlock.2.11.0": "/usr/local/bin/vdb-unlock.2.11.0", + "vdb-validate": "/usr/local/bin/vdb-validate", + "vdb-validate.2": "/usr/local/bin/vdb-validate.2", + "vdb-validate.2.11.0": "/usr/local/bin/vdb-validate.2.11.0", + "wget": "/usr/local/bin/wget", + "xgettext": "/usr/local/bin/xgettext", + "xml2-config": "/usr/local/bin/xml2-config", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xsubpp": "/usr/local/bin/xsubpp", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zipdetails": "/usr/local/bin/zipdetails", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/s/scoring-matrices:0.2.0--py39hf95cd2a_0.json b/quay.io/biocontainers/s/scoring-matrices:0.2.0--py39hf95cd2a_0.json new file mode 100644 index 0000000..e6dbe77 --- /dev/null +++ b/quay.io/biocontainers/s/scoring-matrices:0.2.0--py39hf95cd2a_0.json @@ -0,0 +1,73 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.9": "/usr/local/bin/2to3-3.9", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "clear": "/usr/local/bin/clear", + "idle3": "/usr/local/bin/idle3", + "idle3.9": "/usr/local/bin/idle3.9", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "openssl": "/usr/local/bin/openssl", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.9": "/usr/local/bin/pydoc3.9", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.9": "/usr/local/bin/python3.9", + "python3.9-config": "/usr/local/bin/python3.9-config", + "reset": "/usr/local/bin/reset", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "toe": "/usr/local/bin/toe", + 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0000000..70a82fc --- /dev/null +++ b/quay.io/biocontainers/s/sincei:0.3.1--pyhdfd78af_0.json @@ -0,0 +1,246 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.10": "/usr/local/bin/2to3-3.10", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "alignmentSieve": "/usr/local/bin/alignmentSieve", + "bamCompare": "/usr/local/bin/bamCompare", + "bamCoverage": "/usr/local/bin/bamCoverage", + "bamPEFragmentSize": "/usr/local/bin/bamPEFragmentSize", + "bigwigAverage": "/usr/local/bin/bigwigAverage", + "bigwigCompare": "/usr/local/bin/bigwigCompare", + "brotli": "/usr/local/bin/brotli", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "computeGCBias": "/usr/local/bin/computeGCBias", + "computeMatrix": "/usr/local/bin/computeMatrix", + "computeMatrixOperations": "/usr/local/bin/computeMatrixOperations", + "correctGCBias": "/usr/local/bin/correctGCBias", + "curl-config": "/usr/local/bin/curl-config", + "deeptools": "/usr/local/bin/deeptools", + "derb": "/usr/local/bin/derb", + "djpeg": "/usr/local/bin/djpeg", + "docutils": "/usr/local/bin/docutils", + "estimateReadFiltering": "/usr/local/bin/estimateReadFiltering", + "estimateScaleFactor": "/usr/local/bin/estimateScaleFactor", + "f2py": "/usr/local/bin/f2py", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "genbrk": "/usr/local/bin/genbrk", + "gencfu": "/usr/local/bin/gencfu", + "gencnval": 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"/usr/local/bin/h5repart", + "h5stat": "/usr/local/bin/h5stat", + "h5tools_test_utils": "/usr/local/bin/h5tools_test_utils", + "h5unjam": "/usr/local/bin/h5unjam", + "h5watch": "/usr/local/bin/h5watch", + "hwloc-annotate": "/usr/local/bin/hwloc-annotate", + "hwloc-bind": "/usr/local/bin/hwloc-bind", + "hwloc-calc": "/usr/local/bin/hwloc-calc", + "hwloc-compress-dir": "/usr/local/bin/hwloc-compress-dir", + "hwloc-diff": "/usr/local/bin/hwloc-diff", + "hwloc-distrib": "/usr/local/bin/hwloc-distrib", + "hwloc-gather-cpuid": "/usr/local/bin/hwloc-gather-cpuid", + "hwloc-gather-topology": "/usr/local/bin/hwloc-gather-topology", + "hwloc-info": "/usr/local/bin/hwloc-info", + "hwloc-ls": "/usr/local/bin/hwloc-ls", + "hwloc-patch": "/usr/local/bin/hwloc-patch", + "hwloc-ps": "/usr/local/bin/hwloc-ps", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "idle3": "/usr/local/bin/idle3", + "idle3.10": 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"openssl": "/usr/local/bin/openssl", + "opj_compress": "/usr/local/bin/opj_compress", + "opj_decompress": "/usr/local/bin/opj_decompress", + "opj_dump": "/usr/local/bin/opj_dump", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pkgdata": "/usr/local/bin/pkgdata", + "plotCorrelation": "/usr/local/bin/plotCorrelation", + "plotCoverage": "/usr/local/bin/plotCoverage", + "plotEnrichment": "/usr/local/bin/plotEnrichment", + "plotFingerprint": "/usr/local/bin/plotFingerprint", + "plotHeatmap": "/usr/local/bin/plotHeatmap", + "plotPCA": "/usr/local/bin/plotPCA", + "plotProfile": "/usr/local/bin/plotProfile", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "psicc": "/usr/local/bin/psicc", + "pybabel": "/usr/local/bin/pybabel", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.10": "/usr/local/bin/pydoc3.10", + "pyftmerge": "/usr/local/bin/pyftmerge", + "pyftsubset": "/usr/local/bin/pyftsubset", + 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"/usr/local/bin/scCountQC", + "scCountReads": "/usr/local/bin/scCountReads", + "scFilterBarcodes": "/usr/local/bin/scFilterBarcodes", + "scFilterStats": "/usr/local/bin/scFilterStats", + "scJSD": "/usr/local/bin/scJSD", + "scanpy": "/usr/local/bin/scanpy", + "sclient": "/usr/local/bin/sclient", + "sim_client": "/usr/local/bin/sim_client", + "sincei": "/usr/local/bin/sincei", + "sphinx-apidoc": "/usr/local/bin/sphinx-apidoc", + "sphinx-autogen": "/usr/local/bin/sphinx-autogen", + "sphinx-build": "/usr/local/bin/sphinx-build", + "sphinx-quickstart": "/usr/local/bin/sphinx-quickstart", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tabulate": "/usr/local/bin/tabulate", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tqdm": "/usr/local/bin/tqdm", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "validate-docstrings": "/usr/local/bin/validate-docstrings", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xml2-config": "/usr/local/bin/xml2-config", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/s/squigualiser:0.6.3--pyhca03a8a_0.json b/quay.io/biocontainers/s/squigualiser:0.6.3--pyhca03a8a_0.json new file mode 100644 index 0000000..03c00c2 --- /dev/null +++ b/quay.io/biocontainers/s/squigualiser:0.6.3--pyhca03a8a_0.json @@ -0,0 +1,143 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.10": "/usr/local/bin/2to3-3.10", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "bokeh": "/usr/local/bin/bokeh", + "brotli": "/usr/local/bin/brotli", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "curl-config": "/usr/local/bin/curl-config", + "djpeg": "/usr/local/bin/djpeg", + "f2py": "/usr/local/bin/f2py", + "faidx": "/usr/local/bin/faidx", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "gss-client": "/usr/local/bin/gss-client", + "idle3": "/usr/local/bin/idle3", + "idle3.10": "/usr/local/bin/idle3.10", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "openssl": "/usr/local/bin/openssl", + "opj_compress": "/usr/local/bin/opj_compress", + "opj_decompress": "/usr/local/bin/opj_decompress", + "opj_dump": "/usr/local/bin/opj_dump", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "psicc": "/usr/local/bin/psicc", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.10": "/usr/local/bin/pydoc3.10", + "pyfastx": "/usr/local/bin/pyfastx", + "pyftmerge": "/usr/local/bin/pyftmerge", + "pyftsubset": "/usr/local/bin/pyftsubset", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.10": "/usr/local/bin/python3.10", + "python3.10-config": "/usr/local/bin/python3.10-config", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "reset": "/usr/local/bin/reset", + "sclient": "/usr/local/bin/sclient", + "selenium-manager": "/usr/local/bin/selenium-manager", + "sim_client": "/usr/local/bin/sim_client", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "squigualiser": "/usr/local/bin/squigualiser", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "vcf_filter.py": "/usr/local/bin/vcf_filter.py", + "vcf_melt": "/usr/local/bin/vcf_melt", + "vcf_sample_filter.py": "/usr/local/bin/vcf_sample_filter.py", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/t/tadrep:0.9.2--pyhdfd78af_0.json b/quay.io/biocontainers/t/tadrep:0.9.2--pyhdfd78af_0.json new file mode 100644 index 0000000..494b89d --- /dev/null +++ b/quay.io/biocontainers/t/tadrep:0.9.2--pyhdfd78af_0.json @@ -0,0 +1,386 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.11": "/usr/local/bin/2to3-3.11", + "FET.pl": "/usr/local/bin/FET.pl", + "accn-at-a-time": "/usr/local/bin/accn-at-a-time", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "align-columns": "/usr/local/bin/align-columns", + "amino-acid-composition": "/usr/local/bin/amino-acid-composition", + "archive-ncbinlp": "/usr/local/bin/archive-ncbinlp", + "archive-nihocc": "/usr/local/bin/archive-nihocc", + "archive-nmcds": "/usr/local/bin/archive-nmcds", + "archive-pmc": "/usr/local/bin/archive-pmc", + "archive-pubmed": "/usr/local/bin/archive-pubmed", + "archive-taxonomy": "/usr/local/bin/archive-taxonomy", + "archspec": "/usr/local/bin/archspec", + "args2slice": "/usr/local/bin/args2slice", + "asn2ref": "/usr/local/bin/asn2ref", + "asn2xml": "/usr/local/bin/asn2xml", + "autopoint": "/usr/local/bin/autopoint", + "between-two-genes": "/usr/local/bin/between-two-genes", + "blast_formatter": "/usr/local/bin/blast_formatter", + "blastdb_aliastool": "/usr/local/bin/blastdb_aliastool", + "blastdbcheck": "/usr/local/bin/blastdbcheck", + "blastdbcmd": "/usr/local/bin/blastdbcmd", + "blastn": "/usr/local/bin/blastn", + "blastn_vdb": "/usr/local/bin/blastn_vdb", + "blastp": "/usr/local/bin/blastp", + "blastx": "/usr/local/bin/blastx", + "blst2gm": "/usr/local/bin/blst2gm", + "blst2tkns": "/usr/local/bin/blst2tkns", + "brotli": "/usr/local/bin/brotli", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "cd-hit": "/usr/local/bin/cd-hit", + "cd-hit-2d": "/usr/local/bin/cd-hit-2d", + "cd-hit-2d-para.pl": "/usr/local/bin/cd-hit-2d-para.pl", + "cd-hit-454": "/usr/local/bin/cd-hit-454", + "cd-hit-clstr_2_blm8.pl": "/usr/local/bin/cd-hit-clstr_2_blm8.pl", + "cd-hit-div": "/usr/local/bin/cd-hit-div", + "cd-hit-div.pl": "/usr/local/bin/cd-hit-div.pl", + "cd-hit-est": "/usr/local/bin/cd-hit-est", + "cd-hit-est-2d": "/usr/local/bin/cd-hit-est-2d", + "cd-hit-para.pl": "/usr/local/bin/cd-hit-para.pl", + "cit2pmid": "/usr/local/bin/cit2pmid", + "cjpeg": "/usr/local/bin/cjpeg", + "cleanup-blastdb-volumes.py": "/usr/local/bin/cleanup-blastdb-volumes.py", + "clear": "/usr/local/bin/clear", + "clstr2tree.pl": "/usr/local/bin/clstr2tree.pl", + "clstr2txt.pl": "/usr/local/bin/clstr2txt.pl", + "clstr2xml.pl": "/usr/local/bin/clstr2xml.pl", + "clstr_cut.pl": "/usr/local/bin/clstr_cut.pl", + "clstr_list.pl": "/usr/local/bin/clstr_list.pl", + "clstr_list_sort.pl": "/usr/local/bin/clstr_list_sort.pl", + "clstr_merge.pl": "/usr/local/bin/clstr_merge.pl", + "clstr_merge_noorder.pl": "/usr/local/bin/clstr_merge_noorder.pl", + "clstr_quality_eval.pl": "/usr/local/bin/clstr_quality_eval.pl", + "clstr_quality_eval_by_link.pl": "/usr/local/bin/clstr_quality_eval_by_link.pl", + "clstr_reduce.pl": "/usr/local/bin/clstr_reduce.pl", + "clstr_renumber.pl": "/usr/local/bin/clstr_renumber.pl", + "clstr_rep.pl": "/usr/local/bin/clstr_rep.pl", + "clstr_reps_faa_rev.pl": "/usr/local/bin/clstr_reps_faa_rev.pl", + "clstr_rev.pl": "/usr/local/bin/clstr_rev.pl", + "clstr_select.pl": "/usr/local/bin/clstr_select.pl", + "clstr_select_rep.pl": "/usr/local/bin/clstr_select_rep.pl", + "clstr_size_histogram.pl": "/usr/local/bin/clstr_size_histogram.pl", + "clstr_size_stat.pl": "/usr/local/bin/clstr_size_stat.pl", + "clstr_sort_by.pl": "/usr/local/bin/clstr_sort_by.pl", + "clstr_sort_prot_by.pl": "/usr/local/bin/clstr_sort_prot_by.pl", + "clstr_sql_tbl.pl": "/usr/local/bin/clstr_sql_tbl.pl", + "clstr_sql_tbl_sort.pl": "/usr/local/bin/clstr_sql_tbl_sort.pl", + "combine-uid-lists": "/usr/local/bin/combine-uid-lists", + "compile_et": "/usr/local/bin/compile_et", + "convert2blastmask": "/usr/local/bin/convert2blastmask", + "corelist": "/usr/local/bin/corelist", + "cpan": "/usr/local/bin/cpan", + "csv2xml": "/usr/local/bin/csv2xml", + "curl": "/usr/local/bin/curl", + "curl-config": "/usr/local/bin/curl-config", + "datatool": "/usr/local/bin/datatool", + "deltablast": "/usr/local/bin/deltablast", + "difference-uid-lists": "/usr/local/bin/difference-uid-lists", + "disambiguate-nucleotides": "/usr/local/bin/disambiguate-nucleotides", + "djpeg": "/usr/local/bin/djpeg", + "download-ncbi-data": "/usr/local/bin/download-ncbi-data", + "download-ncbi-software": "/usr/local/bin/download-ncbi-software", + "download-pmc": "/usr/local/bin/download-pmc", + "download-pubmed": "/usr/local/bin/download-pubmed", + "download-sequence": "/usr/local/bin/download-sequence", + "ds2pme": "/usr/local/bin/ds2pme", + "dustmasker": "/usr/local/bin/dustmasker", + "ecommon.sh": "/usr/local/bin/ecommon.sh", + "efetch": "/usr/local/bin/efetch", + "efilter": "/usr/local/bin/efilter", + "einfo": "/usr/local/bin/einfo", + "elink": "/usr/local/bin/elink", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "envsubst": "/usr/local/bin/envsubst", + "epost": "/usr/local/bin/epost", + "esample": "/usr/local/bin/esample", + "esearch": "/usr/local/bin/esearch", + "esummary": "/usr/local/bin/esummary", + "exclude-uid-lists": "/usr/local/bin/exclude-uid-lists", + "expand-current": "/usr/local/bin/expand-current", + "f2py": "/usr/local/bin/f2py", + "fetch-local": "/usr/local/bin/fetch-local", + "fetch-nmcds": "/usr/local/bin/fetch-nmcds", + "fetch-pmc": "/usr/local/bin/fetch-pmc", + "fetch-pubmed": "/usr/local/bin/fetch-pubmed", + "fetch-taxonomy": "/usr/local/bin/fetch-taxonomy", + "filter-columns": "/usr/local/bin/filter-columns", + "filter-genbank": "/usr/local/bin/filter-genbank", + "filter-record": "/usr/local/bin/filter-record", + "filter-stop-words": "/usr/local/bin/filter-stop-words", + "find-in-gene": "/usr/local/bin/find-in-gene", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "fuse-ranges": "/usr/local/bin/fuse-ranges", + "fuse-segments": "/usr/local/bin/fuse-segments", + "gbf2fsa": "/usr/local/bin/gbf2fsa", + "gbf2ref": "/usr/local/bin/gbf2ref", + "gbf2xml": "/usr/local/bin/gbf2xml", + "gene2range": "/usr/local/bin/gene2range", + "get_species_taxids.sh": "/usr/local/bin/get_species_taxids.sh", + "get_species_taxids.sh.bak": "/usr/local/bin/get_species_taxids.sh.bak", + "gettext": "/usr/local/bin/gettext", + "gettext.sh": "/usr/local/bin/gettext.sh", + "gettextize": "/usr/local/bin/gettextize", + "gm2ranges": "/usr/local/bin/gm2ranges", + "gm2segs": "/usr/local/bin/gm2segs", + "gss-client": "/usr/local/bin/gss-client", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "hgvs2spdi": "/usr/local/bin/hgvs2spdi", + "idle3": "/usr/local/bin/idle3", + "idle3.11": "/usr/local/bin/idle3.11", + "idn2": "/usr/local/bin/idn2", + "igzip": "/usr/local/bin/igzip", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "ini2xml": "/usr/local/bin/ini2xml", + "instmodsh": "/usr/local/bin/instmodsh", + "intersect-uid-lists": "/usr/local/bin/intersect-uid-lists", + "join-into-groups-of": "/usr/local/bin/join-into-groups-of", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "json2xml": "/usr/local/bin/json2xml", + "json_pp": "/usr/local/bin/json_pp", + "json_xs": "/usr/local/bin/json_xs", + "jsonl2xml": "/usr/local/bin/jsonl2xml", + "just-first-key": "/usr/local/bin/just-first-key", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "legacy_blast.pl": "/usr/local/bin/legacy_blast.pl", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libnetcfg": "/usr/local/bin/libnetcfg", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "make_multi_seq.pl": "/usr/local/bin/make_multi_seq.pl", + "makeblastdb": "/usr/local/bin/makeblastdb", + "makembindex": "/usr/local/bin/makembindex", + "makeprofiledb": "/usr/local/bin/makeprofiledb", + "msgattrib": "/usr/local/bin/msgattrib", + "msgcat": "/usr/local/bin/msgcat", + "msgcmp": "/usr/local/bin/msgcmp", + "msgcomm": "/usr/local/bin/msgcomm", + "msgconv": "/usr/local/bin/msgconv", + "msgen": "/usr/local/bin/msgen", + "msgexec": "/usr/local/bin/msgexec", + "msgfilter": "/usr/local/bin/msgfilter", + "msgfmt": "/usr/local/bin/msgfmt", + "msggrep": "/usr/local/bin/msggrep", + "msginit": "/usr/local/bin/msginit", + "msgmerge": "/usr/local/bin/msgmerge", + "msgunfmt": "/usr/local/bin/msgunfmt", + "msguniq": "/usr/local/bin/msguniq", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "ngettext": "/usr/local/bin/ngettext", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "nhance.sh": "/usr/local/bin/nhance.sh", + "nquire": "/usr/local/bin/nquire", + "openssl": "/usr/local/bin/openssl", + "opj_compress": "/usr/local/bin/opj_compress", + "opj_decompress": "/usr/local/bin/opj_decompress", + "opj_dump": "/usr/local/bin/opj_dump", + "pbunzip2": "/usr/local/bin/pbunzip2", + "pbzcat": "/usr/local/bin/pbzcat", + "pbzip2": "/usr/local/bin/pbzip2", + "pcre-config": "/usr/local/bin/pcre-config", + "pcregrep": "/usr/local/bin/pcregrep", + "pcretest": "/usr/local/bin/pcretest", + "perl": "/usr/local/bin/perl", + "perl5.32.1": "/usr/local/bin/perl5.32.1", + "perlbug": "/usr/local/bin/perlbug", + "perldoc": "/usr/local/bin/perldoc", + "perlivp": "/usr/local/bin/perlivp", + "perlthanks": "/usr/local/bin/perlthanks", + "pgv-download-dataset": "/usr/local/bin/pgv-download-dataset", + "pgv-gui": "/usr/local/bin/pgv-gui", + "pgv-mmseqs": "/usr/local/bin/pgv-mmseqs", + "pgv-mummer": "/usr/local/bin/pgv-mummer", + "pgv-pmauve": "/usr/local/bin/pgv-pmauve", + "pgv-simpleplot": "/usr/local/bin/pgv-simpleplot", + "phrase-search": "/usr/local/bin/phrase-search", + "piconv": "/usr/local/bin/piconv", + "pigz": "/usr/local/bin/pigz", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pl2pm": "/usr/local/bin/pl2pm", + "plot_2d.pl": "/usr/local/bin/plot_2d.pl", + "plot_len1.pl": "/usr/local/bin/plot_len1.pl", + "pma2apa": "/usr/local/bin/pma2apa", + "pma2pme": "/usr/local/bin/pma2pme", + "pmc2bioc": "/usr/local/bin/pmc2bioc", + "pmc2info": "/usr/local/bin/pmc2info", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "pod2html": "/usr/local/bin/pod2html", + "pod2man": "/usr/local/bin/pod2man", + "pod2text": "/usr/local/bin/pod2text", + "pod2usage": "/usr/local/bin/pod2usage", + "podchecker": "/usr/local/bin/podchecker", + "print-columns": "/usr/local/bin/print-columns", + "project_tree_builder": "/usr/local/bin/project_tree_builder", + "prove": "/usr/local/bin/prove", + "psiblast": "/usr/local/bin/psiblast", + "psicc": "/usr/local/bin/psicc", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.11": "/usr/local/bin/pydoc3.11", + "pyftmerge": "/usr/local/bin/pyftmerge", + "pyftsubset": "/usr/local/bin/pyftsubset", + "pyrodigal": "/usr/local/bin/pyrodigal", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.11": "/usr/local/bin/python3.11", + "python3.11-config": "/usr/local/bin/python3.11-config", + "quote-grouped-elements": "/usr/local/bin/quote-grouped-elements", + "rchive": "/usr/local/bin/rchive", + "rchive.Linux": "/usr/local/bin/rchive.Linux", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "recode-sr-latin": "/usr/local/bin/recode-sr-latin", + "ref2pmid": "/usr/local/bin/ref2pmid", + "refseq-nm-cds": "/usr/local/bin/refseq-nm-cds", + "reorder-columns": "/usr/local/bin/reorder-columns", + "reset": "/usr/local/bin/reset", + "rpsblast": "/usr/local/bin/rpsblast", + "rpsbproc": "/usr/local/bin/rpsbproc", + "rpstblastn": "/usr/local/bin/rpstblastn", + "run-ncbi-converter": "/usr/local/bin/run-ncbi-converter", + "run_with_lock": "/usr/local/bin/run_with_lock", + "sclient": "/usr/local/bin/sclient", + "scn2xml": "/usr/local/bin/scn2xml", + "segmasker": "/usr/local/bin/segmasker", + "shasum": "/usr/local/bin/shasum", + "sim_client": "/usr/local/bin/sim_client", + "skip-if-file-exists": "/usr/local/bin/skip-if-file-exists", + "snp2hgvs": "/usr/local/bin/snp2hgvs", + "snp2tbl": "/usr/local/bin/snp2tbl", + "sort-table": "/usr/local/bin/sort-table", + "sort-uniq-count": "/usr/local/bin/sort-uniq-count", + "sort-uniq-count-rank": "/usr/local/bin/sort-uniq-count-rank", + "spdi2tbl": "/usr/local/bin/spdi2tbl", + "splain": "/usr/local/bin/splain", + "split-at-intron": "/usr/local/bin/split-at-intron", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "stream-local": "/usr/local/bin/stream-local", + "stream-pubmed": "/usr/local/bin/stream-pubmed", + "streamzip": "/usr/local/bin/streamzip", + "tabs": "/usr/local/bin/tabs", + "tadrep": "/usr/local/bin/tadrep", + "tbl2prod": "/usr/local/bin/tbl2prod", + "tbl2xml": "/usr/local/bin/tbl2xml", + "tblastn": "/usr/local/bin/tblastn", + "tblastn_vdb": "/usr/local/bin/tblastn_vdb", + "tblastx": "/usr/local/bin/tblastx", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "test-edirect": "/usr/local/bin/test-edirect", + "test-eutils": "/usr/local/bin/test-eutils", + "test-pmc-index": "/usr/local/bin/test-pmc-index", + "test-pubmed-index": "/usr/local/bin/test-pubmed-index", + "test_pcre": "/usr/local/bin/test_pcre", + "tic": "/usr/local/bin/tic", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "toml2xml": "/usr/local/bin/toml2xml", + "tput": "/usr/local/bin/tput", + "transicc": "/usr/local/bin/transicc", + "transmute": "/usr/local/bin/transmute", + "transmute.Linux": "/usr/local/bin/transmute.Linux", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "uniq-table": "/usr/local/bin/uniq-table", + "unlzma": "/usr/local/bin/unlzma", + "unpigz": "/usr/local/bin/unpigz", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "update_blastdb.pl": "/usr/local/bin/update_blastdb.pl", + "update_blastdb.pl.bak": "/usr/local/bin/update_blastdb.pl.bak", + "uuclient": "/usr/local/bin/uuclient", + "wget": "/usr/local/bin/wget", + "wheel": "/usr/local/bin/wheel", + "windowmasker": "/usr/local/bin/windowmasker", + "windowmasker_2.2.22_adapter.py": "/usr/local/bin/windowmasker_2.2.22_adapter.py", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "word-at-a-time": "/usr/local/bin/word-at-a-time", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xgettext": "/usr/local/bin/xgettext", + "xml2fsa": "/usr/local/bin/xml2fsa", + "xml2json": "/usr/local/bin/xml2json", + "xml2tbl": "/usr/local/bin/xml2tbl", + "xsubpp": "/usr/local/bin/xsubpp", + "xtract": "/usr/local/bin/xtract", + "xtract.Linux": "/usr/local/bin/xtract.Linux", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "yaml2xml": "/usr/local/bin/yaml2xml", + "zipdetails": "/usr/local/bin/zipdetails", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/w/wgatools:0.1.0--h7c767d4_1.json b/quay.io/biocontainers/w/wgatools:0.1.0--h7c767d4_1.json new file mode 100644 index 0000000..73adbbe --- /dev/null +++ b/quay.io/biocontainers/w/wgatools:0.1.0--h7c767d4_1.json @@ -0,0 +1,37 @@ +{ + "c_rehash": "/usr/local/bin/c_rehash", + "corelist": "/usr/local/bin/corelist", + "cpan": "/usr/local/bin/cpan", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "instmodsh": "/usr/local/bin/instmodsh", + "json_pp": "/usr/local/bin/json_pp", + "libnetcfg": "/usr/local/bin/libnetcfg", + "openssl": "/usr/local/bin/openssl", + "perl": "/usr/local/bin/perl", + "perl5.32.1": "/usr/local/bin/perl5.32.1", + "perlbug": "/usr/local/bin/perlbug", + "perldoc": "/usr/local/bin/perldoc", + "perlivp": "/usr/local/bin/perlivp", + "perlthanks": "/usr/local/bin/perlthanks", + "piconv": "/usr/local/bin/piconv", + "pl2pm": "/usr/local/bin/pl2pm", + "pod2html": "/usr/local/bin/pod2html", + "pod2man": "/usr/local/bin/pod2man", + "pod2text": "/usr/local/bin/pod2text", + "pod2usage": "/usr/local/bin/pod2usage", + "podchecker": "/usr/local/bin/podchecker", + "prove": "/usr/local/bin/prove", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "shasum": "/usr/local/bin/shasum", + "splain": "/usr/local/bin/splain", + "streamzip": "/usr/local/bin/streamzip", + "wgatools": "/usr/local/bin/wgatools", + "xsubpp": "/usr/local/bin/xsubpp", + "zipdetails": "/usr/local/bin/zipdetails", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file