From 81dd30defe57f2ef05de015b6621f438388070b9 Mon Sep 17 00:00:00 2001 From: github-actions Date: Mon, 27 May 2024 00:57:49 +0000 Subject: [PATCH] Automated deployment with updated cache 2024-05-27 --- counts.json | 2437 +++++++++-------- .../c/colorid_bv:0.1.0--h4c94732_0.json | 4 + .../c/cured:1.05--hdfd78af_0.json | 521 ++++ .../g/gapseq:1.2--h9ee0642_0.json | 720 +++++ .../g/get_orfs:1.0.0--hdcf5f25_0.json | 4 + ...ndyreadgenotyper:0.1.13--pyhdfd78af_0.json | 151 + .../m/mgikit:0.1.5--h4c94732_0.json | 4 + .../mmseqs2-server:8.c4b9644--he881be0_0.json | 130 + .../r/rnavirhost:1.0.5--pyh7cba7a3_0.json | 306 +++ .../s/shigapass:1.5.0--hdfd78af_0.json | 257 ++ ...neakernet-qc:0.25.0--pl5321hdfd78af_0.json | 892 ++++++ .../s/sspace_basic:2.1.1--hdfd78af_0.json | 165 ++ 12 files changed, 4418 insertions(+), 1173 deletions(-) create mode 100644 quay.io/biocontainers/c/colorid_bv:0.1.0--h4c94732_0.json create mode 100644 quay.io/biocontainers/c/cured:1.05--hdfd78af_0.json create mode 100644 quay.io/biocontainers/g/gapseq:1.2--h9ee0642_0.json create mode 100644 quay.io/biocontainers/g/get_orfs:1.0.0--hdcf5f25_0.json create mode 100644 quay.io/biocontainers/h/handyreadgenotyper:0.1.13--pyhdfd78af_0.json create mode 100644 quay.io/biocontainers/m/mgikit:0.1.5--h4c94732_0.json create mode 100644 quay.io/biocontainers/m/mmseqs2-server:8.c4b9644--he881be0_0.json create mode 100644 quay.io/biocontainers/r/rnavirhost:1.0.5--pyh7cba7a3_0.json create mode 100644 quay.io/biocontainers/s/shigapass:1.5.0--hdfd78af_0.json create mode 100644 quay.io/biocontainers/s/sneakernet-qc:0.25.0--pl5321hdfd78af_0.json create mode 100644 quay.io/biocontainers/s/sspace_basic:2.1.1--hdfd78af_0.json diff --git a/counts.json b/counts.json index bc0e35d..e270cca 100644 --- a/counts.json +++ b/counts.json @@ -2326,15 +2326,15 @@ "2csfastq_1csfastq": 1, "2ft": 2, "2ndscore": 1, - "2to3": 3631, - "2to3-3.10": 802, + "2to3": 3637, + "2to3-3.10": 805, "2to3-3.11": 264, - "2to3-3.12": 175, + "2to3-3.12": 177, "2to3-3.4": 6, "2to3-3.5": 103, "2to3-3.6": 342, "2to3-3.7": 383, - "2to3-3.8": 574, + "2to3-3.8": 575, "2to3-3.9": 651, "3EdgeTests": 1, "3_1_filter_mapQ_for_sam.pl": 1, @@ -2419,8 +2419,8 @@ "AminoExtract": 2, "AmpliGone": 1, "AmpliconSuite-pipeline.py": 1, - "AnalyseDists": 46, - "AnalyseSeqs": 46, + "AnalyseDists": 48, + "AnalyseSeqs": 48, "AnnotSV": 1, "AnnotateInexactHomology": 1, "AnnotateInexactHomologyBedpe": 1, @@ -2525,7 +2525,7 @@ "BedpeGeneAnnotation": 1, "BedpeSort": 1, "BedpeToBed": 1, - "Bifrost": 6, + "Bifrost": 7, "Binner": 1, "Binning_refiner": 1, "Binsanity": 1, @@ -2622,6 +2622,8 @@ "CRISPRlungo": 1, "CRISPRlungoBatch": 1, "CRISPRlungoCompare": 1, + "CURED_FindREs.py": 1, + "CURED_Main.py": 1, "CVInspector": 2, "CalcDelta.py": 1, "CalcGeneCov.py": 1, @@ -2913,6 +2915,8 @@ "ExpansionHunter": 1, "ExpansionHunterDenovo": 1, "ExpressBetaDiversity": 2, + "ExtendOrFormatContigs.pl": 1, + "ExtendOrFormatContigs.pl.bak": 1, "ExternalCalibration": 2, "ExtractCogs.py": 1, "ExtractCountFreqGenes.py": 1, @@ -3277,7 +3281,7 @@ "KatComp": 1, "KatGC": 1, "KinamineY-shaker": 1, - "Kinfold": 55, + "Kinfold": 57, "Kmasker": 1, "KmerCount.py": 1, "KmerFilter": 5, @@ -3742,6 +3746,8 @@ "PaReBrick": 1, "PaReBrick-Charts": 1, "PairSeq.py": 3, + "PairingAndScaffolding.pl": 1, + "PairingAndScaffolding.pl.bak": 1, "PanACoTA": 1, "ParDRe": 1, "ParaFly": 2, @@ -3904,7 +3910,7 @@ "QueueingSystem.dll": 1, "QuickDeconvolution": 1, "QuickSNP.py": 1, - "R": 4647, + "R": 4648, "R-scape": 2, "R-scape-sim": 2, "R-scape-sim-nobps": 2, @@ -3934,19 +3940,19 @@ "RKP.py": 1, "RLPipes": 1, "RM2Bed.py": 12, - "RNA2Dfold": 53, + "RNA2Dfold": 55, "RNADigestor": 2, - "RNALalifold": 53, - "RNALfold": 55, + "RNALalifold": 55, + "RNALfold": 57, "RNAMassCalculator": 1, - "RNAPKplex": 53, + "RNAPKplex": 55, "RNAPhylo": 1, "RNARedPrint": 1, "RNARedPrintSampler.py": 1, "RNARedPrintStructure.py": 1, "RNA_fragment_size.py": 3, - "RNAaliduplex": 55, - "RNAalifold": 55, + "RNAaliduplex": 57, + "RNAalifold": 57, "RNAalisplit.pl": 1, "RNAblueprint": 2, "RNAcalibrate": 1, @@ -3954,32 +3960,32 @@ "RNAcentralHTTPRequest-bin": 1, "RNAclust.pl": 1, "RNAcode": 2, - "RNAcofold": 55, - "RNAdistance": 55, - "RNAdos": 38, - "RNAduplex": 55, + "RNAcofold": 57, + "RNAdistance": 57, + "RNAdos": 40, + "RNAduplex": 57, "RNAeffective": 1, - "RNAeval": 55, - "RNAfold": 54, - "RNAforester": 55, - "RNAheat": 55, + "RNAeval": 57, + "RNAfold": 56, + "RNAforester": 57, + "RNAheat": 57, "RNAhybrid": 1, - "RNAinverse": 55, + "RNAinverse": 57, "RNAlien": 1, "RNAlien-bin": 1, "RNAlienScan": 1, "RNAlienScan-bin": 1, "RNAlienStatistics": 1, "RNAlienStatistics-bin": 1, - "RNAlocmin": 46, - "RNAmultifold": 23, - "RNApaln": 55, - "RNAparconv": 53, - "RNApdist": 55, - "RNAplex": 53, - "RNAplfold": 55, - "RNAplot": 55, - "RNApvmin": 48, + "RNAlocmin": 48, + "RNAmultifold": 25, + "RNApaln": 57, + "RNAparconv": 55, + "RNApdist": 57, + "RNAplex": 55, + "RNAplfold": 57, + "RNAplot": 57, + "RNApvmin": 50, "RNAshapes": 4, "RNAshapes_eval_macrostate": 1, "RNAshapes_eval_microstate": 1, @@ -4050,11 +4056,11 @@ "RNAshapes_subopt_nodangle_window": 1, "RNAshapes_subopt_overdangle": 1, "RNAshapes_subopt_overdangle_window": 1, - "RNAsnoop": 53, + "RNAsnoop": 55, "RNAsnp": 1, "RNAsoup": 1, - "RNAsubopt": 55, - "RNAup": 55, + "RNAsubopt": 57, + "RNAup": 57, "RNAz": 3, "RNAz.pm": 4, "RNPxlSearch": 2, @@ -4134,7 +4140,7 @@ "Rprof": 1, "Rsample": 4, "Rsample-smp": 4, - "Rscript": 4648, + "Rscript": 4649, "RunTHetA.py": 1, "SAGE": 1, "SAMMPileUpReader.py": 1, @@ -4181,6 +4187,8 @@ "SRC_linker": 1, "SRC_linker_ram": 3, "SSAKE": 2, + "SSPACE_Basic.pl": 1, + "SSPACE_Basic.pl.bak": 1, "SSRCalc3.par": 2, "SSRCalc3.pl": 2, "SSeq_tsv2vcf.py": 1, @@ -4218,7 +4226,7 @@ "SVmerge": 1, "SVrefine": 1, "SVwiden": 1, - "SalmID.py": 2, + "SalmID.py": 3, "SamHaplotag": 1, "SamToNavBasics.py": 1, "SampleAncestry": 1, @@ -4275,6 +4283,7 @@ "ShapeKnots": 4, "ShapeKnots-smp": 4, "ShapeMapper.py": 1, + "ShigaPass.sh": 1, "ShortStack": 1, "ShortTracks": 1, "ShortestPathTN93": 1, @@ -4296,6 +4305,11 @@ "SmartMapPrep": 1, "SmartMapRNAPrep": 1, "Smoother": 1, + "SneakerNet.checkdeps.pl": 1, + "SneakerNet.ionTorrent.ro.pl": 1, + "SneakerNet.pl": 1, + "SneakerNet.roRun.pl": 1, + "SneakerNetPlugins.pl": 1, "SnpSift": 1, "SoftClipsToSplitReads": 1, "SolexaQA++": 1, @@ -4398,7 +4412,7 @@ "THESIAS": 1, "TICCalculator": 2, "TIR-Learner": 1, - "TMalign": 15, + "TMalign": 17, "TMscore": 6, "TNS": 2, "TOBIAS": 2, @@ -4407,10 +4421,11 @@ "TPSI_btab_to_gff3.pl": 1, "TPSI_chains_to_fasta.pl": 1, "TPSI_chains_to_gff3.pl": 1, - "TQS.py": 2, - "TQSexport.py": 2, + "TQS.py": 3, + "TQS.readme": 1, + "TQSexport.py": 3, "TQSfastq.pl": 2, - "TQSfastq.py": 2, + "TQSfastq.py": 3, "TRAPmulti": 1, "TRAPmulti.cpp": 1, "TREE-QMC": 1, @@ -4900,7 +4915,7 @@ "abyss-tofastq": 17, "ac-diamond": 1, "accession_retrieve": 1, - "accn-at-a-time": 258, + "accn-at-a-time": 263, "accurate_bkp.py": 1, "acdc": 25, "acdc-filter-fasta-by-name.awk": 1, @@ -4913,7 +4928,7 @@ "acdvalid": 24, "ace.pl": 56, "ace2contig": 2, - "ace2sam": 504, + "ace2sam": 507, "aci": 1, "aclocal.bak": 11, "acountry": 4272, @@ -4927,7 +4942,7 @@ "actc": 1, "action_report.py": 1, "activate": 1342, - "activate-global-python-argcomplete": 337, + "activate-global-python-argcomplete": 338, "acyclic": 198, "adVNTR-Filtering": 1, "ada_model_builder_ntChange.R": 1, @@ -4952,6 +4967,7 @@ "addNH": 1, "addOligos.pl": 5, "addRNAoptions.pl": 3, + "addReadMetrics.pl": 1, "addReadsToUnitigs": 3, "addSurrogatesToFrgCtgFile": 1, "addSurrogatesToFrgctg.perl": 1, @@ -5002,7 +5018,7 @@ "addtit.pl": 2, "adf_checker.pl": 1, "adhocfilelist": 1, - "adig": 4493, + "adig": 4500, "adjustPeakFile.pl": 5, "adjustRedunGroupFile.pl": 5, "adjustScanRankerScoreByGroup": 2, @@ -5118,7 +5134,7 @@ "agrvate": 1, "agtsampleinforw.dll": 2, "ahmm-s": 1, - "ahost": 4493, + "ahost": 4500, "airr-tools": 5, "akita_data.py": 1, "akita_data_read.py": 1, @@ -5161,7 +5177,7 @@ "align-cache.2.11.0": 10, "align-cache.3": 2, "align-cache.3.0.0": 2, - "align-columns": 201, + "align-columns": 206, "align-ema.smk": 1, "align-families.py": 1, "align-info": 22, @@ -5225,7 +5241,7 @@ "alignoth": 1, "aligns_to": 1, "alignstats": 1, - "alimask": 174, + "alimask": 175, "alistat": 4, "all-interval": 2, "allVsAll.sh": 2, @@ -5285,7 +5301,7 @@ "amdgpu-arch": 1, "ame": 13, "amgr": 1, - "amino-acid-composition": 289, + "amino-acid-composition": 294, "aminoextract": 2, "amk_ccc": 2, "amk_fft2": 2, @@ -5389,14 +5405,14 @@ "annembed": 1, "annonars": 1, "annosine2": 1, - "annot-tsv": 22, + "annot-tsv": 25, "annot_blast_btop2.pl": 7, - "annotate": 246, + "annotate": 247, "annotate-partitions.py": 7, "annotate.py": 39, "annotate.pyc": 1, "annotateBAM.py": 1, - "annotateBed": 269, + "annotateBed": 271, "annotateBed_2way.pl": 1, "annotateInteractions.pl": 5, "annotatePeaks.pl": 5, @@ -5611,7 +5627,7 @@ "anvi-update-db-description": 2, "anvi-update-structure-database": 2, "anvi-upgrade": 2, - "any2fasta": 20, + "any2fasta": 22, "aodp": 1, "aomdec": 19, "aomenc": 19, @@ -5716,12 +5732,12 @@ "arcasHLA": 1, "archer": 1, "architeuthis": 1, - "archive-ncbinlp": 13, - "archive-nihocc": 13, - "archive-nmcds": 13, - "archive-pmc": 13, - "archive-pubmed": 288, - "archive-taxonomy": 13, + "archive-ncbinlp": 18, + "archive-nihocc": 18, + "archive-nmcds": 18, + "archive-pmc": 18, + "archive-pubmed": 293, + "archive-taxonomy": 18, "archive_directory.py": 2, "archosv": 2, "archspec": 8, @@ -5732,9 +5748,9 @@ "argnorm": 1, "argparse2tool": 1, "argparse2tool_check_path": 1, - "args2slice": 13, + "args2slice": 18, "args_oap": 1, - "aria2c": 19, + "aria2c": 20, "ariba": 3, "arlatex": 1, "array-as-vcf": 1, @@ -5783,7 +5799,7 @@ "ase-gui": 3, "ase-info": 3, "ase-run": 3, - "aserver": 431, + "aserver": 432, "asession": 3, "asgal": 1, "asgal_BitVector.py": 1, @@ -5809,8 +5825,8 @@ "asn2ff": 1, "asn2gb": 2, "asn2idx": 1, - "asn2ref": 13, - "asn2xml": 202, + "asn2ref": 18, + "asn2xml": 207, "asndhuff": 1, "asntool": 1, "asp-cp": 87, @@ -5821,6 +5837,7 @@ "asscom2": 1, "assemble-complexSVs": 1, "assemble-routed-files.sh": 1, + "assembleAll.pl": 1, "assembleRNAs": 2, "assemblerflow": 1, "assembly-scan": 3, @@ -5913,7 +5930,7 @@ "autometa-taxonomy-majority-vote": 2, "autometa-unclustered-recruitment": 2, "autometa-update-databases": 2, - "autopoint": 5275, + "autopoint": 5281, "autoreconf.bak": 10, "autoscan.bak": 10, "autoupdate.bak": 10, @@ -5927,7 +5944,7 @@ "avgEpsGrid": 2, "aviary": 1, "avro": 13, - "awk": 89, + "awk": 93, "aws": 6, "aws-create-elastic-blast-janitor-role.sh": 1, "aws-delete-elastic-blast-janitor-role.sh": 1, @@ -5963,8 +5980,8 @@ "axt_to_lav.py": 59, "axt_to_maf.py": 59, "b2": 2, - "b2ct": 48, - "b2sum": 81, + "b2ct": 50, + "b2sum": 82, "b2w": 1, "bFst": 31, "bPTR": 1, @@ -6097,10 +6114,10 @@ "bamCoverage": 11, "bamFlags": 3, "bamPEFragmentSize": 11, - "bamToBed": 269, + "bamToBed": 271, "bamToBw.pl": 3, - "bamToFastq": 269, - "bamToGBrowse.pl": 85, + "bamToFastq": 271, + "bamToGBrowse.pl": 87, "bamToPsl": 1, "bamToWig.py": 11, "bam_accuracy.py": 1, @@ -6248,25 +6265,26 @@ "baredSC_2d": 1, "barriers": 2, "barriers-RNA2": 1, - "barrnap": 33, + "barrnap": 34, "barrnap.py": 1, "barseqcount": 1, "bart": 1, "bart-profile": 1, "bart-update": 1, - "base32": 82, + "base32": 83, "base3s": 1, "base58": 3, - "base64": 82, + "base64": 83, + "baseBalance.pl": 1, "baseCalling_Matrix_analyzer": 1, "baseCalling_Matrix_calculator": 1, "baseCalling_Matrix_merger": 1, "base_evolve": 2, "basecall_network.py": 1, - "baseml": 65, - "basemlg": 65, - "basename": 82, - "basenc": 79, + "baseml": 67, + "basemlg": 67, + "basename": 83, + "basenc": 80, "basenji_annot_chr.py": 1, "basenji_bench_classify.py": 1, "basenji_bench_gtex.py": 1, @@ -6384,7 +6402,7 @@ "bbstats.sh": 30, "bbversion.sh": 30, "bbwrap.sh": 30, - "bc": 26, + "bc": 27, "bcalm": 5, "bcbio-prioritize": 1, "bcbio-rnaseq": 1, @@ -6403,8 +6421,8 @@ "bdbag-utils": 1, "bdbloader_unit_test": 5, "bdf2gdfont.PLS": 5, - "bdf2gdfont.pl": 89, - "bdftogd": 232, + "bdf2gdfont.pl": 90, + "bdftogd": 233, "beacon": 1, "beacon2-import": 1, "beacon2-search": 1, @@ -6418,7 +6436,7 @@ "beav_db": 1, "bed-to-bigBed": 1, "bed12-to-gtf": 3, - "bed12ToBed6": 269, + "bed12ToBed6": 271, "bed2DtoUCSCbed.pl": 5, "bed2associated_genes.py": 1, "bed2bedGraph.pl": 1, @@ -6437,10 +6455,10 @@ "bedGraphPack": 1, "bedGraphToBigWig": 18, "bedSort": 2, - "bedToBam": 269, + "bedToBam": 271, "bedToBigBed": 18, "bedToGenePred": 6, - "bedToIgv": 269, + "bedToIgv": 271, "bed_bigwig_profile.py": 59, "bed_build_windows.py": 59, "bed_complement.py": 59, @@ -6475,12 +6493,12 @@ "bedops-typical": 14, "bedoverlap": 1, "bedparse": 2, - "bedpeToBam": 269, + "bedpeToBam": 271, "bedpeToBam.py": 1, "bedpeToBed12.py": 1, "bedtk": 2, "bedtobigbed": 1, - "bedtools": 269, + "bedtools": 271, "bedutils": 1, "bedx-to-bedy": 3, "beeline": 6, @@ -6506,7 +6524,7 @@ "beta_diversity.py": 4, "beta_diversity_through_plots.py": 1, "beta_significance.py": 1, - "between-two-genes": 289, + "between-two-genes": 294, "bf.sh": 1, "bfc": 1, "bfconvert": 1, @@ -6521,7 +6539,7 @@ "bgenFileInfo": 1, "bgenix": 1, "bgreat": 4, - "bgzip": 696, + "bgzip": 699, "bgzip.pl": 4, "bgziptabix": 31, "bialign.py": 1, @@ -6686,7 +6704,7 @@ "bl-pileup-stats": 1, "bl-randomize": 1, "bl-threshold": 1, - "bl2seq": 30, + "bl2seq": 32, "bl2seq_unit_test": 5, "black": 11, "black-hole": 2, @@ -6705,7 +6723,7 @@ "blast2lca": 1, "blast2rma": 1, "blast2sam": 1, - "blast2sam.pl": 504, + "blast2sam.pl": 507, "blastMapAnalyzer2.pl": 1, "blastMining": 1, "blastMining_lca.sh": 1, @@ -6715,7 +6733,7 @@ "blast_check_pair.pl": 1, "blast_filter.pl": 1, "blast_format_unit_test": 5, - "blast_formatter": 321, + "blast_formatter": 326, "blast_names_mapping.tsv": 1, "blast_outfmt6_replace_trans_id_w_gene_symbol.pl": 1, "blast_report": 20, @@ -6726,16 +6744,16 @@ "blast_to_link.sh": 1, "blast_unit_test": 5, "blast_wrapper.py": 1, - "blastall": 30, + "blastall": 32, "blastbesties": 1, "blastcl3": 1, - "blastclust": 30, - "blastdb_aliastool": 321, + "blastclust": 32, + "blastdb_aliastool": 326, "blastdb_convert": 20, "blastdb_format_unit_test": 5, "blastdb_path": 20, - "blastdbcheck": 321, - "blastdbcmd": 321, + "blastdbcheck": 326, + "blastdbcmd": 326, "blastdbcp": 52, "blastdiag_unit_test": 5, "blastengine_unit_test": 5, @@ -6743,13 +6761,13 @@ "blastfilter_unit_test": 5, "blasthits_unit_test": 5, "blastinput_unit_test": 5, - "blastn": 321, - "blastn_vdb": 36, + "blastn": 326, + "blastn_vdb": 41, "blastoptions_unit_test": 5, - "blastp": 321, - "blastpgp": 30, + "blastp": 326, + "blastpgp": 32, "blastsetup_unit_test": 5, - "blastx": 321, + "blastx": 326, "blastzWrapper": 1, "blat": 19, "blat2gbrowse.pl": 14, @@ -6772,8 +6790,8 @@ "blossom5": 1, "blossom_randGraph.py": 1, "blosum62.fas": 2, - "blst2gm": 13, - "blst2tkns": 201, + "blst2gm": 18, + "blst2tkns": 206, "bmaToLinks.pl": 1, "bmfilter": 4, "bmge": 1, @@ -6807,27 +6825,27 @@ "boquila": 1, "borf": 1, "bottle.py": 4, - "bowtie": 39, - "bowtie-align-l": 34, + "bowtie": 40, + "bowtie-align-l": 35, "bowtie-align-reads.py": 1, - "bowtie-align-s": 34, - "bowtie-build": 39, - "bowtie-build-l": 34, - "bowtie-build-s": 34, - "bowtie-inspect": 39, - "bowtie-inspect-l": 34, - "bowtie-inspect-s": 34, - "bowtie2": 110, - "bowtie2-align-l": 110, - "bowtie2-align-s": 110, - "bowtie2-build": 110, - "bowtie2-build-l": 110, - "bowtie2-build-s": 110, - "bowtie2-inspect": 110, - "bowtie2-inspect-l": 110, - "bowtie2-inspect-s": 110, + "bowtie-align-s": 35, + "bowtie-build": 40, + "bowtie-build-l": 35, + "bowtie-build-s": 35, + "bowtie-inspect": 40, + "bowtie-inspect-l": 35, + "bowtie-inspect-s": 35, + "bowtie2": 111, + "bowtie2-align-l": 111, + "bowtie2-align-s": 111, + "bowtie2-build": 111, + "bowtie2-build-l": 111, + "bowtie2-build-s": 111, + "bowtie2-inspect": 111, + "bowtie2-inspect-l": 111, + "bowtie2-inspect-s": 111, "bowtie2_stuff.py": 1, - "bowtie2sam.pl": 504, + "bowtie2sam.pl": 507, "bowtie_PE_separate_then_join.pl": 1, "bowtie_mapper.sh": 1, "box": 1, @@ -6835,12 +6853,12 @@ "boxplot_ng": 1, "bp": 2, "bp-analyze": 1, - "bp_aacomp": 48, + "bp_aacomp": 50, "bp_aacomp.pl": 73, "bp_biofetch_genbank_proxy.pl": 73, - "bp_bioflat_index": 48, + "bp_bioflat_index": 50, "bp_bioflat_index.pl": 73, - "bp_biogetseq": 48, + "bp_biogetseq": 50, "bp_biogetseq.pl": 73, "bp_blast2tree.pl": 73, "bp_bulk_load_gff.pl": 73, @@ -6848,107 +6866,107 @@ "bp_classify_hits_kingdom.pl": 73, "bp_composite_LD.pl": 73, "bp_das_server.pl": 73, - "bp_dbsplit": 48, + "bp_dbsplit": 50, "bp_dbsplit.pl": 73, "bp_download_query_genbank.pl": 73, "bp_einfo": 3, "bp_export_proteins.py": 1, "bp_export_tags.py": 1, - "bp_extract_feature_seq": 48, + "bp_extract_feature_seq": 50, "bp_extract_feature_seq.pl": 73, "bp_fast_load_gff.pl": 73, "bp_fasta_prepare.py": 1, - "bp_fastam9_to_table": 48, + "bp_fastam9_to_table": 50, "bp_fastam9_to_table.pl": 73, - "bp_fetch": 48, + "bp_fetch": 50, "bp_fetch.pl": 73, - "bp_filter_search": 48, + "bp_filter_search": 50, "bp_filter_search.pl": 73, - "bp_find-blast-matches": 48, + "bp_find-blast-matches": 50, "bp_find-blast-matches.pl": 51, "bp_flanks.pl": 73, - "bp_gccalc": 48, + "bp_gccalc": 50, "bp_gccalc.pl": 73, "bp_genbank2gff.pl": 73, - "bp_genbank2gff3": 48, + "bp_genbank2gff3": 50, "bp_genbank2gff3.pl": 73, "bp_genbank_ref_extractor": 3, "bp_generate_histogram.pl": 73, "bp_heterogeneity_test.pl": 73, "bp_hivq.pl": 73, - "bp_hmmer_to_table.pl": 94, - "bp_index": 48, + "bp_hmmer_to_table.pl": 96, + "bp_index": 50, "bp_index.pl": 73, "bp_load_gff.pl": 73, - "bp_local_taxonomydb_query": 48, + "bp_local_taxonomydb_query": 50, "bp_local_taxonomydb_query.pl": 73, - "bp_make_mrna_protein": 48, + "bp_make_mrna_protein": 50, "bp_make_mrna_protein.pl": 73, "bp_mapped_tags.py": 1, - "bp_mask_by_search": 48, + "bp_mask_by_search": 50, "bp_mask_by_search.pl": 73, "bp_meta_gff.pl": 73, - "bp_mrtrans": 48, + "bp_mrtrans": 50, "bp_mrtrans.pl": 73, - "bp_mutate": 48, + "bp_mutate": 50, "bp_mutate.pl": 73, "bp_netinstall.pl": 73, - "bp_nexus2nh": 48, + "bp_nexus2nh": 50, "bp_nexus2nh.pl": 73, - "bp_nrdb": 48, + "bp_nrdb": 50, "bp_nrdb.pl": 73, - "bp_oligo_count": 48, + "bp_oligo_count": 50, "bp_oligo_count.pl": 73, - "bp_pairwise_kaks": 62, + "bp_pairwise_kaks": 64, "bp_pairwise_kaks.pl": 22, - "bp_parse_hmmsearch.pl": 94, + "bp_parse_hmmsearch.pl": 96, "bp_parse_tags.py": 1, - "bp_process_gadfly": 48, + "bp_process_gadfly": 50, "bp_process_gadfly.pl": 73, - "bp_process_sgd": 48, + "bp_process_sgd": 50, "bp_process_sgd.pl": 73, "bp_process_wormbase.pl": 73, "bp_query_entrez_taxa.pl": 73, "bp_remote_blast.pl": 76, - "bp_revtrans-motif": 48, + "bp_revtrans-motif": 50, "bp_revtrans-motif.pl": 73, "bp_search2BSML.pl": 22, - "bp_search2alnblocks": 48, + "bp_search2alnblocks": 50, "bp_search2alnblocks.pl": 73, - "bp_search2gff": 48, + "bp_search2gff": 50, "bp_search2gff.pl": 73, - "bp_search2table": 48, + "bp_search2table": 50, "bp_search2table.pl": 73, - "bp_search2tribe": 48, + "bp_search2tribe": 50, "bp_search2tribe.pl": 73, - "bp_seq_length": 48, + "bp_seq_length": 50, "bp_seq_length.pl": 73, - "bp_seqconvert": 48, + "bp_seqconvert": 50, "bp_seqconvert.pl": 73, - "bp_seqcut": 48, + "bp_seqcut": 50, "bp_seqcut.pl": 73, "bp_seqfeature_delete.pl": 73, "bp_seqfeature_gff3.pl": 73, "bp_seqfeature_load.pl": 73, - "bp_seqpart": 48, + "bp_seqpart": 50, "bp_seqpart.pl": 73, - "bp_seqret": 48, + "bp_seqret": 50, "bp_seqret.pl": 73, - "bp_seqretsplit": 48, + "bp_seqretsplit": 50, "bp_seqretsplit.pl": 73, - "bp_split_seq": 48, + "bp_split_seq": 50, "bp_split_seq.pl": 73, - "bp_sreformat": 48, + "bp_sreformat": 50, "bp_sreformat.pl": 73, - "bp_taxid4species": 48, + "bp_taxid4species": 50, "bp_taxid4species.pl": 73, - "bp_taxonomy2tree": 48, + "bp_taxonomy2tree": 50, "bp_taxonomy2tree.pl": 73, - "bp_translate_seq": 48, + "bp_translate_seq": 50, "bp_translate_seq.pl": 73, - "bp_tree2pag": 48, + "bp_tree2pag": 50, "bp_tree2pag.pl": 73, - "bp_unflatten_seq": 48, + "bp_unflatten_seq": 50, "bp_unflatten_seq.pl": 73, "bpcomp": 1, "bpipe": 4, @@ -6991,7 +7009,7 @@ "broad_utils.py": 1, "brockman_pipeline": 1, "brooklyn_plot": 1, - "brotli": 412, + "brotli": 413, "browse": 18, "bs_call": 2, "bs_seeker2-align.py": 1, @@ -7051,12 +7069,15 @@ "buildG-MPI": 1, "buildG-MPIRMA": 1, "buildH": 1, + "buildKraken1.sh": 1, + "buildKraken2.sh": 1, "buildMetaphyler.pl": 1, "buildPosMap": 3, "buildRMLibFromEMBL.pl": 12, "buildRefContigs": 3, "buildSNPDB.pl": 1, "buildSummary.pl": 12, + "buildTaxonomy.sh": 1, "buildUnitigs": 3, "build_DE_cache_tables.pl": 1, "build_agp.smk": 1, @@ -7088,7 +7109,7 @@ "bundlelinks": 1, "bundler": 19, "bunwarpj": 4, - "bunzip2": 6581, + "bunzip2": 6589, "burden_test_vase": 1, "burst_linux_DB12": 1, "burst_linux_DB15": 1, @@ -7097,7 +7118,7 @@ "buscolite": 1, "bustools": 2, "bvop": 1, - "bwa": 161, + "bwa": 163, "bwa-mem2": 7, "bwa-mem2.avx": 7, "bwa-mem2.avx2": 7, @@ -7139,16 +7160,16 @@ "bxStats.py": 1, "bxcl_seqqc": 1, "bxtools": 1, - "bzcat": 6581, - "bzcmp": 6581, - "bzdiff": 6581, - "bzegrep": 6581, - "bzfgrep": 6581, - "bzgrep": 6581, - "bzip2": 6581, - "bzip2recover": 6581, - "bzless": 6581, - "bzmore": 6581, + "bzcat": 6589, + "bzcmp": 6589, + "bzdiff": 6589, + "bzegrep": 6589, + "bzfgrep": 6589, + "bzgrep": 6589, + "bzip2": 6589, + "bzip2recover": 6589, + "bzless": 6589, + "bzmore": 6589, "c++": 5, "c++filt": 8, "c-index-test": 8, @@ -7165,7 +7186,7 @@ "cPecanLibTests": 1, "cPecanModifyHmm": 1, "cPecanRealign": 1, - "c_rehash": 7733, + "c_rehash": 7741, "ca2ace.pl": 3, "ca2ctg": 2, "ca2mates": 2, @@ -7239,7 +7260,7 @@ "cage-classify.py": 1, "cagee": 1, "cai": 25, - "cairo-trace": 5106, + "cairo-trace": 5108, "cairosvg": 6, "cal": 13, "calD": 1, @@ -7336,12 +7357,12 @@ "capCpileup2binned": 1, "capcruncher": 1, "caper": 2, - "capnp": 53, - "capnpc": 53, - "capnpc-c++": 53, - "capnpc-capnp": 53, + "capnp": 54, + "capnpc": 54, + "capnpc-c++": 54, + "capnpc-capnp": 54, "capnpc-cython": 1, - "captoinfo": 7664, + "captoinfo": 7672, "captus_assembly": 1, "caqc.pl": 3, "caqc_help.ini": 3, @@ -7388,7 +7409,7 @@ "cassiopeeknife": 2, "cassis": 1, "castats": 2, - "cat": 82, + "cat": 83, "cat-bgen": 1, "cat-corrects": 3, "cat-erates": 3, @@ -7482,8 +7503,8 @@ "cdna_alignment_orf_to_genome_orf.pl": 5, "cdna_classifier.py": 1, "cdo": 1, - "cds-mapping-stats": 35, - "cds-subgraphs": 35, + "cds-mapping-stats": 36, + "cds-subgraphs": 36, "cds-trainer.pl": 2, "cdscan": 1, "ceas": 2, @@ -7534,7 +7555,7 @@ "cert2spc": 15, "certmgr": 15, "certtool": 31, - "certutil": 167, + "certutil": 168, "cesar": 1, "cestat-cov": 2, "cestats": 6, @@ -7598,7 +7619,7 @@ "charge": 24, "charmmlipid2amber.py": 6, "chartex": 58, - "chcon": 82, + "chcon": 83, "check": 2, "check-assembly-accession.py": 2, "check-corrupt": 4, @@ -7692,8 +7713,8 @@ "chewiesnake_join": 1, "chexalign": 1, "chexmix": 1, - "chgrp": 82, - "chi2": 65, + "chgrp": 83, + "chi2": 67, "chimChe": 3, "chimera": 3, "chimerascan-exclude-transcriptome-events": 2, @@ -7719,7 +7740,7 @@ "chisel_rdr": 1, "chktrust": 15, "chmem": 13, - "chmod": 82, + "chmod": 83, "choom": 13, "chooseK.py": 1, "chooseLines": 2, @@ -7728,10 +7749,10 @@ "chopify.pl": 5, "chopin2": 1, "chopper": 1, - "chown": 82, + "chown": 83, "chroder": 1, "chromRegionLength.r": 1, - "chrom_sizes.pl": 85, + "chrom_sizes.pl": 87, "chromap": 1, "chromatiblock": 1, "chromograph": 1, @@ -7741,7 +7762,7 @@ "chromosomer": 1, "chronic": 3, "chronumental": 1, - "chroot": 82, + "chroot": 83, "chrpath": 16, "chrt": 13, "chunked-scatter": 1, @@ -7754,8 +7775,8 @@ "circledetector.py": 1, "circminer": 1, "circo": 198, - "circos": 19, - "circos.exe": 19, + "circos": 20, + "circos.exe": 20, "circtools": 1, "circtools_circtest_wrapper.R": 1, "circtools_detect_write_skip_tracks.pl": 1, @@ -7775,12 +7796,12 @@ "circulocov": 1, "cirdna": 24, "cirtap": 1, - "cit2pmid": 13, + "cit2pmid": 18, "civicpy": 1, "cjk-gs-integrate": 1, - "cjpeg": 5740, + "cjpeg": 5742, "ckeygen": 1, - "cksum": 82, + "cksum": 83, "claMLST": 1, "cladebreaker": 1, "cladeomatic": 1, @@ -7854,7 +7875,10 @@ "classification_predict": 1, "classifier": 5, "classifier.jar": 2, + "classifier_report.py": 1, + "classify": 1, "classify-ali.pl": 1, + "classify.py": 1, "classifyMates": 3, "classifyMatesApply": 3, "classifyMatesPairwise": 3, @@ -7880,11 +7904,11 @@ "cleanmap.awk": 1, "cleanme.pl": 1, "cleanpp.sh": 3, - "cleanup-blastdb-volumes.py": 250, + "cleanup-blastdb-volumes.py": 255, "cleanup-coverage.py": 2, "cleanup-stale-gcp-resources.py": 1, "cleanup.py": 1, - "clear": 7664, + "clear": 7672, "clearCNV": 1, "clearcut": 1, "cleric": 1, @@ -7930,7 +7954,7 @@ "closest-features-float128": 14, "closest-features-megarow": 14, "closest-features-typical": 14, - "closestBed": 269, + "closestBed": 271, "closest_residues": 1, "cloudgene.yaml": 1, "clove": 1, @@ -7964,9 +7988,9 @@ "clust": 1, "clustal2link": 1, "clustal_to_alma.py": 1, - "clustalo": 27, - "clustalw": 72, - "clustalw2": 73, + "clustalo": 29, + "clustalw": 74, + "clustalw2": 75, "clustalw2fasta": 13, "clustalw2phylip": 13, "cluster": 203, @@ -7974,7 +7998,7 @@ "cluster2bed.pl": 5, "cluster2bedgraph.pl": 5, "clusterAndSplitGenes.pl": 14, - "clusterBed": 269, + "clusterBed": 271, "clusterGenes": 1, "clusterHeatmap.R": 1, "clusterSnps": 2, @@ -8072,7 +8096,7 @@ "codcmp": 24, "codcopy": 24, "codecov": 2, - "codeml": 65, + "codeml": 67, "coderet": 24, "codes_bufr_filter": 1, "codes_count": 1, @@ -8122,7 +8146,8 @@ "colorcet": 3, "colord": 1, "colored-matrix": 2, - "coloredlogs": 73, + "coloredlogs": 74, + "colorid_bv": 1, "colorinterpolate": 1, "colorrna.pl": 1, "colrm": 13, @@ -8137,7 +8162,7 @@ "combine": 4, "combine-assembled-files.sh": 1, "combine-subexons": 1, - "combine-uid-lists": 13, + "combine-uid-lists": 18, "combineAndAnnotateReferences.pl": 1, "combineFile": 2, "combineFragandDBGraph_fastg.py": 1, @@ -8173,7 +8198,7 @@ "comet": 2, "comet.exe": 2, "comgen": 1, - "comm": 82, + "comm": 83, "commandline.sh": 1, "comment_out_assays.pl": 1, "common.go": 14, @@ -8234,15 +8259,15 @@ "comparison.sh": 1, "compile-et.pl": 43, "compile-rpbp-models": 2, - "compile.bat": 19, - "compile.make": 19, + "compile.bat": 20, + "compile.make": 20, "compileSpliceCands": 12, "compile_STARE_Linux.sh": 1, "compile_STARE_macOS.sh": 1, - "compile_et": 5775, + "compile_et": 5781, "compiled_table.py": 1, "compleasm": 1, - "complementBed": 269, + "complementBed": 271, "complete-ant-cmd.pl": 1, "complete_locus": 1, "completion.bash": 1, @@ -8330,7 +8355,7 @@ "config.py": 1, "config.sh": 1, "configManta.py": 1, - "config_data": 59, + "config_data": 61, "config_parser.py": 1, "configure": 1, "configureESTmapper.pl": 3, @@ -8422,7 +8447,7 @@ "convert2bed-float128": 14, "convert2bed-megarow": 14, "convert2bed-typical": 14, - "convert2blastmask": 321, + "convert2blastmask": 326, "convert2snns": 2, "convertCoordinates.pl": 5, "convertFastaQualToFastQ.rb": 1, @@ -8532,13 +8557,13 @@ "copycat.3.0.0": 2, "copyfile.sh": 1, "copylink": 1, - "copymat": 30, + "copymat": 32, "coral": 1, "core-only.pl": 1, "core_diversity_analyses.py": 1, "core_methods.py": 1, "core_overlap_plot.py": 1, - "corelist": 1681, + "corelist": 1688, "corepack": 11, "coreprocess.pl": 3, "coresnpfilter": 1, @@ -8618,7 +8643,7 @@ "coverage.py": 1, "coverage2cytosine": 2, "coverage3": 2, - "coverageBed": 269, + "coverageBed": 271, "coverage_estimator.py": 1, "coverage_from_bam": 1, "coverage_from_fastx": 1, @@ -8635,16 +8660,16 @@ "covid-spike-classification": 1, "covtobed": 1, "covtotarget": 1, - "cp": 82, + "cp": 83, "cp2k.sopt": 1, "cp2k.ssmp": 1, "cp2k_prep": 1, "cp2k_run": 1, "cp2k_shell.ssmp": 1, "cpack": 11, - "cpan": 1681, + "cpan": 1688, "cpancover": 6, - "cpanm": 243, + "cpanm": 244, "cpat.py": 1, "cpeinutil.py": 6, "cpgcdifenrich": 1, @@ -8825,7 +8850,7 @@ "csfasta_to_fastq": 1, "csharp": 15, "csi": 13, - "csplit": 82, + "csplit": 83, "csslint-0.6": 8, "cstacks": 1, "cstag": 1, @@ -8835,7 +8860,7 @@ "csv2rdf": 32, "csv2tsv": 1, "csv2xlsx": 1, - "csv2xml": 201, + "csv2xml": 206, "csvExtractBorders": 1, "csvFrags2text": 1, "csv_to_tsv": 1, @@ -8843,7 +8868,7 @@ "ct-energy": 3, "ct-ng.config": 1, "ct2bp": 1, - "ct2db": 48, + "ct2db": 50, "ct2dot": 4, "ct2rnaml": 3, "ct_boxplot_ng": 1, @@ -8875,20 +8900,20 @@ "cuffquant": 2, "cuppa": 1, "cuppa-chart": 1, - "cups-config": 187, + "cups-config": 188, "curare": 1, "curare_wizard": 1, "curate_database.py": 1, "curate_universe": 1, "curesim": 2, - "curl": 5091, - "curl-config": 5891, + "curl": 5096, + "curl-config": 5897, "curlywhirly": 1, "curve_keygen": 68, "cusp": 24, "custom.py": 1, "custom_logger.py": 1, - "cut": 82, + "cut": 83, "cut-range": 1, "cut.pl": 1, "cut.pl.bak": 1, @@ -8929,7 +8954,7 @@ "cw_get_uniprot_data": 1, "cw_query_database": 1, "cweave": 1, - "cwebp": 348, + "cwebp": 349, "cwl-cite-extract": 1, "cwl-docker-extract": 1, "cwl-explode": 1, @@ -9009,6 +9034,7 @@ "dask-worker": 45, "dask_utils.py": 1, "data.py": 1, + "data_classes.py": 1, "data_filter": 1, "data_import_post_install_tests.bats": 1, "data_import_post_install_tests.sh": 1, @@ -9019,7 +9045,7 @@ "database_modules.py": 1, "databases.py": 1, "databricks": 2, - "dataformat": 2, + "dataformat": 3, "dataframeSumAllValues.r": 1, "datafunk": 1, "datamash": 3, @@ -9028,11 +9054,11 @@ "dataset": 1, "dataset.py": 2, "dataset_manager.py": 1, - "datasets": 2, + "datasets": 3, "datasets-cli": 2, - "datatool": 321, + "datatool": 326, "datavzrd": 2, - "date": 82, + "date": 83, "datma.py": 1, "datma_seq.py": 1, "dav1d": 13, @@ -9050,23 +9076,23 @@ "dazcon": 4, "dbSNP_idx": 2, "dbTestScript": 1, - "db_archive": 119, - "db_checkpoint": 119, - "db_convert": 97, - "db_deadlock": 119, - "db_dump": 119, + "db_archive": 121, + "db_checkpoint": 121, + "db_convert": 99, + "db_deadlock": 121, + "db_dump": 121, "db_exclude.locs.tsv": 1, "db_graph.jl": 2, - "db_hotbackup": 119, - "db_load": 119, - "db_log_verify": 119, - "db_printlog": 119, - "db_recover": 119, - "db_replicate": 119, - "db_stat": 119, - "db_tuner": 119, - "db_upgrade": 119, - "db_verify": 119, + "db_hotbackup": 121, + "db_load": 121, + "db_log_verify": 121, + "db_printlog": 121, + "db_recover": 121, + "db_replicate": 121, + "db_stat": 121, + "db_tuner": 121, + "db_upgrade": 121, + "db_verify": 121, "dba": 3, "dbcanLight": 1, "dbcanLight-hmmparser": 1, @@ -9079,9 +9105,9 @@ "dbifasta": 24, "dbiflat": 24, "dbigcg": 24, - "dbilogstrip": 111, - "dbiprof": 111, - "dbiproxy": 111, + "dbilogstrip": 112, + "dbiprof": 112, + "dbiproxy": 112, "dbkit_create.py": 1, "dbkit_extract.py": 1, "dbkit_merge.py": 1, @@ -9110,7 +9136,7 @@ "dbxstat": 24, "dbxtax": 24, "dbxuncompress": 24, - "dc": 26, + "dc": 27, "dc_remapper": 1, "dca": 6, "dcm2json": 1, @@ -9162,7 +9188,7 @@ "dcmtls_tests": 1, "dcod2lum": 1, "dconvlum": 1, - "dd": 82, + "dd": 83, "ddls": 2, "ddv": 1, "de-macro": 1, @@ -9268,7 +9294,7 @@ "deltaBS.pl": 1, "delta_filter_wrapper.py": 5, "delta_unit_test": 5, - "deltablast": 321, + "deltablast": 326, "deltapd": 1, "demes": 4, "demesdraw": 1, @@ -9319,7 +9345,7 @@ "depth_calc.py": 1, "depth_estim_from_vcf.sh": 1, "depythontex": 1, - "derb": 5801, + "derb": 5805, "derep_stuff.py": 1, "deripcal": 1, "derna": 1, @@ -9366,7 +9392,7 @@ "dexqv": 1, "dexta": 3, "dextract": 1, - "df": 82, + "df": 83, "dfamscan.pl": 1, "dfast": 2, "dfast_file_downloader.py": 2, @@ -9404,7 +9430,7 @@ "diff_iso_usage": 1, "diff_motif": 1, "diffacto": 1, - "difference-uid-lists": 13, + "difference-uid-lists": 18, "difference_from_first_TSS_script_mordor.r": 1, "difference_from_first_TSS_script_mordor_chrom_wide.r": 1, "differentialBindingAffinity_multipleSNPs": 1, @@ -9434,16 +9460,16 @@ "dipenum": 1, "dipspades": 3, "dipspades.py": 5, - "dir": 82, - "dircolors": 82, + "dir": 83, + "dircolors": 83, "directag": 2, "directories.py": 1, "diri_sampler": 1, "dirmngr": 2, "dirmngr-client": 2, - "dirname": 82, + "dirname": 83, "dirseq": 2, - "disambiguate-nucleotides": 201, + "disambiguate-nucleotides": 206, "disco": 17, "disco.cfg": 1, "disco_2.cfg": 1, @@ -9483,7 +9509,7 @@ "django-admin": 4, "django-admin.py": 3, "django-admin.pyc": 1, - "djpeg": 5740, + "djpeg": 5742, "dkfzbiasfilter.py": 1, "dkfzbiasfilter_summarize.py": 1, "dlcoal_to_dlcpar": 1, @@ -9594,23 +9620,23 @@ "download-db.sh": 9, "download-dfam.py": 1, "download-entities.pl": 2, - "download-ncbi-data": 274, + "download-ncbi-data": 279, "download-ncbi-genomes": 1, - "download-ncbi-software": 201, + "download-ncbi-software": 206, "download-ncbi-taxa.sh": 1, "download-ncbi-taxmaps": 1, "download-ncbi-taxonomy": 1, - "download-pmc": 13, - "download-pubmed": 288, - "download-sequence": 288, + "download-pmc": 18, + "download-pubmed": 293, + "download-sequence": 293, "download-spatypes.sh": 1, "download-srr-files": 3, "download-taxonomy.sh": 1, "download-uniprot-taxa.sh": 1, "download-vadr-models.sh": 1, "download-virulence-db.sh": 1, - "downloadKalamari.pl": 1, - "downloadKalamari.sh": 1, + "downloadKalamari.pl": 2, + "downloadKalamari.sh": 2, "downloadRefSeq.pl": 1, "download_and_set_models.py": 1, "download_assemblies_from_genbank.py": 2, @@ -9702,7 +9728,7 @@ "drtext": 24, "drttest": 1, "drugbank": 1, - "ds2pme": 13, + "ds2pme": 18, "dsCompareCurves": 1, "dsComputeBEDDensity": 1, "dsComputeGCCoverage": 1, @@ -9789,7 +9815,7 @@ "dtd2rng": 15, "dtd2xsd": 15, "dtxgen": 1, - "du": 82, + "du": 83, "dual.py": 1, "duck_chunk": 1, "duck_prepare_sys": 1, @@ -9839,7 +9865,7 @@ "dupre": 1, "dupsifter": 1, "dust": 13, - "dustmasker": 321, + "dustmasker": 326, "dv_call_variants.py": 1, "dv_make_examples.py": 1, "dv_postprocess_variants.py": 1, @@ -9854,7 +9880,7 @@ "dvitomp": 1, "dvitype": 1, "dvorfs": 1, - "dwebp": 348, + "dwebp": 349, "dwgsim": 4, "dwgsim_eval": 4, "dwgsim_eval_plot.py": 1, @@ -9903,7 +9929,7 @@ "eaddress": 88, "eagle": 1, "earlGrey": 1, - "easel": 147, + "easel": 148, "easy-fuse": 1, "easy.py": 1, "easy_install": 1727, @@ -9917,7 +9943,7 @@ "ebisearch": 1, "eblast": 86, "ebong": 1, - "echo": 82, + "echo": 83, "echoscu": 1, "ecitmatch": 88, "ecoPCR": 1, @@ -9928,7 +9954,7 @@ "ecodbtaxstat": 1, "ecofind": 1, "ecogrep": 1, - "ecommon.sh": 201, + "ecommon.sh": 206, "econtact": 88, "ecotag": 1, "ecotaxspecificity": 1, @@ -9964,9 +9990,9 @@ "edonr256-hash": 9, "edonr512-hash": 9, "eel": 1, - "efetch": 289, + "efetch": 294, "effectivet3": 1, - "efilter": 289, + "efilter": 294, "efishent": 1, "efn": 1, "efn2": 5, @@ -9974,7 +10000,7 @@ "efpa": 2, "ega2": 1, "eggnog_to_sqlite3.py": 2, - "egrep": 19, + "egrep": 20, "ehhbin": 1, "eido": 9, "eigenstrat": 1, @@ -9982,8 +10008,8 @@ "eigenstrat_database_tools": 1, "eigenstrat_rename_snps": 1, "eigenstrat_snp_coverage": 1, - "einfo": 289, - "einsi": 98, + "einfo": 294, + "einsi": 100, "einverted": 24, "eject": 13, "eklipseHeader.png": 1, @@ -10011,13 +10037,14 @@ "elfedit": 8, "elgato_report.py": 1, "eliminateBadSuperReadsUsingList": 1, - "elink": 289, + "elink": 294, "elm2meme": 13, "elprep": 1, "elsize": 6, "ema": 1, "ema-h": 1, "email.sh": 1, + "emailWhoever.pl": 1, "email_validator": 1, "emapper.py": 3, "embl-api-validator": 1, @@ -10046,8 +10073,8 @@ "enano": 1, "enasearch": 1, "enc": 1, - "enc2xs": 1681, - "encguess": 1681, + "enc2xs": 1688, + "encguess": 1688, "encode2var": 1, "encode_dir": 1, "encode_exclude_loci": 1, @@ -10078,25 +10105,25 @@ "entrypoint.py": 1, "enumall": 1, "enumerate_paths.py": 1, - "env": 82, - "env-execute": 6828, + "env": 83, + "env-execute": 6839, "env.yml": 1, - "env_parallel": 99, - "env_parallel.ash": 99, - "env_parallel.bash": 99, - "env_parallel.csh": 99, - "env_parallel.dash": 99, - "env_parallel.fish": 99, - "env_parallel.ksh": 99, - "env_parallel.mksh": 99, - "env_parallel.pdksh": 99, - "env_parallel.sh": 99, - "env_parallel.tcsh": 99, - "env_parallel.zsh": 99, + "env_parallel": 102, + "env_parallel.ash": 102, + "env_parallel.bash": 102, + "env_parallel.csh": 102, + "env_parallel.dash": 102, + "env_parallel.fish": 102, + "env_parallel.ksh": 102, + "env_parallel.mksh": 102, + "env_parallel.pdksh": 102, + "env_parallel.sh": 102, + "env_parallel.tcsh": 102, + "env_parallel.zsh": 102, "environment.yml": 1, "envpath": 3, "envset.cmd": 1, - "envsubst": 5275, + "envsubst": 5281, "eoulsan.sh": 1, "epa-ng": 4, "epestfind": 24, @@ -10112,7 +10139,7 @@ "epimuller-define": 1, "epimuller-draw": 1, "epimuller-parse": 1, - "epost": 289, + "epost": 294, "eprimer3": 24, "eprimer32": 24, "eproxy": 88, @@ -10147,38 +10174,38 @@ "errno": 3, "errorEstimate": 6, "error_corrected2frg": 1, - "esample": 274, + "esample": 279, "esbuild": 1, - "esd2esi": 10, + "esd2esi": 11, "esdcompat": 12, - "esearch": 289, + "esearch": 294, "esh": 1, "esimsa": 1, - "esl-afetch": 164, + "esl-afetch": 165, "esl-alidepair.pl": 2, - "esl-alimanip": 162, - "esl-alimap": 162, - "esl-alimask": 162, - "esl-alimerge": 162, - "esl-alipid": 162, - "esl-alirev": 162, - "esl-alistat": 162, - "esl-compalign": 162, - "esl-compstruct": 162, - "esl-construct": 162, - "esl-histplot": 162, - "esl-mask": 162, - "esl-mixdchlet": 147, - "esl-reformat": 164, - "esl-selectn": 162, - "esl-seqrange": 162, - "esl-seqstat": 162, - "esl-sfetch": 162, - "esl-shuffle": 162, - "esl-ssdraw": 162, + "esl-alimanip": 163, + "esl-alimap": 163, + "esl-alimask": 163, + "esl-alimerge": 163, + "esl-alipid": 163, + "esl-alirev": 163, + "esl-alistat": 163, + "esl-compalign": 163, + "esl-compstruct": 163, + "esl-construct": 163, + "esl-histplot": 163, + "esl-mask": 163, + "esl-mixdchlet": 148, + "esl-reformat": 165, + "esl-selectn": 163, + "esl-seqrange": 163, + "esl-seqstat": 163, + "esl-sfetch": 163, + "esl-shuffle": 163, + "esl-ssdraw": 163, "esl-ssplit.pl": 2, - "esl-translate": 162, - "esl-weight": 162, + "esl-translate": 163, + "esl-weight": 163, "espell": 88, "espgen": 6, "espgen.py": 6, @@ -10203,6 +10230,8 @@ "estimateScaleFactor": 11, "estimateScalePerMotif.sh": 1, "estimateSelfSimilarity.pl": 1, + "estimate_insert_size.pl": 1, + "estimate_insert_size.pl.bak": 1, "estimate_observation_richness.py": 1, "estimate_sequencing_error_effects.py": 1, "estimator_ckpt_converter": 51, @@ -10210,7 +10239,7 @@ "estscan": 1, "estwise": 3, "estwisedb": 3, - "esummary": 289, + "esummary": 294, "etandem": 24, "ete": 2, "ete3": 57, @@ -10249,7 +10278,7 @@ "eviplot.py": 1, "evol": 3, "evoluzer": 1, - "evolver": 65, + "evolver": 67, "exact-tandems": 57, "exactSNP": 6, "examine": 1, @@ -10265,7 +10294,7 @@ "excise_precursors.pl": 1, "excise_precursors_iterative_final.pl": 1, "excl_seqs": 2, - "exclude-uid-lists": 274, + "exclude-uid-lists": 279, "exclude_N": 1, "exclude_loci": 1, "exclude_loci_backup": 1, @@ -10281,8 +10310,8 @@ "existDB": 5, "exomiser-rest-prioritiser": 1, "exon_utils": 1, - "exonerate": 10, - "exonerate-server": 10, + "exonerate": 11, + "exonerate-server": 11, "exonerate2hints.pl": 14, "exoniphy": 2, "exoniphyDb2hints.pl": 14, @@ -10290,9 +10319,9 @@ "exp_up_ensg.pl": 7, "expam": 1, "expam_limit": 1, - "expand": 82, - "expand-current": 274, - "expandCols": 269, + "expand": 83, + "expand-current": 279, + "expandCols": 271, "expand_fastq": 1, "expand_links.pl": 7, "expand_refseq_isoforms.pl": 1, @@ -10309,11 +10338,11 @@ "exporTPP.pl": 2, "export-itol.pl": 1, "export2graphlan.py": 1, - "export2sam.pl": 504, + "export2sam.pl": 507, "exportTools.sh": 1, "export_mitochondrial_contigs.py": 1, "export_norm_data": 1, - "expr": 82, + "expr": 83, "express": 1, "expressionFromGenomicSet.py": 1, "exprop": 1, @@ -10469,15 +10498,15 @@ "ezez4makefile_v4.pl": 1, "ezez4qsub_vx1.pl": 1, "ezez_vx1.pl": 1, - "f2py": 2028, + "f2py": 2032, "f2py2": 135, "f2py2.7": 135, - "f2py3": 1591, + "f2py3": 1592, "f2py3.10": 445, "f2py3.11": 110, "f2py3.6": 126, "f2py3.7": 257, - "f2py3.8": 244, + "f2py3.8": 245, "f2py3.9": 409, "f4ratio": 2, "f5c": 1, @@ -10505,7 +10534,7 @@ "faToVcf": 3, "fa_coords": 11, "fab": 2, - "factor": 92, + "factor": 93, "fade": 1, "fadvise": 1, "fahash": 1, @@ -10535,7 +10564,7 @@ "falconc": 4, "falconsense": 6, "fallocate": 13, - "false": 82, + "false": 83, "famap": 1, "famdef": 4, "famsa": 4, @@ -10591,7 +10620,7 @@ "fasta-most": 13, "fasta-nr": 4, "fasta-re-match": 8, - "fasta-sanitize.pl": 303, + "fasta-sanitize.pl": 306, "fasta-shuffle-letters": 13, "fasta-splitter": 1, "fasta-strip-identifier": 2, @@ -10605,7 +10634,7 @@ "fasta2ali.pl": 1, "fasta2bed.py": 1, "fasta2col": 1, - "fasta2esd": 10, + "fasta2esd": 11, "fasta2frag.tcl": 1, "fasta2frg.pl": 1, "fasta2frg_m.pl": 1, @@ -10628,7 +10657,7 @@ "fasta2tab.pl": 5, "fasta2upper": 1, "fasta36": 7, - "fastaFromBed": 269, + "fastaFromBed": 271, "fastaToCA": 3, "fastaToRead": 1, "fasta_base_content.py": 2, @@ -10669,27 +10698,27 @@ "fasta_tool": 2, "fasta_ushuffle": 2, "fasta_windows": 1, - "fastaannotatecdna": 10, - "fastachecksum": 10, - "fastaclean": 11, - "fastaclip": 10, - "fastacmd": 30, - "fastacomposition": 10, - "fastadiff": 10, + "fastaannotatecdna": 11, + "fastachecksum": 11, + "fastaclean": 12, + "fastaclip": 11, + "fastacmd": 32, + "fastacomposition": 11, + "fastadiff": 11, "fastadigest.py": 2, "fastadigeststats.py": 2, - "fastaexplode": 10, - "fastafetch": 10, + "fastaexplode": 11, + "fastafetch": 11, "fastafunk": 1, "fastagap": 1, "fastahack": 1, - "fastahardmask": 10, + "fastahardmask": 11, "fastail": 2, - "fastaindex": 10, + "fastaindex": 11, "fastainfo": 1, - "fastalength": 10, - "fastanrdb": 10, - "fastaoverlap": 10, + "fastalength": 11, + "fastanrdb": 11, + "fastaoverlap": 11, "fastaparse.pl": 1, "fastaptamer_cluster": 1, "fastaptamer_cluster_xs": 1, @@ -10698,17 +10727,17 @@ "fastaptamer_enrich": 1, "fastaptamer_search": 1, "fastaq": 20, - "fastareformat": 10, - "fastaremove": 10, - "fastarevcomp": 10, + "fastareformat": 11, + "fastaremove": 11, + "fastarevcomp": 11, "fastaselect.pl": 1, - "fastasoftmask": 10, - "fastasort": 10, - "fastasplit": 11, - "fastasubseq": 10, + "fastasoftmask": 11, + "fastasort": 11, + "fastasplit": 12, + "fastasubseq": 11, "fastatrans": 1, - "fastatranslate": 10, - "fastavalidcds": 10, + "fastatranslate": 11, + "fastavalidcds": 11, "fastax": 2, "fastaxsort": 2, "fastconv": 2, @@ -10870,7 +10899,7 @@ "fastq_trim_poly_at": 3, "fastq_truncate": 3, "fastq_validator.sh": 3, - "fastqc": 37, + "fastqc": 38, "fastqc_report.Rmd": 1, "fastqc_single_report.Rmd": 1, "fastqe": 1, @@ -10918,19 +10947,19 @@ "fasxl": 2, "fathom": 2, "favites_lite.py": 1, - "fax2ps": 5293, - "fax2tiff": 5293, + "fax2ps": 5294, + "fax2tiff": 5294, "fba": 1, "fc": 1, - "fc-cache": 5305, - "fc-cat": 5305, - "fc-conflist": 4822, - "fc-list": 5305, - "fc-match": 5305, - "fc-pattern": 5305, - "fc-query": 5305, - "fc-scan": 5305, - "fc-validate": 5305, + "fc-cache": 5307, + "fc-cat": 5307, + "fc-conflist": 4824, + "fc-list": 5307, + "fc-match": 5307, + "fc-pattern": 5307, + "fc-query": 5307, + "fc-scan": 5307, + "fc-validate": 5307, "fc_actg_coordinate": 1, "fc_calc_cutoff": 1, "fc_consensus": 1, @@ -11011,12 +11040,12 @@ "fermi2.pl": 2, "fetch": 4, "fetch-extras": 73, - "fetch-local": 13, - "fetch-nmcds": 13, - "fetch-pmc": 13, - "fetch-pubmed": 288, + "fetch-local": 18, + "fetch-nmcds": 18, + "fetch-pmc": 18, + "fetch-pubmed": 293, "fetch-tax.pl": 1, - "fetch-taxonomy": 13, + "fetch-taxonomy": 18, "fetchChromSizes": 5, "fetchEnaLibraryFastqs.sh": 1, "fetchFastq.sh": 1, @@ -11049,8 +11078,8 @@ "ffprobe": 10, "ffq": 1, "ffreqboot": 2, - "fftns": 98, - "fftnsi": 98, + "fftns": 100, + "fftnsi": 100, "fftw-wisdom": 167, "fftw-wisdom-to-conf": 167, "fftwf-wisdom": 167, @@ -11059,7 +11088,7 @@ "fgbio": 3, "fgendist": 2, "fgmp": 1, - "fgrep": 19, + "fgrep": 20, "fgsv": 1, "fgwas": 1, "fido2-assert": 4, @@ -11095,18 +11124,18 @@ "filter-alignments.py": 1, "filter-bam": 2, "filter-bam-by-ids": 3, - "filter-columns": 189, - "filter-genbank": 13, + "filter-columns": 194, + "filter-genbank": 18, "filter-gff": 1, "filter-nonunique-peptide-matches": 2, "filter-positions.pl": 1, "filter-ppx.pl": 14, - "filter-record": 13, + "filter-record": 18, "filter-sort": 1, "filter-stage-1.prl": 4, "filter-stage-2.prl": 4, "filter-stats.pl": 1, - "filter-stop-words": 289, + "filter-stop-words": 294, "filter-stoptags.py": 7, "filter-table": 12, "filter-variations": 2, @@ -11151,6 +11180,7 @@ "filterTADsAndCPs.pl": 5, "filterTADsAndLoops.pl": 5, "filterTagDirectory.pl": 3, + "filterTaxonomy.sh": 1, "filterVcf.pl": 1, "filter_1hits": 1, "filter_FP.py": 1, @@ -11282,7 +11312,7 @@ "find-all-symbols": 2, "find-compounds.pl": 1, "find-duplicate-reads": 2, - "find-in-gene": 201, + "find-in-gene": 206, "find-knots.py": 7, "find-mango-assembly.sh": 1, "find-mango-home": 1, @@ -11430,10 +11460,10 @@ "flaimapper": 1, "flair": 1, "flake8": 4, - "flankBed": 269, + "flankBed": 271, "flanker": 1, "flapjack": 1, - "flash": 15, + "flash": 16, "flash2": 4, "flask": 49, "flatc": 12, @@ -11476,7 +11506,7 @@ "fmlrc2-convert": 1, "fmove": 2, "fmplot.py": 3, - "fmt": 82, + "fmt": 83, "fmtutil": 1, "fmtutil-sys": 1, "fmtutil-user": 1, @@ -11484,14 +11514,14 @@ "fnj": 1, "focus": 1, "focus_database_utils": 1, - "fold": 82, + "fold": 83, "foldFasta.pl": 1, "foldcomp": 1, - "foldseek": 2, + "foldseek": 3, "font-awesome-to-png": 2, "font2c": 3, "fontinst": 1, - "fonttools": 386, + "fonttools": 387, "fop": 1, "forceOneClusterPerPairMem.py": 1, "forest.py": 1, @@ -11508,9 +11538,9 @@ "format_sintax.py": 1, "format_xml.pl": 1, "format_xml.pl.bak": 1, - "formatdb": 30, + "formatdb": 32, "formatlist": 1, - "formatrpsdb": 30, + "formatrpsdb": 32, "formcon": 2, "forwardGenomics.R": 1, "forwardGenomics_fullAnalysis.R": 1, @@ -11540,6 +11570,8 @@ "fq2psmcfa": 1, "fq2psmcfa.c": 1, "fq2psmcfa.o": 1, + "fq_all2std.pl": 1, + "fq_all2std.pl.bak": 1, "fq_deinterleave": 1, "fq_interleave": 1, "fqc": 5, @@ -11578,7 +11610,7 @@ "freec": 1, "freec2bed.pl": 1, "freec2circos.pl": 1, - "freetype-config": 5801, + "freetype-config": 5803, "freeze_graph": 25, "freq2group.pl": 5, "frequency.py": 1, @@ -11592,7 +11624,7 @@ "frg2fastq": 2, "frg2ta": 2, "frgs2clones": 3, - "fribidi": 3998, + "fribidi": 3999, "frictionless": 1, "frm_admin": 1, "frm_purged": 1, @@ -11722,8 +11754,8 @@ "funr": 1, "funzip": 25, "fuse": 1, - "fuse-ranges": 201, - "fuse-segments": 189, + "fuse-ranges": 206, + "fuse-segments": 194, "fuse.sh": 30, "fusion-bloom": 1, "fusion-bloom.makefile": 1, @@ -11964,7 +11996,8 @@ "gapless.sh": 1, "gapmm2": 1, "gappa": 2, - "gapplication": 2345, + "gapplication": 2346, + "gapseq": 1, "garnett_check_markers.R": 1, "garnett_classify_cells.R": 1, "garnett_cli_post_install_tests.bats": 1, @@ -11989,22 +12022,22 @@ "gatk3": 5, "gatk3-register": 3, "gatk_to_gvcf": 1, - "gawk": 89, + "gawk": 93, "gawk-4.1.3": 1, "gawk-4.2.1": 2, "gawk-5.0.0": 1, "gawk-5.0.1": 6, "gawk-5.1.0": 64, "gawk-5.2.2": 1, - "gawk-5.3.0": 14, - "gawkbug": 15, + "gawk-5.3.0": 18, + "gawkbug": 19, "gb2fas": 1, "gb2fasta": 1, "gbSmallDNA2gff.pl": 14, "gbase": 2, - "gbf2fsa": 13, - "gbf2ref": 13, - "gbf2xml": 288, + "gbf2fsa": 18, + "gbf2ref": 18, + "gbf2xml": 293, "gbf2xml.bak": 1, "gbfalncut": 2, "gbfcut": 2, @@ -12051,9 +12084,9 @@ "gctb": 1, "gctx2gct": 2, "gcv": 2, - "gd2copypal": 232, - "gd2togif": 232, - "gd2topng": 232, + "gd2copypal": 233, + "gd2togif": 233, + "gd2topng": 233, "gdal-config": 36, "gdal2tiles.py": 4, "gdal2xyz.py": 4, @@ -12104,11 +12137,11 @@ "gdbm_dump": 25, "gdbm_load": 25, "gdbmtool": 25, - "gdbus": 1652, - "gdbus-codegen": 1650, + "gdbus": 1653, + "gdbus-codegen": 1651, "gdc-client": 1, - "gdcmpgif": 232, - "gddiag": 19, + "gdcmpgif": 233, + "gddiag": 20, "gdi": 1, "gdiff": 1, "gdistribution": 1, @@ -12119,12 +12152,12 @@ "gdlib-config": 44, "gdmicro": 1, "gdown": 3, - "gdparttopng": 232, + "gdparttopng": 233, "gdrive": 1, "gdsctools_anova": 1, "gdsctools_regression": 1, "gdtools": 1, - "gdtopng": 232, + "gdtopng": 233, "gecco": 1, "geckodriver": 2, "geecee": 24, @@ -12158,20 +12191,20 @@ "genbank_to": 1, "genblastG": 1, "genbox": 1, - "genbrk": 5801, - "gencfu": 5801, + "genbrk": 5805, + "gencfu": 5805, "genclust": 1, - "gencnval": 5801, + "gencnval": 5805, "gencode_extract_relevant_gtf_exons.pl": 1, "gencode_singleton_unit_test": 5, "genconf": 1, "gencore": 1, "gencove": 1, "gendb": 13, - "gendict": 5801, + "gendict": 5805, "gendist": 10, "gene2protein.db3": 2, - "gene2range": 189, + "gene2range": 194, "gene2xml": 1, "geneAssociationZscore.py": 1, "geneBody_coverage.py": 3, @@ -12249,7 +12282,7 @@ "generate_report.py.bak": 1, "generate_report.pyc.bak": 1, "generate_run_scripts.py": 1, - "generate_sepia_reference.py": 1, + "generate_sepia_reference.py": 2, "generate_ska_alignment.py": 1, "generate_training_data": 1, "generate_transcripts_gff.py": 1, @@ -12283,8 +12316,8 @@ "genome-complexity-fast": 2, "genome-to-blast-db": 1, "genome2cg": 1, - "genomeCoverageBed": 269, - "genomeCoverageBed.pl": 85, + "genomeCoverageBed": 271, + "genomeCoverageBed.pl": 87, "genomeOntology": 5, "genome_LenFilter_stats.pl": 3, "genome_anno.py": 2, @@ -12316,11 +12349,12 @@ "genotype.pl": 1, "genotypeSummary": 31, "genotyper": 3, + "genotyper_data_classes.py": 1, "genotyphi": 1, "genotyphi.py": 1, "genpcz": 2, "genpept2gsi.pl": 2, - "genrb": 5801, + "genrb": 5805, "genreflex": 3, "genremdinputs.py": 6, "genrestr": 4, @@ -12378,7 +12412,7 @@ "getDifferentialPeaksReplicates.pl": 5, "getDistalPeaks.pl": 5, "getEndSequencesOfContigs.perl": 1, - "getExactTaxonomy.pl": 1, + "getExactTaxonomy.pl": 2, "getFCSheader.R": 1, "getFCSheaders.py": 1, "getFRCvalues": 2, @@ -12406,7 +12440,7 @@ "getOntology.R": 1, "getOntology.py": 1, "getOrthologList": 4, - "getOverlap": 269, + "getOverlap": 271, "getPartOfPromoter.pl": 5, "getPatch": 2, "getPeakTags": 5, @@ -12491,6 +12525,7 @@ "get_obsolete_term_id_vs_name_in_go.pl": 1, "get_obsolete_terms.pl": 1, "get_ont_flowcell": 1, + "get_orfs": 1, "get_organelle_config.py": 1, "get_organelle_from_assembly.py": 1, "get_organelle_from_reads.py": 1, @@ -12519,8 +12554,8 @@ "get_sequence_type": 1, "get_sequences_for_meme.py": 1, "get_simple_cycs.py": 1, - "get_species_taxids.sh": 288, - "get_species_taxids.sh.bak": 283, + "get_species_taxids.sh": 293, + "get_species_taxids.sh.bak": 288, "get_standard_headers": 1, "get_stats_summary.pl": 1, "get_subontology_from.pl": 1, @@ -12590,9 +12625,9 @@ "getscu": 1, "getsize": 13, "getsnvfreq_by_interval": 1, - "gettext": 5275, - "gettext.sh": 5275, - "gettextize": 5275, + "gettext": 5281, + "gettext.sh": 5281, + "gettextize": 5281, "getuniqgenomealign": 1, "getuniqgenomealign_interval": 1, "getuniqgenomealign_sample_names": 1, @@ -12605,6 +12640,7 @@ "gfServer": 12, "gfa1tofasta.py": 1, "gfa2tofasta.py": 1, + "gfa_connector": 1, "gfa_to_fasta.py": 1, "gfa_to_fastg.py": 1, "gfaffix": 2, @@ -12694,14 +12730,14 @@ "gie": 39, "gif2h5": 535, "gif2hdf": 122, - "gif2rgb": 738, + "gif2rgb": 739, "gif2tiff": 189, - "gif2webp": 348, - "gifbuild": 738, - "gifclrmp": 738, + "gif2webp": 349, + "gifbuild": 739, + "gifclrmp": 739, "gifecho": 39, "giffilter": 25, - "giffix": 738, + "giffix": 739, "gifinto": 39, "gifmaker.py": 20, "gifrop": 1, @@ -12712,31 +12748,31 @@ "gifrop_pannotate.R": 1, "gifrop_plots.R": 1, "gifsponge": 25, - "giftext": 738, - "giftogd2": 232, - "giftool": 738, + "giftext": 739, + "giftogd2": 233, + "giftool": 739, "gigrnd.py": 1, "gil2bin": 1, "gimbleprep": 1, "gimme": 4, "gimme_taxa.py": 7, - "ginsi": 98, - "gio": 1540, + "ginsi": 100, + "gio": 1541, "gio-launch-desktop": 668, - "gio-querymodules": 1652, - "git": 28, + "gio-querymodules": 1653, + "git": 29, "git-clang-format": 7, - "git-cvsserver": 28, + "git-cvsserver": 29, "git-lfs": 3, - "git-receive-pack": 28, - "git-shell": 28, - "git-upload-archive": 28, - "git-upload-pack": 28, + "git-receive-pack": 29, + "git-shell": 29, + "git-upload-archive": 29, + "git-upload-pack": 29, "git2": 13, "git2_cli": 7, "git_test.py": 1, "gitable.sh": 30, - "gitk": 28, + "gitk": 29, "gkmpredict": 1, "gkmtrain": 1, "gkpStoreCreate": 3, @@ -12750,26 +12786,26 @@ "glam2scan": 13, "glam2scan2html": 13, "glewinfo": 1, - "glib-compile-resources": 1650, - "glib-compile-schemas": 1652, - "glib-genmarshal": 1650, - "glib-gettextize": 1650, - "glib-mkenums": 1650, + "glib-compile-resources": 1651, + "glib-compile-schemas": 1653, + "glib-genmarshal": 1651, + "glib-gettextize": 1651, + "glib-mkenums": 1651, "glim-diff.awk": 2, "glimmer3": 2, - "glimmerhmm": 15, - "glimmhmm.pl": 15, + "glimmerhmm": 16, + "glimmhmm.pl": 16, "glistcompare": 2, "glistmaker": 2, "glistquery": 2, "glnexus_cli": 1, "glob_res.pl": 1, "global.json": 1, - "glpsol": 226, + "glpsol": 227, "glsearch36": 7, "gm": 2, - "gm2ranges": 13, - "gm2segs": 13, + "gm2ranges": 18, + "gm2segs": 18, "gmap": 13, "gmap.nosimd": 8, "gmap.sse42": 11, @@ -12882,7 +12918,7 @@ "goalign": 1, "goalign_test.sh": 1, "goat-cli": 1, - "gobject-query": 1650, + "gobject-query": 1651, "goblin": 1, "gocr": 2, "gocr.tcl": 2, @@ -13012,10 +13048,10 @@ "green3": 1, "green3.10": 1, "greenhill": 1, - "grep": 19, + "grep": 20, "grep.py": 1, "grepf": 1, - "gresource": 1652, + "gresource": 1653, "gretel": 1, "gretel-snpper": 1, "grf-alignment": 5, @@ -13057,14 +13093,14 @@ "groopm": 1, "groot": 2, "groovy_script": 4, - "groupBy": 269, + "groupBy": 271, "groupSequences.pl": 5, "group_ORF_sequences.py": 1, "group_bp_reads.pl": 1, "group_humann2_uniref_abundances_to_GO.sh": 1, "group_process.pl": 1, "group_significance.py": 1, - "groups": 82, + "groups": 83, "grow-readbank": 2, "grpc_cpp_plugin": 136, "grpc_csharp_plugin": 136, @@ -13082,13 +13118,13 @@ "gsea": 1, "gsea-cli": 1, "gseapy": 4, - "gsettings": 1652, + "gsettings": 1653, "gsf": 1, "gsf-office-thumbnailer": 1, "gsf-vba-dump": 1, - "gsl-config": 4541, - "gsl-histogram": 4541, - "gsl-randist": 4541, + "gsl-config": 4543, + "gsl-histogram": 4543, + "gsl-randist": 4543, "gslj": 104, "gslp": 104, "gsnap": 11, @@ -13099,7 +13135,7 @@ "gsnapl.sse42": 11, "gsnd": 104, "gsort": 5, - "gss-client": 5775, + "gss-client": 5781, "gss-server": 2, "gst-completion-helper": 1, "gst-device-monitor-1.0": 229, @@ -13117,8 +13153,8 @@ "gt_lods": 1, "gtdbtk": 2, "gtest": 3, - "gtester": 1650, - "gtester-report": 1650, + "gtester": 1651, + "gtester-report": 1651, "gtf-to-bed12": 3, "gtf2aa.pl": 12, "gtf2bed": 15, @@ -13320,8 +13356,8 @@ "h264dec": 10, "h264enc": 10, "h2load": 3929, - "h2ph": 1681, - "h2xs": 1681, + "h2ph": 1688, + "h2xs": 1688, "h4_ncdump": 122, "h4_ncgen": 122, "h4cc": 122, @@ -13494,11 +13530,11 @@ "haystack_pipeline": 1, "haystack_run_test": 1, "haystack_tf_activity_plane": 1, - "hb-info": 256, - "hb-ot-shape-closure": 5050, - "hb-shape": 5050, - "hb-subset": 4614, - "hb-view": 5007, + "hb-info": 258, + "hb-ot-shape-closure": 5052, + "hb-shape": 5052, + "hb-subset": 4616, + "hb-view": 5009, "hbvblast.sh": 1, "hca-matrix-downloader": 1, "hca-mtx-to-10x": 1, @@ -13525,7 +13561,7 @@ "hdiff": 122, "hdp": 122, "hdrcopy": 1, - "head": 82, + "head": 83, "headPolishes": 3, "heartbeat-wrapper": 2, "heatmap.R": 1, @@ -13551,7 +13587,7 @@ "hexdump": 13, "hgGcPercent": 3, "hgvs-shell": 1, - "hgvs2spdi": 201, + "hgvs2spdi": 206, "hhalign": 4, "hhalign_omp": 4, "hhblits": 4, @@ -13691,15 +13727,15 @@ "hmm_vali.py": 2, "hmm_view": 2, "hmm_worker.py": 3, - "hmmalign": 180, + "hmmalign": 181, "hmmalign2": 6, - "hmmbuild": 180, + "hmmbuild": 181, "hmmbuild2": 6, "hmmc2": 13, "hmmcalibrate2": 6, - "hmmconvert": 174, + "hmmconvert": 175, "hmmconvert2": 6, - "hmmemit": 174, + "hmmemit": 175, "hmmemit2": 6, "hmmer2filtered_best.py": 1, "hmmer2gff": 1, @@ -13707,25 +13743,25 @@ "hmmeralign": 7, "hmmerbuild": 7, "hmmerfm-exactmatch": 13, - "hmmfetch": 174, + "hmmfetch": 175, "hmmfetch2": 6, "hmmgs": 5, "hmmindex2": 6, "hmmlib_to_sqlite3.py": 2, - "hmmlogo": 174, + "hmmlogo": 175, "hmmpair": 1, "hmmpfam2": 6, - "hmmpgmd": 174, - "hmmpgmd_shard": 146, - "hmmpress": 174, - "hmmscan": 174, + "hmmpgmd": 175, + "hmmpgmd_shard": 147, + "hmmpress": 175, + "hmmscan": 175, "hmmscan-parser.py": 1, "hmmscan_parser.py": 2, - "hmmsearch": 174, + "hmmsearch": 175, "hmmsearch2": 6, "hmmsearch_run.py": 2, - "hmmsim": 174, - "hmmstat": 174, + "hmmsim": 175, + "hmmstat": 175, "hmnfusion": 1, "hmnqc": 1, "hmoment": 24, @@ -13743,7 +13779,7 @@ "homopolish": 1, "hopla": 1, "hops": 1, - "hostid": 82, + "hostid": 83, "hostile": 1, "hotspot3d": 1, "howdesbt": 1, @@ -13800,7 +13836,7 @@ "htseq-count": 22, "htseq-count-barcodes": 14, "htseq-qa": 22, - "htsfile": 692, + "htsfile": 695, "htsget": 2, "htsinfer": 1, "httpcfg": 15, @@ -13814,7 +13850,7 @@ "huge-split.pl": 1, "huggingface-cli": 2, "hulk": 1, - "humanfriendly": 102, + "humanfriendly": 103, "humann": 1, "humann2": 2, "humann2_associate": 1, @@ -13863,21 +13899,21 @@ "humann_unpack_pathways": 1, "humid": 1, "hv-pipeline.py": 1, - "hwloc-annotate": 61, + "hwloc-annotate": 63, "hwloc-assembler": 2, "hwloc-assembler-remote": 2, - "hwloc-bind": 61, - "hwloc-calc": 61, - "hwloc-compress-dir": 61, - "hwloc-diff": 61, + "hwloc-bind": 63, + "hwloc-calc": 63, + "hwloc-compress-dir": 63, + "hwloc-diff": 63, "hwloc-distances": 2, - "hwloc-distrib": 61, - "hwloc-gather-cpuid": 59, - "hwloc-gather-topology": 61, - "hwloc-info": 61, - "hwloc-ls": 61, - "hwloc-patch": 61, - "hwloc-ps": 61, + "hwloc-distrib": 63, + "hwloc-gather-cpuid": 61, + "hwloc-gather-topology": 63, + "hwloc-info": 63, + "hwloc-ls": 63, + "hwloc-patch": 63, + "hwloc-ps": 63, "hyb_analyze": 1, "hyb_check": 1, "hyb_eval": 1, @@ -13931,7 +13967,7 @@ "ic.tsv": 1, "ic_mep": 1, "ic_mes": 1, - "icarus.py": 10, + "icarus.py": 11, "icc2ps": 1, "icclink": 1, "icctrans": 1, @@ -13944,10 +13980,10 @@ "ichar": 1, "icon-font-to-png": 2, "iconv": 5462, - "icu-config": 5801, - "icuexportdata": 2017, - "icuinfo": 5801, - "id": 82, + "icu-config": 5805, + "icuexportdata": 2021, + "icuinfo": 5805, + "id": 83, "idba": 10, "idba.o": 10, "idba_hybrid": 10, @@ -13976,20 +14012,20 @@ "idfetch": 1, "idiag-socket-details": 9, "idle": 332, - "idle3": 3300, - "idle3.10": 802, + "idle3": 3306, + "idle3.10": 805, "idle3.11": 264, - "idle3.12": 175, + "idle3.12": 177, "idle3.4": 6, "idle3.5": 103, "idle3.6": 342, "idle3.7": 383, - "idle3.8": 574, + "idle3.8": 575, "idle3.9": 651, "idlj": 117, "idmatrix.sh": 30, "idn": 30, - "idn2": 262, + "idn2": 268, "idpAssemble": 2, "idpQonvert": 2, "idpQuery": 2, @@ -14106,7 +14142,7 @@ "img2dcm": 1, "img2png": 5, "img2py": 5, - "img2webp": 339, + "img2webp": 340, "img2xpm": 5, "imgcmp": 6, "imginfo": 6, @@ -14118,7 +14154,7 @@ "imode_gcc": 2, "imodview": 2, "imove": 2, - "impala": 30, + "impala": 32, "impg": 1, "import": 75, "import-html-template": 13, @@ -14182,7 +14218,7 @@ "infer_bp_v4.pl": 1, "infer_experiment.py": 3, "infer_sv.pl": 1, - "infinitesites": 65, + "infinitesites": 67, "inflate_denoiser_output.py": 1, "influx_i": 1, "influx_i.py": 1, @@ -14193,12 +14229,12 @@ "infoalign": 24, "infoassembly": 24, "infobase": 24, - "infocmp": 7664, + "infocmp": 7672, "inforesidue": 24, "informant.py": 1, "infoseq": 24, - "infotocap": 7664, - "ini2xml": 13, + "infotocap": 7672, + "ini2xml": 18, "init_Trinotate_sqlite_db.pl": 1, "init_db.sh": 1, "initdb": 45, @@ -14214,7 +14250,9 @@ "innochecksum": 10, "input_commands.py": 2, "input_output.py": 1, + "input_processing.py": 1, "inputgui.f": 1, + "inputs_validation.py": 1, "insert-length-histogram": 2, "insert-sizes": 2, "insert_mol_no_vmd.py": 1, @@ -14232,12 +14270,13 @@ "inst-qual-filter.pl": 1, "inst-split-seqs.pl": 1, "inst-tax-filter.pl": 1, - "install": 82, + "install": 83, "install.db.tables.r": 5, "install.pl": 2, - "installBiocDataPackage.sh": 289, + "installBiocDataPackage.sh": 290, "installMetaphyler.pl": 1, "installPackages.R": 1, + "install_archived_sybilSBML.sh": 1, "install_cmdstan": 2, "install_compass": 2, "install_cxx_toolchain": 2, @@ -14256,7 +14295,7 @@ "installpackages.R": 1, "installvst": 15, "instance_events": 29, - "instmodsh": 1681, + "instmodsh": 1688, "int_seqs_to_char_strings.py": 59, "intake": 1, "intake-server": 1, @@ -14287,12 +14326,12 @@ "interop_plot_qscore_histogram": 4, "interop_plot_sample_qc": 4, "interop_summary": 4, - "interpolate_sam.pl": 504, + "interpolate_sam.pl": 507, "interprophet.rb": 1, "interproscan.sh": 1, "intersect": 5, - "intersect-uid-lists": 287, - "intersectBed": 269, + "intersect-uid-lists": 292, + "intersectBed": 271, "intersectFiles.py": 2, "intersectGenomicSets.py": 1, "intersect_assembly_errors": 1, @@ -14341,7 +14380,7 @@ "ipcmk": 13, "ipcontroller": 6, "ipcontroller2": 1, - "ipcress": 10, + "ipcress": 11, "ipcrm": 13, "ipcs": 13, "ipengine": 6, @@ -14349,8 +14388,8 @@ "iphop": 1, "ipopt": 1, "ipopt_sens": 1, - "ippeveprinter": 187, - "ipptool": 187, + "ippeveprinter": 188, + "ipptool": 188, "ipr_update_gff": 1, "iprscan2gff3": 1, "iptest": 53, @@ -14503,7 +14542,7 @@ "jack_zombie": 12, "jackd": 25, "jackdiff": 1, - "jackhmmer": 174, + "jackhmmer": 175, "jackknifed_beta_diversity.py": 1, "jaffa-assembly": 1, "jaffa-direct": 1, @@ -14514,8 +14553,8 @@ "jamo-normalize": 1, "jannovar": 1, "jaotc": 310, - "jar": 534, - "jarsigner": 534, + "jar": 535, + "jarsigner": 535, "jasmine": 3, "jasmine.jar": 1, "jasmine_igv.jar": 1, @@ -14526,41 +14565,41 @@ "jaspscan": 24, "jass": 1, "jass_preprocessing": 1, - "java": 534, + "java": 535, "java-rmi.cgi": 112, - "javac": 534, - "javadoc": 534, + "javac": 535, + "javadoc": 535, "javah": 112, - "javap": 534, + "javap": 535, "javareconf": 1, "jbrowse": 1, "jcast": 1, - "jcmd": 534, - "jconsole": 534, - "jdb": 534, - "jdeprscan": 425, - "jdeps": 533, + "jcmd": 535, + "jconsole": 535, + "jdb": 535, + "jdeprscan": 426, + "jdeps": 534, "je": 2, - "jellyfish": 45, + "jellyfish": 46, "jemalloc-config": 14, "jemalloc.sh": 15, "jembossctl": 24, "jeprof": 14, "jf_aligner": 1, - "jfr": 369, + "jfr": 370, "jgi_gc": 1, "jgi_summarize_bam_contig_depths": 6, "jgoslin": 1, "jhat": 112, - "jhsdb": 425, - "jimage": 425, - "jinfo": 534, + "jhsdb": 426, + "jimage": 426, + "jinfo": 535, "jiv": 5, "jjs": 420, - "jlink": 425, + "jlink": 426, "jlpm": 2, - "jmap": 534, - "jmod": 425, + "jmap": 535, + "jmod": 426, "jmztab-m": 1, "job-shop": 1, "jobTreeKill": 2, @@ -14569,8 +14608,8 @@ "jobTreeStats": 2, "jobTreeStatus": 2, "jobTreeTest_Dependencies.py": 1, - "join": 82, - "join-into-groups-of": 289, + "join": 83, + "join-into-groups-of": 294, "join-long-chromosomes": 3, "join.pl": 1, "join.pl.bak": 1, @@ -14592,33 +14631,33 @@ "joint-indels": 1, "joint-parsimony": 1, "jp.py": 100, - "jpackage": 115, + "jpackage": 116, "jpeg2hdf": 122, - "jpegtran": 5740, - "jpgicc": 979, + "jpegtran": 5742, + "jpgicc": 980, "jpredapi": 1, - "jps": 534, - "jq": 300, + "jps": 535, + "jq": 301, "jronn": 1, - "jrunscript": 534, + "jrunscript": 535, "js-beautify": 1, "jsadebugd": 112, "jscan": 1, "jsearch": 1, - "jshell": 425, + "jshell": 426, "json2gff": 1, - "json2xml": 201, + "json2xml": 206, "json_collect_data_source.py": 1, - "json_pp": 1681, - "json_xs": 347, + "json_pp": 1688, + "json_xs": 352, "jsondiff": 8, - "jsonl2xml": 13, + "jsonl2xml": 18, "jsonpatch": 8, "jsonpointer": 10, "jsonschema": 206, - "jstack": 534, - "jstat": 534, - "jstatd": 534, + "jstack": 535, + "jstat": 535, + "jstatd": 535, "juicer": 1, "juicer_shortform2pairs.pl": 22, "julia": 6, @@ -14664,17 +14703,17 @@ "jupyter-serverextension": 37, "jupyter-troubleshoot": 143, "jupyter-trust": 136, - "just-first-key": 13, + "just-first-key": 18, "just_blast_test.pl": 1, - "jwebserver": 33, - "k5srvutil": 5775, - "k8": 159, + "jwebserver": 34, + "k5srvutil": 5781, + "k8": 161, "k8-Linux": 1, "k_means": 1, "k_means_coefficient": 1, "k_neighbors": 1, "k_neighbors_coefficient": 1, - "kadmin": 5775, + "kadmin": 5781, "kadmin.local": 2, "kadmind": 2, "kaiju": 4, @@ -14695,7 +14734,7 @@ "kaijup": 4, "kaijux": 4, "kakuro": 2, - "kaleido": 10, + "kaleido": 11, "kalign": 9, "kallisto": 10, "kanji-config-updmap": 1, @@ -14768,7 +14807,7 @@ "kdbmeta.3.0.0": 2, "kdbmeta.3.0.3": 1, "kdbmeta.3.1.0": 1, - "kdestroy": 5775, + "kdestroy": 5781, "kea-config": 35, "keep-header": 1, "keep-ribo-periodic": 1, @@ -14778,10 +14817,10 @@ "keggcharter.py": 1, "keggpathway_map.py": 1, "keyFreq": 1, - "keyctl": 2405, + "keyctl": 2411, "keygen": 1, "keyring": 10, - "keytool": 534, + "keytool": 535, "kget": 18, "kget.2": 18, "kget.2.10.0": 1, @@ -14797,7 +14836,7 @@ "khist.sh": 30, "kid": 1, "kidc": 1, - "kill": 93, + "kill": 94, "killBadKUnitigs": 1, "kill_instance": 29, "kill_pyro_mip_servers": 3, @@ -14809,10 +14848,10 @@ "kinSimRiboswitch": 1, "king": 1, "kingfisher": 1, - "kinit": 5775, + "kinit": 5781, "kinship-read": 1, "kinshipDecompose": 1, - "kinwalker": 48, + "kinwalker": 50, "kipoi": 2, "kissnp2": 1, "kissplice": 1, @@ -14822,14 +14861,14 @@ "kitsch": 10, "kitsune": 1, "kleborate": 1, - "klist": 5775, - "kma": 18, - "kma_index": 18, - "kma_shm": 18, - "kma_update": 18, - "kmc": 20, - "kmc_dump": 20, - "kmc_tools": 20, + "klist": 5781, + "kma": 19, + "kma_index": 19, + "kma_shm": 19, + "kma_update": 19, + "kmc": 21, + "kmc_dump": 21, + "kmc_tools": 21, "kmcp": 2, "kmds": 1, "kmer-count": 2, @@ -14847,6 +14886,7 @@ "kmer_nt_stuff.py": 1, "kmer_nt_stuff_threader.py": 1, "kmer_repeat_counter.py": 2, + "kmercounter": 1, "kmercountexact.sh": 30, "kmercountmulti.sh": 30, "kmercoverage": 1, @@ -14907,7 +14947,7 @@ "kp1mer_to_kmer.py": 1, "kp2np.py": 1, "kpal": 2, - "kpasswd": 5775, + "kpasswd": 5781, "kpileup.py": 1, "kprop": 2, "kpropd": 2, @@ -14920,18 +14960,18 @@ "kpsewhere": 1, "kpsewhich": 1, "kpsexpand": 1, - "kraken": 11, + "kraken": 12, "kraken-biom": 1, "kraken-bracken-summary.py": 1, - "kraken-build": 11, + "kraken-build": 12, "kraken-build.bak": 1, - "kraken-filter": 11, + "kraken-filter": 12, "kraken-filter.bak": 1, - "kraken-mpa-report": 11, + "kraken-mpa-report": 12, "kraken-mpa-report.bak": 1, - "kraken-report": 11, + "kraken-report": 12, "kraken-report.bak": 1, - "kraken-translate": 11, + "kraken-translate": 12, "kraken-translate.bak": 1, "kraken.bak": 1, "kraken2": 17, @@ -14954,7 +14994,7 @@ "krakenuniq-report": 1, "krakenuniq-translate": 1, "krakmeopen": 1, - "krb5-config": 5775, + "krb5-config": 5781, "krb5-send-pr": 2, "krb5kdc": 2, "kreport2krona.py": 3, @@ -14970,45 +15010,45 @@ "kseq_split": 1, "ksnp": 1, "kssd": 1, - "ksu": 5775, + "ksu": 5781, "ksw": 1, - "kswitch": 5775, - "ktClassifyBLAST": 16, - "ktClassifyHits": 12, - "ktGetContigMagnitudes": 16, - "ktGetLCA": 16, - "ktGetLibPath": 16, - "ktGetTaxIDFromAcc": 16, - "ktGetTaxInfo": 16, - "ktImportBLAST": 16, - "ktImportDiskUsage": 16, - "ktImportEC": 16, - "ktImportFCP": 16, - "ktImportGalaxy": 16, - "ktImportHits": 12, - "ktImportKrona": 16, - "ktImportMETAREP-BLAST": 16, - "ktImportMETAREP-EC": 16, - "ktImportMGRAST": 16, - "ktImportPhymmBL": 16, - "ktImportRDP": 16, - "ktImportRDPComparison": 16, - "ktImportTaxonomy": 16, - "ktImportText": 16, - "ktImportXML": 16, - "ktUpdateTaxonomy.sh": 16, + "kswitch": 5781, + "ktClassifyBLAST": 17, + "ktClassifyHits": 13, + "ktGetContigMagnitudes": 17, + "ktGetLCA": 17, + "ktGetLibPath": 17, + "ktGetTaxIDFromAcc": 17, + "ktGetTaxInfo": 17, + "ktImportBLAST": 17, + "ktImportDiskUsage": 17, + "ktImportEC": 17, + "ktImportFCP": 17, + "ktImportGalaxy": 17, + "ktImportHits": 13, + "ktImportKrona": 17, + "ktImportMETAREP-BLAST": 17, + "ktImportMETAREP-EC": 17, + "ktImportMGRAST": 17, + "ktImportPhymmBL": 17, + "ktImportRDP": 17, + "ktImportRDPComparison": 17, + "ktImportTaxonomy": 17, + "ktImportText": 17, + "ktImportXML": 17, + "ktUpdateTaxonomy.sh": 17, "ktremotemgr": 2, "ktremotetest": 2, "ktrimfrg": 2, "ktserver": 2, "kttimedmgr": 2, "kttimedtest": 2, - "ktutil": 5775, + "ktutil": 5781, "ktutilmgr": 2, "ktutilserv": 2, "ktutiltest": 2, "kubectl": 1, - "kvno": 5775, + "kvno": 5781, "kwip": 2, "kwip-stats": 2, "l4p-tmpl": 32, @@ -15126,7 +15166,7 @@ "lefse_plot_features.py": 1, "lefse_plot_res.py": 1, "lefse_run.py": 1, - "legacy_blast.pl": 321, + "legacy_blast.pl": 326, "legsta": 1, "lemon-0.x-to-1.x.sh": 4, "lemur": 1, @@ -15160,8 +15200,8 @@ "libclair3.cpython-36m-x86_64-linux-gnu.so": 1, "libclair3.o": 1, "libclair3.so": 1, - "libdeflate-gunzip": 4102, - "libdeflate-gzip": 4102, + "libdeflate-gunzip": 4106, + "libdeflate-gzip": 4106, "libdrawgram.so": 5, "libdrawtree.so": 5, "libfile.pl": 1, @@ -15170,9 +15210,9 @@ "libiomp5md.dll": 1, "liblist.pl": 1, "liblist.pl.bak": 1, - "libnetcfg": 1681, - "libpng-config": 5854, - "libpng16-config": 5854, + "libnetcfg": 1688, + "libpng-config": 5856, + "libpng16-config": 5856, "libpypy-c.so": 1, "libpypy-c.so.debug": 1, "libpypy3-c.so.debug": 3, @@ -15197,7 +15237,7 @@ "liftofftools": 1, "liftover.awk": 1, "ligand": 1, - "lighter": 9, + "lighter": 10, "lightning_predict": 2, "lightning_train": 2, "lighttpd": 2, @@ -15224,16 +15264,16 @@ "linguist-qt4": 3, "linguist6": 1, "linguistic_sequence_complexity.py": 1, - "link": 82, + "link": 83, "link_bin_sequences.py": 1, "link_ssv.py": 1, "linkage2allegro": 1, "linkhsp_unit_test": 5, - "linkicc": 979, + "linkicc": 980, "linknets": 2, "links2sql.pl": 7, - "linksBed": 269, - "linsi": 98, + "linksBed": 271, + "linsi": 100, "linux32": 13, "linux64": 13, "linx": 1, @@ -15244,7 +15284,7 @@ "lissero": 1, "list-linked-contigs": 2, "list-products": 1, - "list.modules": 19, + "list.modules": 20, "list2mapper.pl": 1, "listAllGenomesInDirectory.py": 1, "listGCContent": 2, @@ -15352,7 +15392,7 @@ "llvm-undname": 3, "llvm-windres": 1, "llvm-xray": 5, - "ln": 82, + "ln": 83, "lncrna": 1, "lndir": 1, "lneato": 4, @@ -15428,7 +15468,7 @@ "logging_utils.py": 1, "logistic_regression": 1, "loglog.sh": 30, - "logname": 82, + "logname": 83, "long-orfs": 2, "long-to-linked-pe": 2, "longQC.py": 1, @@ -15484,7 +15524,7 @@ "lrzip": 9, "lrztar": 9, "lrzuntar": 9, - "ls": 81, + "ls": 82, "lsblk": 13, "lscpu": 13, "lsd": 1, @@ -15497,8 +15537,8 @@ "lsmem": 13, "lsns": 13, "lss3": 29, - "lstopo": 61, - "lstopo-no-graphics": 61, + "lstopo": 63, + "lstopo-no-graphics": 63, "ltqnorm.pl": 1, "ltqnorm.pl.bak": 1, "ltr_finder": 3, @@ -15529,26 +15569,26 @@ "lut_pdiffCI.dat": 4, "lut_pdiffInRegion.dat": 4, "lwarpmk": 1, - "lwp-download": 193, - "lwp-dump": 193, - "lwp-mirror": 193, - "lwp-request": 193, + "lwp-download": 195, + "lwp-dump": 195, + "lwp-mirror": 195, + "lwp-request": 195, "lyner": 1, - "lz4": 3501, + "lz4": 3502, "lz4_decompress": 2, - "lz4c": 3500, - "lz4cat": 3500, - "lzcat": 7489, - "lzcmp": 7489, - "lzdiff": 7489, - "lzegrep": 7489, - "lzfgrep": 7489, - "lzgrep": 7489, - "lzless": 7489, - "lzma": 7489, - "lzmadec": 7489, - "lzmainfo": 7489, - "lzmore": 7489, + "lz4c": 3501, + "lz4cat": 3501, + "lzcat": 7496, + "lzcmp": 7496, + "lzdiff": 7496, + "lzegrep": 7496, + "lzfgrep": 7496, + "lzgrep": 7496, + "lzless": 7496, + "lzma": 7496, + "lzmadec": 7496, + "lzmainfo": 7496, + "lzmore": 7496, "lzop_build_offset_table.py": 59, "m-party": 1, "m-tx": 1, @@ -15666,22 +15706,22 @@ "maf_translate_chars.py": 59, "maf_truncate.py": 59, "maf_word_frequency.py": 59, - "mafft": 99, - "mafft-distance": 98, - "mafft-einsi": 98, - "mafft-fftns": 98, - "mafft-fftnsi": 98, - "mafft-ginsi": 98, - "mafft-homologs.rb": 98, - "mafft-linsi": 98, - "mafft-nwns": 98, - "mafft-nwnsi": 98, - "mafft-profile": 98, - "mafft-qinsi": 98, - "mafft-sparsecore.rb": 96, - "mafft-xinsi": 98, + "mafft": 101, + "mafft-distance": 100, + "mafft-einsi": 100, + "mafft-fftns": 100, + "mafft-fftnsi": 100, + "mafft-ginsi": 100, + "mafft-homologs.rb": 100, + "mafft-linsi": 100, + "mafft-nwns": 100, + "mafft-nwnsi": 100, + "mafft-profile": 100, + "mafft-qinsi": 100, + "mafft-sparsecore.rb": 98, + "mafft-xinsi": 100, "mafft.yaml": 1, - "mag-improve": 35, + "mag-improve": 36, "mag2gfa": 1, "magcluster": 1, "mageck": 1, @@ -15709,7 +15749,7 @@ "main_html_generator.py": 1, "makblk.pl": 4, "makdbs": 4, - "make": 4136, + "make": 4138, "make-barcodes.awk": 1, "make-cluster.R": 1, "make-conf": 1, @@ -15842,7 +15882,7 @@ "make_pp_rst_file.py": 1, "make_prefs_file.py": 1, "make_prg": 2, - "make_pscores.pl": 16, + "make_pscores.pl": 18, "make_qiime_py_file.py": 1, "make_rarefaction_plots.py": 1, "make_rejoin_links.pl": 1, @@ -15859,27 +15899,27 @@ "makeagp2.awk": 1, "makeagp_full.awk": 1, "makeagp_full2.awk": 1, - "makeblastdb": 323, + "makeblastdb": 328, "makecert": 15, "makechimeras.sh": 30, "makeclusterdb": 4, "makecontaminatedgenomes.sh": 30, - "makeconv": 5801, + "makeconv": 5805, "makedtx": 1, "makefasta.awk": 1, "makegeo": 35, "makeglossaries": 1, "makeglossaries-lite": 1, - "makehmmerdb": 174, + "makehmmerdb": 175, "makeidx.pl": 4, - "makemat": 30, - "makembindex": 321, + "makemat": 32, + "makembindex": 326, "makenucseq": 24, "makepBAM_genome.sh": 1, "makepBAM_transcriptome.sh": 1, "makeplot.pl": 3, "makepolymers.sh": 30, - "makeprofiledb": 321, + "makeprofiledb": 326, "makeprotseq": 24, "maker": 1, "maker2chado": 1, @@ -15923,11 +15963,12 @@ "manualcompile.sh": 1, "map": 57, "map-fastq.pl": 5, + "map.py": 1, "map2assembly": 1, "map2bed.pl": 2, "map2gtf": 3, "map2slim": 1, - "mapBed": 269, + "mapBed": 271, "mapCounter": 1, "mapDIA": 1, "mapDamage": 2, @@ -15977,8 +16018,8 @@ "mapula": 1, "mapview": 44, "mapviewToBed.pl": 1, - "maq2sam-long": 504, - "maq2sam-short": 504, + "maq2sam-long": 507, + "maq2sam-short": 507, "mareymaps_untrimmed.smk": 1, "marge": 1, "margin_cons": 2, @@ -15990,8 +16031,8 @@ "mark_partial_genes.py": 2, "mark_productivity": 1, "mark_prophage_features.py": 2, - "markdown-it": 45, - "markdown_py": 118, + "markdown-it": 46, + "markdown_py": 119, "markdups": 1, "markermagu": 1, "marko": 1, @@ -16002,7 +16043,7 @@ "marvel_prokka": 1, "mascot_search.rb": 1, "mascot_to_pepxml.rb": 1, - "mash": 56, + "mash": 57, "mash_screener.sh": 1, "mashclust.py": 1, "mashmap": 1, @@ -16016,7 +16057,7 @@ "mask-ali.pl": 1, "mask-consensus.py": 2, "maskAlignedReads.py": 1, - "maskFastaFromBed": 269, + "maskFastaFromBed": 271, "maskFile.pl": 10, "maskNregions.pl": 14, "mask_and_chain.smk": 1, @@ -16065,7 +16106,7 @@ "mateclever": 2, "mateclever-compute-rois": 2, "math_utils.py": 1, - "mathjax-path": 10, + "mathjax-path": 11, "mathspic": 1, "matplotlib": 10, "matrix-scan-quick": 1, @@ -16192,7 +16233,7 @@ "mclcm": 23, "mclpipeline": 23, "mcmc_gtb.py": 1, - "mcmctree": 65, + "mcmctree": 67, "mcomp": 4, "mconfig": 15, "mcookie": 13, @@ -16217,9 +16258,9 @@ "md5cp.2.11.0": 10, "md5cp.3": 2, "md5cp.3.0.0": 2, - "md5fa": 504, - "md5sum": 82, - "md5sum-lite": 504, + "md5fa": 507, + "md5sum": 83, + "md5sum-lite": 507, "md_coords": 11, "mdasim": 1, "mdassembler": 15, @@ -16307,17 +16348,17 @@ "mega_reads_assemble_cluster2.sh": 1, "mega_reads_assemble_polish.sh": 1, "mega_reads_assemble_ref.sh": 1, - "megablast": 30, + "megablast": 32, "megadepth": 1, "megagta": 1, "megagta.py": 1, - "megahit": 20, + "megahit": 21, "megahit_asm_core": 1, - "megahit_core": 19, - "megahit_core_no_hw_accel": 19, - "megahit_core_popcnt": 19, + "megahit_core": 20, + "megahit_core_no_hw_accel": 20, + "megahit_core_popcnt": 20, "megahit_sdbg_build": 1, - "megahit_toolkit": 20, + "megahit_toolkit": 21, "megalodon": 1, "megalodon_extras": 1, "megamerger": 24, @@ -16391,7 +16432,7 @@ "merge.py": 1, "merge2Dbed.pl": 5, "mergeBamWithSameSM.pl": 1, - "mergeBed": 269, + "mergeBed": 271, "mergeBreakpoints.py": 1, "mergeCharges.pl": 2, "mergeCounts": 3, @@ -16567,8 +16608,8 @@ "metaprokka": 1, "metaquant": 1, "metaquantome": 1, - "metaquast": 10, - "metaquast.py": 10, + "metaquast": 11, + "metaquast.py": 11, "metar_compare": 1, "metar_copy": 1, "metar_dump": 1, @@ -16576,7 +16617,7 @@ "metar_get": 1, "metar_ls": 1, "metaseq-cli": 1, - "metaspades.py": 46, + "metaspades.py": 47, "metatree": 1, "metatwist": 6, "metaviralspades.py": 10, @@ -16636,6 +16677,7 @@ "mgcod.py": 1, "mge_cluster": 1, "mgf-formatter": 1, + "mgikit": 1, "mglbabel": 1, "mglenv.csh": 2, "mglenv.sh": 2, @@ -16728,7 +16770,7 @@ "minigzip": 2, "minimap": 1, "minimap-lite": 1, - "minimap2": 160, + "minimap2": 162, "minimap2-coverage": 2, "minimap2.py": 26, "minimap2_genome": 1, @@ -16804,10 +16846,10 @@ "mkbitmap": 2, "mkbundle": 15, "mkbwt": 2, - "mkdir": 82, + "mkdir": 83, "mkdna6idx": 3, "mkfake": 1, - "mkfifo": 82, + "mkfifo": 83, "mkfmi": 2, "mkgraticule.py": 4, "mkgrkindex": 1, @@ -16816,7 +16858,7 @@ "mkjobtexmf": 1, "mklml.dll": 1, "mkmapfile": 57, - "mknod": 82, + "mknod": 83, "mkocp": 1, "mkoctfile": 1, "mkoctfile-4.2.1": 1, @@ -16830,7 +16872,7 @@ "mkselect": 1, "mksquashfs": 3, "mkt1font": 1, - "mktemp": 82, + "mktemp": 83, "mktexfmt": 1, "mktexlsr": 1, "mktexmf": 1, @@ -16845,8 +16887,13 @@ "mloc2stockholm.pl": 1, "mlocarna": 4, "mlocarna_nnames": 4, - "mlst": 7, + "mlst": 9, + "mlst-ST_mini_genomes": 2, "mlst-blast.py": 1, + "mlst-consistency_checker": 2, + "mlst-download_pub_mlst": 2, + "mlst-make_blast_db": 2, + "mlst-show_seqs": 2, "mlst.py": 2, "mlst_download_functions.jl": 2, "mltree": 1, @@ -16862,7 +16909,8 @@ "mmpbsa_py_energy": 6, "mmpbsa_py_nabnmode": 6, "mmquant": 1, - "mmseqs": 41, + "mmseqs": 42, + "mmseqs-server": 1, "mmseqs2.sh": 1, "mmvc": 1, "moabs": 4, @@ -16872,7 +16920,7 @@ "mob_typer": 1, "mobster": 1, "mobster-to-vcf": 1, - "mobsuiteRepresentativeFasta.pl": 1, + "mobsuiteRepresentativeFasta.pl": 2, "moc": 245, "moc-qt4": 3, "moca": 1, @@ -16890,6 +16938,7 @@ "model.r.bak": 1, "model_P": 1, "model_datasets_concatenator.py": 1, + "model_manager.py": 1, "model_postpro.py": 1, "modeltest-ng": 5, "modeltest-ng-mpi": 2, @@ -17063,24 +17112,24 @@ "mseqtools": 1, "msformatter": 1, "msfragger": 2, - "msgattrib": 5275, - "msgcat": 5275, - "msgcmp": 5275, - "msgcomm": 5275, - "msgconv": 5275, - "msgen": 5275, - "msgexec": 5275, + "msgattrib": 5281, + "msgcat": 5281, + "msgcmp": 5281, + "msgcomm": 5281, + "msgconv": 5281, + "msgen": 5281, + "msgexec": 5281, "msgf2pin": 1, "msgf_plus": 3, - "msgfilter": 5275, - "msgfmt": 5275, + "msgfilter": 5281, + "msgfmt": 5281, "msgfplus_search.rb": 1, - "msggrep": 5275, - "msginit": 5275, - "msgmerge": 5275, + "msggrep": 5281, + "msginit": 5281, + "msgmerge": 5281, "msgserv": 1, - "msgunfmt": 5275, - "msguniq": 5275, + "msgunfmt": 5281, + "msguniq": 5281, "msi": 1, "msi_cluster2reads": 1, "msi_clustr2map.pl": 1, @@ -17153,10 +17202,10 @@ "mult-mix-lwt": 1, "multi-bin-packing": 2, "multi-extract": 2, - "multiBamCov": 269, + "multiBamCov": 271, "multiBamSummary": 11, "multiBigwigSummary": 11, - "multiIntersectBed": 269, + "multiIntersectBed": 271, "multiSub": 1, "multi_length_hist.py": 1, "multi_parallel_pick_otus.py": 1, @@ -17189,7 +17238,7 @@ "multiple_split_libraries_fastq.py": 1, "multiple_testing_adjustment.py": 2, "multiprocess_mgcod.py": 1, - "multiqc": 16, + "multiqc": 17, "multivcfanalyzer": 1, "multiz": 1, "mummer": 57, @@ -17197,7 +17246,7 @@ "mummerplot": 57, "munge_sumstats.py": 1, "mupbwt": 1, - "muscle": 66, + "muscle": 68, "musixflx": 1, "musixtex": 1, "muspinsim": 1, @@ -17217,7 +17266,7 @@ "mutselomega": 1, "mutserve.jar": 1, "muxbyname.sh": 30, - "mv": 82, + "mv": 83, "mvicuna": 2, "mvirs": 1, "mvp": 1, @@ -17371,9 +17420,9 @@ "ncrf_to_bed": 2, "ncrf_to_bed.py": 2, "ncurses5-config": 565, - "ncurses6-config": 6957, + "ncurses6-config": 6965, "ncursesw5-config": 703, - "ncursesw6-config": 6958, + "ncursesw6-config": 6966, "ndg_httpclient": 2, "ndisasm": 1, "ndmetis": 58, @@ -17463,7 +17512,7 @@ "nf-test": 1, "nfe-umbrella-slice": 6, "ngd": 9, - "ngettext": 5275, + "ngettext": 5281, "ngg_barabasi_albert": 2, "ngg_barbell": 2, "ngg_complete": 2, @@ -17473,9 +17522,9 @@ "ngg_newman_watts_strogatz": 2, "ngg_path": 2, "ngg_ring_lattice": 2, - "nghttp": 4443, - "nghttpd": 4443, - "nghttpx": 4443, + "nghttp": 4449, + "nghttpd": 4449, + "nghttpx": 4449, "ngless": 2, "ngless-wrapped": 1, "nglview": 2, @@ -17509,9 +17558,9 @@ "ngsngs": 1, "ngsplotdb.py": 5, "ngsutils": 1, - "nhance.sh": 13, - "nhmmer": 174, - "nhmmscan": 174, + "nhance.sh": 18, + "nhmmer": 175, + "nhmmscan": 175, "nib-conform": 2, "nib-convert": 1, "nib-dicomfs": 3, @@ -17527,15 +17576,15 @@ "nib_chrom_intervals_to_fasta.py": 59, "nib_intervals_to_fasta.py": 59, "nib_length.py": 59, - "nice": 82, - "niceload": 99, + "nice": 83, + "niceload": 102, "nighthawk": 1, "nii2dcm": 1, "nimblegen2adf.pl": 1, "nimnexus": 1, "ninety_five_percent.py": 1, "ninja": 34, - "nl": 82, + "nl": 83, "nl-addr-add": 9, "nl-addr-delete": 9, "nl-addr-list": 9, @@ -17590,7 +17639,7 @@ "nohead": 5, "nohtml": 24, "nohuman": 1, - "nohup": 82, + "nohup": 83, "noise2read": 1, "nolb_nma": 1, "noncoding-trainer.pl": 2, @@ -17616,7 +17665,7 @@ "normalize_multicov.pl": 1, "normalize_oneD.R": 1, "normalize_table.py": 1, - "normalizer": 455, + "normalizer": 457, "normandcorrectwrapper.sh": 1, "nose2": 1, "nose2-2.7": 1, @@ -17634,7 +17683,7 @@ "noveliso.py": 1, "novo2maq": 1, "novo2paf": 2, - "novo2sam.pl": 505, + "novo2sam.pl": 508, "novoBreak": 1, "novoalign": 2, "novoalign-license-register": 2, @@ -17654,18 +17703,18 @@ "np-likeness": 1, "npinv": 1, "npm": 16, - "nproc": 82, + "nproc": 83, "npth-config": 2, "npx": 15, - "nquire": 289, + "nquire": 294, "nquire.bak": 1, "nrForwardSplicedReads.pl": 1, "nr_ORFs_gff3.pl": 5, "nrex": 1, "nseg": 5, "nsenter": 8, - "nspr-config": 167, - "nss-config": 167, + "nspr-config": 168, + "nss-config": 168, "ntJoin": 2, "ntLink": 3, "ntLink_rounds": 3, @@ -17698,7 +17747,7 @@ "ntsynt_run.py": 1, "ntsynt_run_pipeline.smk": 1, "ntsynt_synteny.py": 1, - "nucBed": 269, + "nucBed": 271, "nucamino": 1, "nucdiff": 1, "nucfreqsfasta": 1, @@ -17718,7 +17767,7 @@ "numCI": 4, "numba": 132, "number-lines": 1, - "numfmt": 82, + "numfmt": 83, "numlines": 1, "nunit-console": 10, "nunit-console2": 10, @@ -17748,8 +17797,8 @@ "nw_topology": 2, "nw_trim": 2, "nwalign3": 1, - "nwns": 98, - "nwnsi": 98, + "nwns": 100, + "nwnsi": 100, "nxtrim": 2, "o-bars-for-each-column.R": 1, "o-boxplots.R": 1, @@ -17912,7 +17961,7 @@ "octave-config": 1, "octave-config-4.2.1": 1, "octopus": 1, - "od": 82, + "od": 83, "odamnet": 1, "odbc_config": 1, "odbcinst": 1, @@ -17968,7 +18017,7 @@ "oncotator": 1, "one_field_per_line.py": 59, "onehot2seq": 1, - "onig-config": 300, + "onig-config": 301, "onnxruntime_test": 3, "ontime": 1, "ontocount": 24, @@ -17999,11 +18048,11 @@ "openslide-quickhash1sum": 2, "openslide-show-properties": 2, "openslide-write-png": 2, - "openssl": 7733, + "openssl": 7741, "opentargets_validator": 1, - "opj_compress": 633, - "opj_decompress": 633, - "opj_dump": 633, + "opj_compress": 634, + "opj_decompress": 634, + "opj_dump": 634, "opl2ofm": 1, "opsin": 1, "opt": 6, @@ -18194,13 +18243,13 @@ "paf2chain.awk": 1, "paf2gfa": 1, "paf_to_CARNAC.py": 1, - "paftools.js": 159, + "paftools.js": 161, "pager": 1, "painter.py": 20, "pair2tb": 1, "pairDiscordants.py": 1, - "pairToBed": 269, - "pairToPair": 269, + "pairToBed": 271, + "pairToPair": 271, "pair_sequences": 1, "pairalign": 2, "pairaln": 1, @@ -18215,14 +18264,14 @@ "pairtools": 3, "pairwise_comparison": 1, "pal2nal.pl": 7, - "pal2rgb": 5293, + "pal2rgb": 5294, "pal_finder": 1, "paladin": 2, "palindrome": 24, "paltohdf": 122, "pam": 1, "pamon": 40, - "pamp": 65, + "pamp": 67, "panISa.py": 1, "panX.py": 1, "pan_genome_assembly_statistics": 7, @@ -18263,10 +18312,10 @@ "panfeed-get-kmers": 1, "panfeed-plot": 1, "pangenome_variants_to_treeWAS.pl": 1, - "pango-list": 3995, + "pango-list": 3996, "pango-querymodules": 10, - "pango-segmentation": 2821, - "pango-view": 4798, + "pango-segmentation": 2822, + "pango-view": 4799, "pangoLEARN": 1, "pango_designation": 1, "pangolearn.smk": 1, @@ -18301,7 +18350,7 @@ "paragone": 1, "paragraph": 1, "paragraph2dot.py": 1, - "parallel": 100, + "parallel": 103, "parallel-fasta": 11, "parallel-fastq": 11, "parallel-fastq-dump": 1, @@ -18342,7 +18391,7 @@ "paraphase": 1, "parascopy": 1, "paraview-config": 1, - "parcat": 99, + "parcat": 102, "parebrick": 1, "parebrick-charts": 1, "parec": 40, @@ -18394,12 +18443,12 @@ "parse_typhi_mykrobe.py": 1, "parsec": 1, "parsecasm": 2, - "parset": 99, + "parset": 102, "parseval": 1, "parsimplify": 1, "parsing_functions.py": 1, "parsnp": 2, - "parsort": 83, + "parsort": 86, "partial_least_squares.py": 2, "partition": 6, "partition-graph.py": 7, @@ -18415,7 +18464,7 @@ "pash3.0.rb": 1, "pashToLff.rb": 1, "pass": 1, - "paste": 82, + "paste": 83, "pasteseq": 24, "pasteurize": 234, "pastml": 1, @@ -18431,7 +18480,7 @@ "patgen": 1, "path-graph": 1, "path_decompose_sparse.py": 1, - "pathchk": 82, + "pathchk": 83, "patholive": 1, "pathos_connect": 7, "pathoscope": 2, @@ -18507,14 +18556,14 @@ "pcnt_bezier.lua": 1, "pcoaPlot.py": 2, "pcor": 1, - "pcre-config": 4932, - "pcre2-config": 3692, - "pcre2_jit_test": 3678, - "pcre2grep": 3692, + "pcre-config": 4937, + "pcre2-config": 3694, + "pcre2_jit_test": 3679, + "pcre2grep": 3694, "pcre2posix_test": 113, - "pcre2test": 3692, - "pcregrep": 4932, - "pcretest": 4932, + "pcre2test": 3694, + "pcregrep": 4937, + "pcretest": 4937, "pct2rgb.py": 4, "pctid_ani_sample": 1, "pcz_animate": 1, @@ -18712,7 +18761,7 @@ "perf": 1, "perfect-square": 2, "perform_controls.pl": 1, - "perl": 1681, + "perl": 1688, "perl-doc": 2, "perl-reversion": 9, "perl5.22.0": 55, @@ -18720,12 +18769,12 @@ "perl5.26.2": 369, "perl5.30.3": 5, "perl5.32.0": 64, - "perl5.32.1": 1188, - "perlbug": 1681, - "perldoc": 1681, - "perlivp": 1681, + "perl5.32.1": 1195, + "perlbug": 1688, + "perldoc": 1688, + "perlivp": 1688, "perltex": 1, - "perlthanks": 1681, + "perlthanks": 1688, "permuteGPAT++": 31, "permuteSmooth": 31, "permute_structure.pl": 1, @@ -18850,7 +18899,7 @@ "phist.py": 1, "phizz": 1, "phmm": 4, - "phmmer": 174, + "phmmer": 175, "phold": 1, "phonopy": 1, "phonopy-FHI-aims": 1, @@ -18866,7 +18915,7 @@ "phonopy-vasp-born": 1, "phonopy-vasp-efe": 1, "photo": 2, - "phrase-search": 287, + "phrase-search": 292, "phsolverserver": 3, "phy2nex": 1, "phykit": 1, @@ -19060,7 +19109,7 @@ "pickle_cat.py": 1, "pickorientation.awk": 1, "pickout": 1, - "piconv": 1681, + "piconv": 1688, "picopore": 1, "picopore-realtime": 1, "picopore-rename": 1, @@ -19068,7 +19117,7 @@ "picrust2_pipeline.py": 1, "pidof": 1, "pigeon": 1, - "pigz": 116, + "pigz": 117, "pilconvert.py": 23, "pildriver.py": 23, "pilercr": 7, @@ -19086,23 +19135,23 @@ "pileups_to_freq_table.py": 1, "pilfile.py": 23, "pilfont.py": 23, - "pilon": 17, + "pilon": 18, "pilprint.py": 23, "pin_hic": 1, "pin_hic_it": 1, "pindel": 1, "pindel2vcf": 1, "pindel2vcf4tcga": 1, - "pinky": 82, + "pinky": 83, "pint-convert": 4, "pints_boundary_extender": 1, "pints_caller": 1, "pints_normalizer": 1, "pints_visualizer": 1, - "pip": 3632, + "pip": 3638, "pip2": 1, "pip2.7": 1, - "pip3": 2557, + "pip3": 2563, "pipdeptree": 1, "pipelign": 1, "pipeline.py": 2, @@ -19141,7 +19190,7 @@ "pizzly_flatten_json.py.bak": 1, "pizzly_get_fragment_length.py": 1, "pizzly_get_fragment_length.py.bak": 1, - "pk12util": 167, + "pk12util": 168, "pk_al": 1, "pk_alignment_length": 1, "pk_alignment_length_no_gaps": 1, @@ -19255,13 +19304,13 @@ "pkfix-helper": 1, "pkg-config": 76, "pkg-config.bin": 76, - "pkgdata": 5801, + "pkgdata": 5805, "pkginfo": 10, "pkill": 1, "pktogf": 1, "pktype": 1, - "pl2bat.pl": 3, - "pl2pm": 1681, + "pl2bat.pl": 4, + "pl2pm": 1688, "plaScope.sh": 1, "plac_runner.py": 60, "place_orient1.smk": 1, @@ -19278,7 +19327,7 @@ "plasmidID": 1, "plasmidfinder.py": 1, "plasmidhawk": 1, - "plasmidspades.py": 46, + "plasmidspades.py": 47, "plasmidtron": 1, "plass": 1, "plassembler.py": 1, @@ -19296,8 +19345,8 @@ "plip": 1, "plncpro": 1, "plncpro_format_ff.sh": 1, - "plot-ampliconstats": 309, - "plot-bamstats": 504, + "plot-ampliconstats": 312, + "plot-bamstats": 507, "plot-bmprobs": 4, "plot-cnv": 1, "plot-insert-size-distribution": 2, @@ -19424,11 +19473,11 @@ "pm4ngs-rnaseq-demo": 1, "pm4ngs-server": 1, "pm_which": 2, - "pma2apa": 13, - "pma2pme": 13, + "pma2apa": 18, + "pma2pme": 18, "pmap": 1, - "pmc2bioc": 13, - "pmc2info": 13, + "pmc2bioc": 18, + "pmc2info": 18, "pmd": 1, "pmdtools": 1, "pmemd_mdrun": 1, @@ -19454,21 +19503,21 @@ "pmxmutate": 1, "pn2pdf": 1, "pneumo-typer": 1, - "png-fix-itxt": 5854, + "png-fix-itxt": 5856, "pngcp": 89, - "pngfix": 5854, - "pngtogd": 232, - "pngtogd2": 232, + "pngfix": 5856, + "pngtogd": 233, + "pngtogd2": 233, "pnps-gen": 1, - "poa": 17, + "poa": 19, "pocheck": 1, "poclcc": 3, - "pod2html": 1681, - "pod2man": 1681, - "pod2text": 1681, - "pod2usage": 1681, + "pod2html": 1688, + "pod2man": 1688, + "pod2text": 1688, + "pod2usage": 1688, "pod_cover": 12, - "podchecker": 1681, + "podchecker": 1688, "podselect": 438, "poetry": 6, "pointwise_datasets_concatenator.py": 1, @@ -19514,7 +19563,7 @@ "poppunk_sketch": 1, "poppunk_visualise": 1, "popscle": 1, - "popt": 48, + "popt": 50, "populations": 1, "pore_c": 1, "porechop": 12, @@ -19566,7 +19615,7 @@ "ppi2html": 2, "pplacer": 21, "ppltotf": 1, - "ppm2tiff": 5293, + "ppm2tiff": 5294, "pprodigal": 1, "pprof": 2, "pprof-symbolize": 1, @@ -19577,7 +19626,7 @@ "pqresolve": 1, "pqsplits": 1, "pqstat": 1, - "pr": 82, + "pr": 83, "prank": 16, "pre.py": 1, "preTA": 2, @@ -19694,7 +19743,7 @@ "prinseq-graphs-noPCA.pl": 3, "prinseq-graphs.pl": 3, "prinseq-lite.pl": 3, - "print-columns": 201, + "print-columns": 206, "print.pl": 1, "printIcounts": 1, "printScaff": 2, @@ -19708,8 +19757,8 @@ "print_qiime_config.py": 1, "print_unique": 1, "printafm": 104, - "printenv": 82, - "printf": 82, + "printenv": 83, + "printf": 83, "printimage": 3, "prints2prfl.pl": 14, "printsextract": 24, @@ -19766,7 +19815,7 @@ "processhi-c.sh": 29, "processspeed.sh": 30, "proda": 1, - "prodigal": 114, + "prodigal": 116, "prodigal-gv": 3, "prodigal.py": 1, "prodigal_stuff.py": 1, @@ -19787,7 +19836,7 @@ "project.sh.orig": 1, "projectAndStrip": 4, "projectFeatures": 3, - "project_tree_builder": 321, + "project_tree_builder": 326, "projinfo": 38, "projsync": 35, "prokka": 23, @@ -19931,7 +19980,7 @@ "protxml_to_table.rb": 1, "prov-compare": 9, "prov-convert": 9, - "prove": 1681, + "prove": 1688, "provean": 1, "provean.sh": 1, "provis": 1, @@ -19975,10 +20024,10 @@ "psiCalculator.py": 1, "psiPerGene.py": 1, "psibl2seq_unit_test": 5, - "psiblast": 321, + "psiblast": 326, "psiblast_iteration_unit_test": 5, "psiblast_unit_test": 5, - "psicc": 979, + "psicc": 980, "psiclass": 1, "psiphi": 24, "psite": 3, @@ -19988,7 +20037,7 @@ "psl2bed-float128": 14, "psl2bed-megarow": 14, "psl2bed-typical": 14, - "psl2sam.pl": 504, + "psl2sam.pl": 507, "psl2starch": 14, "psl2starch-float128": 14, "psl2starch-megarow": 14, @@ -20033,9 +20082,9 @@ "pt2to3": 74, "ptGAUL.sh": 1, "ptangle": 1, - "ptar": 1681, - "ptardiff": 1681, - "ptargrep": 1681, + "ptar": 1688, + "ptardiff": 1688, + "ptargrep": 1688, "ptdump": 74, "ptest": 1, "ptex": 1, @@ -20048,7 +20097,7 @@ "ptrepack": 74, "ptrimmer": 1, "pttree": 74, - "ptx": 82, + "ptx": 83, "publish.py": 2, "pubmlst_download": 1, "pubmlst_list": 1, @@ -20084,7 +20133,7 @@ "pvserver": 1, "pwatcher-main": 2, "pwatcher-pypeflow-example": 2, - "pwd": 82, + "pwd": 83, "pwdx": 1, "pweave": 1, "pweave-convert": 1, @@ -20211,16 +20260,16 @@ "pydamage": 1, "pydemult": 1, "pydicom": 1, - "pydoc": 3631, - "pydoc3": 3300, - "pydoc3.10": 802, + "pydoc": 3637, + "pydoc3": 3306, + "pydoc3.10": 805, "pydoc3.11": 264, - "pydoc3.12": 175, + "pydoc3.12": 177, "pydoc3.4": 6, "pydoc3.5": 103, "pydoc3.6": 342, "pydoc3.7": 383, - "pydoc3.8": 574, + "pydoc3.8": 575, "pydoc3.9": 651, "pydownsampler": 1, "pyega3": 1, @@ -20236,12 +20285,12 @@ "pyflyte-execute": 1, "pyflyte-fast-execute": 1, "pyflyte-map-execute": 1, - "pyftmerge": 386, - "pyftsubset": 386, + "pyftmerge": 387, + "pyftsubset": 387, "pygal_gen.py": 2, "pygenetic_code": 1, "pygmentex": 1, - "pygmentize": 244, + "pygmentize": 245, "pygmes": 1, "pygrun": 1, "pygtail": 2, @@ -20339,8 +20388,8 @@ "pytest": 142, "pytest-benchmark": 1, "pythia8-config": 1, - "python": 3632, - "python-argcomplete-check-easy-install-script": 337, + "python": 3638, + "python-argcomplete-check-easy-install-script": 338, "python-argcomplete-tcsh": 191, "python-build": 2, "python-config": 332, @@ -20350,15 +20399,15 @@ "python2.5-config": 1, "python2.7": 331, "python2.7-config": 314, - "python3": 3301, - "python3-config": 3300, - "python3.1": 1241, - "python3.10": 802, - "python3.10-config": 802, + "python3": 3307, + "python3-config": 3306, + "python3.1": 1246, + "python3.10": 805, + "python3.10-config": 805, "python3.11": 264, "python3.11-config": 264, - "python3.12": 175, - "python3.12-config": 175, + "python3.12": 177, + "python3.12-config": 177, "python3.4": 6, "python3.4-config": 6, "python3.4m": 6, @@ -20375,8 +20424,8 @@ "python3.7-config": 383, "python3.7m": 383, "python3.7m-config": 383, - "python3.8": 574, - "python3.8-config": 574, + "python3.8": 575, + "python3.8-config": 575, "python3.9": 651, "python3.9-config": 651, "pythonsh": 2, @@ -20498,8 +20547,10 @@ "qs": 2, "qscores_from_summary": 1, "qscxmlc": 177, - "qseq2fasta.pl": 2, - "qseq2fastq.pl": 7, + "qseq2fasta.pl": 3, + "qseq2fasta.pl.bak": 1, + "qseq2fastq.pl": 8, + "qseq2fastq.pl.bak": 1, "qsignature": 1, "qt.conf": 247, "qt3to4": 9, @@ -20526,7 +20577,7 @@ "qual-recalib-stat.3.0.0": 2, "qual_offset.py": 2, "qual_trim.py": 2, - "qualfa2fq.pl": 151, + "qualfa2fq.pl": 153, "qualimap": 3, "qualitativeEvaluation.py": 1, "qualityScores": 5, @@ -20545,12 +20596,12 @@ "quarto": 1, "quarto.js": 1, "quasirecomb": 1, - "quast": 10, - "quast-download-busco": 10, - "quast-download-gridss": 10, - "quast-download-silva": 10, - "quast-lg.py": 10, - "quast.py": 10, + "quast": 11, + "quast-download-busco": 11, + "quast-download-gridss": 11, + "quast-download-silva": 11, + "quast-lg.py": 11, + "quast.py": 11, "quastunmap.py": 1, "quatradis.smk": 1, "queen-armies": 2, @@ -20574,7 +20625,7 @@ "quorum": 4, "quorum_create_database": 4, "quorum_error_correct_reads": 4, - "quote-grouped-elements": 13, + "quote-grouped-elements": 18, "qv_to_bqv.py": 59, "qvality": 1, "qvalue": 13, @@ -20639,7 +20690,7 @@ "randRemoveBackground.pl": 5, "rand_sel_reads_from_bam": 1, "randfold": 3, - "randomBed": 269, + "randomBed": 271, "randomFQ": 1, "randomGeneSample": 4, "randomJunctionFilter": 1, @@ -20694,7 +20745,7 @@ "ratt": 2, "rav1e": 5, "raven": 4, - "raw2tiff": 5293, + "raw2tiff": 5294, "raw_n50": 10, "raw_n50.o": 10, "raw_vcf_parse.py": 1, @@ -20743,8 +20794,8 @@ "rcexplain.3.0.3": 1, "rcexplain.3.1.0": 1, "rcf": 1, - "rchive": 288, - "rchive.Linux": 288, + "rchive": 293, + "rchive.Linux": 293, "rchive.go": 14, "rcl": 1, "rcl-dot-resmap.pl": 1, @@ -20760,7 +20811,7 @@ "rdfgraphisomorphism": 32, "rdfpipe": 32, "rdfs2dot": 32, - "rdjpgcom": 5740, + "rdjpgcom": 5742, "rdkit2fps": 1, "rdma_client": 20, "rdma_server": 20, @@ -20788,10 +20839,13 @@ "readCountsMatrix": 1, "readGet.py": 1, "readItAndKeep": 1, + "readLibFiles.pl": 1, + "readLibFiles.pl.bak": 1, "readToMap.pl": 1, "read_GC.py": 3, "read_NVC.py": 3, "read_chromo_size": 1, + "read_classifier.py": 1, "read_distribution.py": 3, "read_duplication.py": 3, "read_fasta.py": 1, @@ -20799,6 +20853,7 @@ "read_file_names": 1, "read_grouping.py": 1, "read_hexamer.py": 3, + "read_length_quality_stats_fastq.py": 1, "read_merger.pl": 2, "read_nt_stuff.py": 1, "read_quality.py": 3, @@ -20810,7 +20865,7 @@ "readfq": 1, "readinfo2cam": 2, "readlength.sh": 30, - "readlink": 82, + "readlink": 83, "readme.pdf": 73, "readmutselomega": 1, "readnodemutsel": 1, @@ -20838,7 +20893,7 @@ "real_time_concatenator.py": 1, "realignPolishes": 3, "realignsamfile": 1, - "realpath": 82, + "realpath": 83, "realphy": 1, "reanalyzer": 1, "reaper": 1, @@ -20853,7 +20908,7 @@ "recgraph": 1, "reciprocal_blast_local": 1, "reciprocal_blast_local.py": 1, - "recode-sr-latin": 5275, + "recode-sr-latin": 5281, "recode_dir": 1, "recode_dir_legacy": 1, "recoder": 24, @@ -20899,7 +20954,7 @@ "ref-variation.3": 2, "ref-variation.3.0.3": 1, "ref-variation.3.1.0": 1, - "ref2pmid": 13, + "ref2pmid": 18, "refFinder": 1, "ref_map.pl": 1, "ref_seqs_from_bam": 1, @@ -20935,12 +20990,12 @@ "refresh-versioned": 1, "refseq-download": 1, "refseq-extract": 1, - "refseq-nm-cds": 13, + "refseq-nm-cds": 18, "refseq_masher": 1, "refseqget": 24, "refseqsplit.py": 2, "regenie": 1, - "register-python-argcomplete": 337, + "register-python-argcomplete": 338, "regression_neural_network": 1, "regression_predict": 1, "regtools": 1, @@ -21149,7 +21204,7 @@ "renumberRMFiles.pl": 3, "renumber_structure": 1, "reorder": 1, - "reorder-columns": 289, + "reorder-columns": 294, "reorder-fasta": 3, "reorder.smk": 1, "reorient_sequences_by_id.py": 2, @@ -21215,7 +21270,7 @@ "rescue_fusion.py": 1, "reseq": 1, "reseq-prepare-names.py": 1, - "reset": 7664, + "reset": 7672, "resetFragLibrary": 2, "reset_array.pl": 1, "reset_experiment.pl": 1, @@ -21320,7 +21375,7 @@ "ribotin-ref": 1, "ribotin-verkko": 1, "ribotish": 1, - "rich-click": 16, + "rich-click": 17, "riostream": 20, "ripcal": 1, "ripcal.bak": 1, @@ -21336,7 +21391,7 @@ "rism3d.thermo": 6, "ristosds": 122, "rls": 1, - "rm": 82, + "rm": 83, "rmOut2Fasta.pl": 14, "rmOutToGFF3.pl": 14, "rmRedundantHints.pl": 14, @@ -21355,10 +21410,10 @@ "rmapbs-pe": 1, "rmats2sashimiplot": 1, "rmblastn": 16, - "rmdir": 82, + "rmdir": 83, "rmic": 421, "rmid": 421, - "rmiregistry": 534, + "rmiregistry": 535, "rmkdepend": 1, "rmlst-api": 1, "rmsk2bed": 14, @@ -21392,8 +21447,9 @@ "rnaseq_peakfinder.pl": 1, "rnaseqc": 1, "rnasoup_consMFE.pl": 1, - "rnaspades.py": 46, + "rnaspades.py": 47, "rnaviralspades.py": 10, + "rnavirhost": 1, "rnazAnnotate.pl": 3, "rnazBEDsort.pl": 3, "rnazBEDstats.pl": 3, @@ -21477,9 +21533,9 @@ "rpkmforgenes.py": 1, "rppr": 17, "rps_unit_test": 5, - "rpsblast": 330, - "rpsbproc": 249, - "rpstblastn": 321, + "rpsblast": 335, + "rpsbproc": 254, + "rpstblastn": 326, "rqcfilter.sh": 30, "rqcfilter2.sh": 29, "rqw": 1, @@ -21551,8 +21607,8 @@ "rstream": 20, "rsv-typer": 1, "rsvg-convert": 165, - "rsync": 25, - "rsync-ssl": 23, + "rsync": 26, + "rsync-ssl": 24, "rtags": 1, "rtc_binner.py": 1, "rtg": 1, @@ -21579,7 +21635,7 @@ "run-htseq-workflow": 1, "run-mummer1": 44, "run-mummer3": 44, - "run-ncbi-converter": 288, + "run-ncbi-converter": 293, "run-ncbi-converter.bak": 1, "run-ntedit": 1, "run-roh.pl": 156, @@ -21782,7 +21838,7 @@ "run_vote.py": 1, "run_voteSpecies.py": 1, "run_vsclust_app.R": 1, - "run_with_lock": 311, + "run_with_lock": 316, "run_workflows.py": 1, "run_x_platform_fuzz_corpus": 37, "runabyss.py": 1, @@ -21791,7 +21847,7 @@ "runbatch": 2, "runbenders": 3, "runcabog.py": 1, - "runcon": 82, + "runcon": 83, "runef": 3, "runerrcor.py": 1, "rungs": 1, @@ -21911,7 +21967,7 @@ "sam2starch-float128": 14, "sam2starch-megarow": 14, "sam2starch-typical": 14, - "sam2vcf.pl": 504, + "sam2vcf.pl": 507, "samFLAGinfo.pl": 1, "samFilter": 1, "samMap.pl": 14, @@ -21919,6 +21975,8 @@ "samToDelta": 1, "sam_add_rg.pl": 16, "sam_addtag": 1, + "sam_bam2tab.pl": 1, + "sam_bam2tab.pl.bak": 1, "sam_compare_w_feature.py": 1, "sam_filter.py": 2, "sam_juncs": 3, @@ -21938,7 +21996,7 @@ "sambamba": 17, "samblaster": 4, "samcat": 2, - "samclip": 19, + "samclip": 20, "samcount": 2, "samcut": 1, "samestr": 1, @@ -21969,8 +22027,8 @@ "samtoh5": 1, "samtom4": 1, "samtom5_dir": 1, - "samtools": 529, - "samtools.pl": 504, + "samtools": 532, + "samtools.pl": 507, "samtools_0.1.18": 3, "samtools_mpileup_to_var": 1, "samtoroc.sh": 30, @@ -22006,6 +22064,8 @@ "sass": 1, "sat": 2, "satrap": 1, + "saute": 1, + "saute_prot": 1, "sav": 2, "sav2p_num": 1, "sav2plot": 1, @@ -22075,7 +22135,7 @@ "scaladoc.bat": 1, "scalap": 1, "scalap.bat": 1, - "scalar": 11, + "scalar": 12, "scale_columns": 1, "scallop-lr": 1, "scallop-umi": 1, @@ -22162,7 +22222,7 @@ "scitokens-test": 1, "scitokens-test-access": 1, "scitokens-verify": 1, - "sclient": 5775, + "sclient": 5781, "sclust_summary.sh": 1, "scluster": 3, "scmap-cli-post-install-tests.bats": 1, @@ -22181,7 +22241,7 @@ "scn-post-install-tests.sh": 1, "scn-predict.R": 1, "scn-train-model.R": 1, - "scn2xml": 13, + "scn2xml": 18, "scoary": 3, "scoary_GUI": 3, "scompare": 6, @@ -22268,7 +22328,7 @@ "sdsort": 2, "sdsplit": 2, "sdtether": 2, - "sdust": 146, + "sdust": 148, "sea": 2, "seagen": 3, "seal.sh": 30, @@ -22287,12 +22347,12 @@ "secondary2split.py": 1, "sectosupp": 1, "secutil": 15, - "sed": 3921, + "sed": 3922, "seealso": 24, "seedRand.py": 1, "seedme": 1, "seedme.py": 1, - "seedtop": 78, + "seedtop": 80, "seeker.pl": 1, "seer": 1, "segToGc": 1, @@ -22300,7 +22360,7 @@ "segalign": 1, "segalign_repeat_masker": 1, "segemehl.x": 1, - "segmasker": 321, + "segmasker": 326, "segment-cnv": 1, "segment.py": 1, "segmentFst": 31, @@ -22357,7 +22417,7 @@ "selene_sdk": 1, "selenium-manager": 1, "selscan": 1, - "sem": 99, + "sem": 102, "send2trash": 20, "sendsketch.sh": 30, "senergy": 6, @@ -22370,7 +22430,7 @@ "seperatePFMs.py": 1, "seperatePFMsAndCheckActivity.py": 1, "seppJsonMerger.jar": 4, - "seq": 82, + "seq": 83, "seq-gen": 3, "seq-seq-pan": 1, "seq-seq-pan-consensus": 1, @@ -22382,7 +22442,7 @@ "seq2onehot": 1, "seq2profile.pl": 5, "seq2science": 2, - "seq_cache_populate.pl": 504, + "seq_cache_populate.pl": 507, "seq_count": 2, "seq_diff": 1, "seq_download.py": 2, @@ -22427,7 +22487,7 @@ "seqstats": 1, "seqstr": 1, "seqtest": 1, - "seqtk": 53, + "seqtk": 54, "seqtk-trinity": 6, "seqtools.py": 1, "seqtovec.sh": 1, @@ -22455,7 +22515,7 @@ "seqxref": 24, "seqxrefget": 24, "seqyclean": 1, - "serialver": 534, + "serialver": 535, "seroba": 1, "serotypefinder": 1, "servertell": 24, @@ -22559,12 +22619,12 @@ "sgldwt.sh": 6, "sgt_constructor.py": 1, "sgt_constructor.smk": 1, - "sha1sum": 82, - "sha224sum": 82, + "sha1sum": 83, + "sha224sum": 83, "sha256_profile": 56, - "sha256sum": 82, - "sha384sum": 82, - "sha512sum": 82, + "sha256sum": 83, + "sha384sum": 83, + "sha512sum": 83, "shannon.py": 1, "shannon_cpp": 1, "shape-it": 1, @@ -22582,12 +22642,12 @@ "sharq.3": 2, "sharq.3.0.0": 2, "shasta": 1, - "shasum": 1681, + "shasum": 1688, "shed-tools": 2, "shell_utils.py": 1, "shiboken2": 2, "shiboken_tool.py": 2, - "shiftBed": 256, + "shiftBed": 258, "shigatyper": 1, "shigeifinder": 1, "shims.py": 1, @@ -22612,7 +22672,7 @@ "short_read_connector_linker.sh": 1, "shortenContigIDs.pl": 1, "shortuuid": 4, - "shovill": 6, + "shovill": 7, "shovill-se": 2, "show": 1, "show-aligns": 57, @@ -22633,17 +22693,17 @@ "showseq": 24, "showserver": 24, "showtable": 3, - "shred": 82, + "shred": 83, "shred.sh": 30, "shrink_bedgraph": 1, "shrink_db.pl": 1, "shrinkaccession.sh": 30, - "shuf": 82, + "shuf": 83, "shuffle": 4, "shuffle.sh": 30, "shuffle2.sh": 29, "shuffleBank": 2, - "shuffleBed": 269, + "shuffleBed": 271, "shuffleCodons.rb": 2, "shuffleCodonsAddMotifs.rb": 2, "shuffleSequences_fasta.pl": 1, @@ -22677,7 +22737,7 @@ "sim-cover2": 2, "sim-shotgun": 2, "sim4db": 3, - "sim_client": 5775, + "sim_client": 5781, "sim_reads": 10, "sim_reads.o": 10, "sim_reads_tran": 10, @@ -22784,7 +22844,7 @@ "skani": 4, "skc": 1, "skera": 1, - "skesa": 9, + "skesa": 10, "sketch.sh": 30, "sketchblacklist.sh": 30, "sketchblacklist2.sh": 27, @@ -22792,7 +22852,7 @@ "sketchy": 1, "skewer": 1, "skg_convert.py": 2, - "skip-if-file-exists": 258, + "skip-if-file-exists": 263, "skip_psl_self.awk": 2, "skip_psl_self_ss.awk": 2, "skip_selfmatches.py": 1, @@ -22807,7 +22867,7 @@ "slamdunk": 1, "slclust": 4, "sldout": 1, - "sleep": 82, + "sleep": 83, "slencheck": 1, "slice2py": 6, "slice_fasta": 1, @@ -22824,7 +22884,7 @@ "slivar": 1, "slncky": 2, "slncky.v1.0": 2, - "slopBed": 269, + "slopBed": 271, "slow5curl": 1, "slow5tools": 1, "slsh": 2, @@ -22865,6 +22925,33 @@ "smudgeplot.py": 2, "smudgeplot_plot.R": 2, "sn": 15, + "sn_SalmID.pl": 1, + "sn_assembleAll_reference.pl": 1, + "sn_assemblyWorkflow_init.pl": 1, + "sn_cleanup.pl": 1, + "sn_createSampleSheet.pl": 1, + "sn_crypto_assembleAll.pl": 1, + "sn_crypto_gp60.pl": 1, + "sn_detectContamination-kraken.pl": 1, + "sn_detectContamination-mlst.pl": 1, + "sn_detectContamination.pl": 1, + "sn_genotype.pl": 1, + "sn_genotype_escherichia.pl": 1, + "sn_helloWorld.pl": 1, + "sn_helloWorld.py": 1, + "sn_helloWorld.sh": 1, + "sn_immediateStatus.pl": 1, + "sn_iontorrent_assembleAll.pl": 1, + "sn_kraken-metagenomics.pl": 1, + "sn_kraken.pl": 1, + "sn_mlst-wg.pl": 1, + "sn_mlst.pl": 1, + "sn_parseSampleSheet.pl": 1, + "sn_passfail.pl": 1, + "sn_report.pl": 1, + "sn_sarscov2_assembleAll.pl": 1, + "sn_saveFailedGenomes.pl": 1, + "sn_staramr.pl": 1, "snakeSV": 1, "snakedeploy": 1, "snakefmt": 1, @@ -22915,8 +23002,8 @@ "snp-pileup": 2, "snp-pileup-quickbam": 1, "snp-sites": 13, - "snp2hgvs": 201, - "snp2tbl": 201, + "snp2hgvs": 206, + "snp2tbl": 206, "snpEff": 23, "snpEffAnnotate.py": 3, "snp_diversity.py": 1, @@ -22941,7 +23028,7 @@ "snver-pool": 1, "soap": 2, "soap.coverage": 2, - "soap2sam.pl": 504, + "soap2sam.pl": 507, "soapcpp2": 1, "soapsplice": 1, "soapsuds": 15, @@ -22980,7 +23067,7 @@ "sonnet_sat_bed.py": 1, "sonnet_sat_vcf.py": 1, "soprano_submitter": 2, - "sort": 82, + "sort": 83, "sort-bed": 14, "sort-bed-float128": 14, "sort-bed-megarow": 14, @@ -22989,11 +23076,11 @@ "sort-last-maf": 1, "sort-snos": 2, "sort-snos.pl": 2, - "sort-table": 201, - "sort-uniq-count": 289, - "sort-uniq-count-rank": 289, + "sort-table": 206, + "sort-uniq-count": 294, + "sort-uniq-count-rank": 294, "sort2": 2, - "sortBed": 269, + "sortBed": 271, "sortByRefAndCor.pl": 1, "sortGeneMark.py": 2, "sortHits": 4, @@ -23026,24 +23113,24 @@ "spacepharer": 1, "spacy": 1, "spades": 3, - "spades-bwa": 43, - "spades-convert-bin-to-fasta": 35, - "spades-core": 43, - "spades-corrector-core": 43, + "spades-bwa": 44, + "spades-convert-bin-to-fasta": 36, + "spades-core": 44, + "spades-corrector-core": 44, "spades-dipspades-core": 2, - "spades-gbuilder": 43, - "spades-gmapper": 43, - "spades-gsimplifier": 35, - "spades-hammer": 43, - "spades-ionhammer": 43, - "spades-kmer-estimating": 35, - "spades-kmercount": 43, - "spades-read-filter": 35, - "spades-truseq-scfcorrection": 43, - "spades.py": 46, + "spades-gbuilder": 44, + "spades-gmapper": 44, + "spades-gsimplifier": 36, + "spades-hammer": 44, + "spades-ionhammer": 44, + "spades-kmer-estimating": 36, + "spades-kmercount": 44, + "spades-read-filter": 36, + "spades-truseq-scfcorrection": 44, + "spades.py": 47, "spades_assembly.sh": 1, - "spades_init.py": 46, - "spaligner": 35, + "spades_init.py": 47, + "spaligner": 36, "spaln": 4, "spamo": 13, "spanner.pl": 1, @@ -23068,7 +23155,7 @@ "sparsetable_unittest": 1, "spatypes.txt": 1, "spdi2prod": 12, - "spdi2tbl": 201, + "spdi2tbl": 206, "specialk": 1, "spectra-cluster-cli": 1, "spectral_clustering": 1, @@ -23090,7 +23177,7 @@ "sphinx-quickstart": 40, "spine.pl": 1, "spinner.py": 1, - "splain": 1681, + "splain": 1688, "splash": 1, "splice_site_summary.pl": 1, "spliceai": 1, @@ -23098,8 +23185,8 @@ "spliced_bam2gff": 1, "splinter.pl": 1, "splinter_scaffolds.pl": 1, - "split": 82, - "split-at-intron": 201, + "split": 83, + "split-at-intron": 206, "split-bed12-blocks": 3, "split-coverages.py": 1, "split-fasta": 1, @@ -23224,11 +23311,11 @@ "sqStoreDumpMetaData": 6, "sqfscat": 1, "sqfstar": 1, - "sql": 99, + "sql": 102, "sqlformat": 9, "sqlite.pl": 1, - "sqlite3": 2709, - "sqlite3_analyzer": 7072, + "sqlite3": 2710, + "sqlite3_analyzer": 7078, "sqlitebrowser": 1, "sqlmetal": 15, "sqlsharp": 15, @@ -23370,6 +23457,7 @@ "sshd": 4, "sslm2sam": 1, "ssm": 1, + "sspace_basic": 1, "sstacks": 1, "sstofa": 14, "ssu": 2, @@ -23496,7 +23584,7 @@ "start_parallel_jobs_torque.py": 1, "start_tassel.pl": 1, "stash-pubmed": 1, - "stat": 82, + "stat": 83, "statSTR": 1, "statSpliceMap": 1, "stat_unit_test": 5, @@ -23515,7 +23603,7 @@ "stats_from_bam": 1, "stats_utils.py": 1, "statswrapper.sh": 30, - "stdbuf": 82, + "stdbuf": 83, "stecfinder": 1, "steel-mill": 2, "steiner": 2, @@ -23556,15 +23644,15 @@ "strainscan_build": 1, "stranger": 1, "stream": 76, - "stream-local": 13, - "stream-pubmed": 287, + "stream-local": 18, + "stream-pubmed": 292, "stream_atac": 1, "stream_run_test": 1, "streamer_1d": 22, "streamlit": 6, "streamlit.cmd": 6, "streamsam.sh": 30, - "streamzip": 1252, + "streamzip": 1259, "streme": 6, "streme_xml_to_html": 6, "stress-ng": 1, @@ -23603,7 +23691,7 @@ "structures.py": 2, "strudel": 1, "stssearch": 24, - "stty": 82, + "stty": 83, "stubgen": 2, "stubmaker.pl": 57, "stubtest": 2, @@ -23637,14 +23725,14 @@ "subsetdb": 2, "subsketch.sh": 29, "subtract-bed": 3, - "subtractBed": 269, + "subtractBed": 271, "subtractBedGraphs.pl": 5, "subtractBedGraphsDirectory.pl": 5, "sucos": 1, "sucos_max": 1, "sudoku": 2, "sudoku-advanced": 1, - "sum": 82, + "sum": 83, "sum_chr_mod.py": 1, "sum_prob.py": 1, "sumaclust": 3, @@ -23789,7 +23877,7 @@ "symilar": 11, "symmetric-cpgs": 1, "synapse": 2, - "sync": 82, + "sync": 83, "sync_files.py": 1, "sync_reads": 1, "synchain-mugsy": 1, @@ -23810,7 +23898,7 @@ "tRNAscan-SE": 14, "tRNAscan-SE.conf": 14, "tRNAscanChecker.py": 1, - "t_coffee": 66, + "t_coffee": 68, "t_coffee_run.py": 2, "ta2ace": 2, "tab-to-vcf": 10, @@ -23820,7 +23908,7 @@ "tab2krona.py": 1, "tab2mapper.pl": 1, "tab2ovls": 2, - "tabix": 696, + "tabix": 699, "tabix++": 23, "table2asn": 2, "table_add_column.py": 59, @@ -23829,13 +23917,13 @@ "tableproxy64": 1, "tableschema": 1, "tablet": 1, - "tabs": 7664, + "tabs": 7672, "tabulate": 128, "tabulate.py": 1, "tabulator": 1, "tabutils": 1, "tabview": 1, - "tac": 82, + "tac": 83, "taco_refcomp": 1, "taco_run": 1, "tad-plot": 2, @@ -23852,7 +23940,7 @@ "tag2bed.pl": 5, "tag2pos.pl": 5, "tag2sort": 1, - "tagBam": 269, + "tagBam": 271, "tagDir2HiCsummary.pl": 5, "tagDir2bed.pl": 5, "tagDir2hicFile.pl": 5, @@ -23861,7 +23949,7 @@ "tagore": 2, "tagrecon": 2, "tagsum-reduce": 2, - "tail": 82, + "tail": 83, "taipale2meme": 13, "tajimas_d": 1, "tal-AA.fa": 1, @@ -23922,7 +24010,7 @@ "tantan": 1, "tap": 1, "tap2": 1, - "tar": 54, + "tar": 55, "taranis.py": 1, "taranis_configuration.py": 1, "tarchive2amos": 2, @@ -23986,20 +24074,20 @@ "tba": 1, "tbl2asn": 29, "tbl2asn-test": 12, - "tbl2prod": 189, - "tbl2xml": 201, - "tblastn": 321, - "tblastn_vdb": 36, - "tblastx": 321, + "tbl2prod": 194, + "tbl2xml": 206, + "tblastn": 326, + "tblastn_vdb": 41, + "tblastx": 326, "tblite": 1, "tbox-scan": 1, "tbpore": 1, "tbtamr": 1, "tbvcfreport": 1, "tcdemux": 1, - "tclsh": 7309, + "tclsh": 7315, "tclsh8.5": 473, - "tclsh8.6": 7072, + "tclsh8.6": 7078, "tcode": 24, "tcsh": 3, "td_bignet": 2, @@ -24008,7 +24096,7 @@ "tease_maker_apart.py": 1, "teckit_compile": 1, "tedna": 1, - "tee": 82, + "tee": 83, "telescope": 1, "teloclip": 1, "teloclip-extract": 1, @@ -24032,16 +24120,16 @@ "termscu": 1, "terrace": 1, "tesseract": 2, - "test": 97, + "test": 98, "test-download": 2, "test-download.3": 2, "test-download.3.0.0": 2, - "test-edirect": 258, - "test-eutils": 287, + "test-edirect": 263, + "test-eutils": 292, "test-gzip": 1, "test-merStream": 5, - "test-pmc-index": 13, - "test-pubmed-index": 287, + "test-pmc-index": 18, + "test-pubmed-index": 292, "test-read-write-cursor": 2, "test-read-write-cursor.3": 2, "test-read-write-cursor.3.0.0": 2, @@ -24060,7 +24148,7 @@ "test-sra.3.1.0": 1, "test-yaml": 1, "test.mgcv.installed.R": 1, - "test.modules": 19, + "test.modules": 20, "test.o": 10, "test.pl": 1, "test.py": 2, @@ -24093,7 +24181,7 @@ "test_install.bak": 1, "test_miso": 1, "test_musicc.py": 2, - "test_pcre": 82, + "test_pcre": 87, "test_proton.bam": 1, "test_proton.bam.bai": 1, "test_regexp": 1, @@ -24196,7 +24284,7 @@ "thumbpdf": 1, "tiara": 2, "tiara-test": 2, - "tic": 7664, + "tic": 7672, "tiddit": 1, "tides": 1, "tidk": 1, @@ -24204,23 +24292,23 @@ "tidygff3": 1, "tidyp": 66, "tie": 1, - "tiff2bw": 5293, + "tiff2bw": 5294, "tiff2fsspec": 17, - "tiff2pdf": 5293, - "tiff2ps": 5293, - "tiff2rgba": 5293, - "tiffcmp": 5293, + "tiff2pdf": 5294, + "tiff2ps": 5294, + "tiff2rgba": 5294, + "tiffcmp": 5294, "tiffcomment": 19, - "tiffcp": 5492, - "tiffcrop": 5293, - "tiffdither": 5293, - "tiffdump": 5492, + "tiffcp": 5494, + "tiffcrop": 5294, + "tiffdither": 5294, + "tiffdump": 5494, "tifffile": 22, - "tiffinfo": 5492, - "tiffmedian": 5293, - "tiffset": 5492, - "tiffsplit": 5492, - "tificc": 979, + "tiffinfo": 5494, + "tiffmedian": 5294, + "tiffset": 5494, + "tiffsplit": 5494, + "tificc": 980, "tigStore": 3, "tiger-hash": 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"xz": 7721, + "xzcat": 7496, + "xzcmp": 7496, + "xzdec": 7496, + "xzdiff": 7496, + "xzegrep": 7496, + "xzfgrep": 7496, + "xzgrep": 7496, + "xzless": 7496, + "xzmore": 7496, "y2racc": 7, "yacc": 4, "yacht": 1, @@ -25886,7 +25977,7 @@ "yak": 2, "yaml2gff.1.4.pl": 14, "yaml2obj": 4, - "yaml2xml": 13, + "yaml2xml": 18, "yamllint": 1, "yamlpp5-events": 4, "yamlpp5-highlight": 4, @@ -25905,12 +25996,12 @@ "yasm": 1, "yass": 1, "yat2m": 30, - "yes": 82, - "yn00": 65, + "yes": 83, + "yn00": 67, "yoyo": 3, "yoyo-migrate": 3, "yplan": 1, - "yq": 289, + "yq": 290, "ytasm": 1, "yte": 58, "zagros": 1, @@ -25936,7 +26027,7 @@ "zipHomerResults.pl": 5, "zipcloak": 2, "zipcmp": 90, - "zipdetails": 1681, + "zipdetails": 1688, "zipgrep": 25, "zipinfo": 25, "zipmerge": 90, @@ -25951,7 +26042,7 @@ "znew": 18, "zol": 1, "zoom": 1, - "zoom2sam.pl": 504, + "zoom2sam.pl": 507, "zopfli": 22, "zopflipng": 22, "zorro": 1, @@ -25961,10 +26052,10 @@ "zrun": 3, "zsh": 3, "zsh-5.8": 3, - "zstd": 5167, - "zstdcat": 5167, - "zstdgrep": 4965, - "zstdless": 4965, - "zstdmt": 5167, + "zstd": 5173, + "zstdcat": 5173, + "zstdgrep": 4971, + "zstdless": 4971, + "zstdmt": 5173, "ztr_dump": 2 } \ No newline at end of file diff --git a/quay.io/biocontainers/c/colorid_bv:0.1.0--h4c94732_0.json b/quay.io/biocontainers/c/colorid_bv:0.1.0--h4c94732_0.json new file mode 100644 index 0000000..caf1a07 --- /dev/null +++ b/quay.io/biocontainers/c/colorid_bv:0.1.0--h4c94732_0.json @@ -0,0 +1,4 @@ +{ + "colorid_bv": "/usr/local/bin/colorid_bv", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/c/cured:1.05--hdfd78af_0.json b/quay.io/biocontainers/c/cured:1.05--hdfd78af_0.json new file mode 100644 index 0000000..a797e52 --- /dev/null +++ b/quay.io/biocontainers/c/cured:1.05--hdfd78af_0.json @@ -0,0 +1,521 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.10": "/usr/local/bin/2to3-3.10", + "AnalyseDists": "/usr/local/bin/AnalyseDists", + "AnalyseSeqs": "/usr/local/bin/AnalyseSeqs", + "Bifrost": "/usr/local/bin/Bifrost", + "CURED_FindREs.py": "/usr/local/bin/CURED_FindREs.py", + "CURED_Main.py": "/usr/local/bin/CURED_Main.py", + "Kinfold": "/usr/local/bin/Kinfold", + "RNA2Dfold": "/usr/local/bin/RNA2Dfold", + "RNALalifold": "/usr/local/bin/RNALalifold", + "RNALfold": "/usr/local/bin/RNALfold", + "RNAPKplex": "/usr/local/bin/RNAPKplex", + "RNAaliduplex": "/usr/local/bin/RNAaliduplex", + "RNAalifold": "/usr/local/bin/RNAalifold", + "RNAcofold": "/usr/local/bin/RNAcofold", + "RNAdistance": "/usr/local/bin/RNAdistance", + "RNAdos": "/usr/local/bin/RNAdos", + "RNAduplex": "/usr/local/bin/RNAduplex", + "RNAeval": "/usr/local/bin/RNAeval", + "RNAfold": "/usr/local/bin/RNAfold", + "RNAforester": "/usr/local/bin/RNAforester", + "RNAheat": "/usr/local/bin/RNAheat", + "RNAinverse": "/usr/local/bin/RNAinverse", + "RNAlocmin": "/usr/local/bin/RNAlocmin", + "RNAmultifold": "/usr/local/bin/RNAmultifold", + "RNApaln": "/usr/local/bin/RNApaln", + "RNAparconv": "/usr/local/bin/RNAparconv", + "RNApdist": "/usr/local/bin/RNApdist", + "RNAplex": "/usr/local/bin/RNAplex", + "RNAplfold": "/usr/local/bin/RNAplfold", + "RNAplot": "/usr/local/bin/RNAplot", + "RNApvmin": "/usr/local/bin/RNApvmin", + "RNAsnoop": "/usr/local/bin/RNAsnoop", + "RNAsubopt": "/usr/local/bin/RNAsubopt", + "RNAup": "/usr/local/bin/RNAup", + "TMalign": "/usr/local/bin/TMalign", + "accn-at-a-time": "/usr/local/bin/accn-at-a-time", + "ace2sam": "/usr/local/bin/ace2sam", + "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", + "annot-tsv": "/usr/local/bin/annot-tsv", + "any2fasta": "/usr/local/bin/any2fasta", + "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", + "args2slice": "/usr/local/bin/args2slice", + "asn2ref": "/usr/local/bin/asn2ref", + "asn2xml": "/usr/local/bin/asn2xml", + "autopoint": "/usr/local/bin/autopoint", + "awk": "/usr/local/bin/awk", + "b2ct": "/usr/local/bin/b2ct", + "bamToGBrowse.pl": "/usr/local/bin/bamToGBrowse.pl", + "baseml": "/usr/local/bin/baseml", + "basemlg": "/usr/local/bin/basemlg", + "between-two-genes": "/usr/local/bin/between-two-genes", + "bgzip": "/usr/local/bin/bgzip", + "bl2seq": "/usr/local/bin/bl2seq", + "blast2sam.pl": "/usr/local/bin/blast2sam.pl", + "blast_formatter": "/usr/local/bin/blast_formatter", + "blastall": "/usr/local/bin/blastall", + "blastclust": "/usr/local/bin/blastclust", + "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", + "blastpgp": "/usr/local/bin/blastpgp", + "blastx": "/usr/local/bin/blastx", + "blst2gm": "/usr/local/bin/blst2gm", + "blst2tkns": "/usr/local/bin/blst2tkns", + "bowtie2sam.pl": "/usr/local/bin/bowtie2sam.pl", + "bp_aacomp": "/usr/local/bin/bp_aacomp", + "bp_bioflat_index": "/usr/local/bin/bp_bioflat_index", + "bp_biogetseq": "/usr/local/bin/bp_biogetseq", + "bp_dbsplit": "/usr/local/bin/bp_dbsplit", + "bp_extract_feature_seq": "/usr/local/bin/bp_extract_feature_seq", + "bp_fastam9_to_table": "/usr/local/bin/bp_fastam9_to_table", + "bp_fetch": "/usr/local/bin/bp_fetch", + "bp_filter_search": "/usr/local/bin/bp_filter_search", + "bp_find-blast-matches": "/usr/local/bin/bp_find-blast-matches", + "bp_gccalc": "/usr/local/bin/bp_gccalc", + "bp_genbank2gff3": "/usr/local/bin/bp_genbank2gff3", + "bp_hmmer_to_table.pl": "/usr/local/bin/bp_hmmer_to_table.pl", + "bp_index": "/usr/local/bin/bp_index", + "bp_local_taxonomydb_query": "/usr/local/bin/bp_local_taxonomydb_query", + "bp_make_mrna_protein": "/usr/local/bin/bp_make_mrna_protein", + "bp_mask_by_search": "/usr/local/bin/bp_mask_by_search", + "bp_mrtrans": "/usr/local/bin/bp_mrtrans", + "bp_mutate": "/usr/local/bin/bp_mutate", + "bp_nexus2nh": "/usr/local/bin/bp_nexus2nh", + "bp_nrdb": "/usr/local/bin/bp_nrdb", + "bp_oligo_count": "/usr/local/bin/bp_oligo_count", + "bp_pairwise_kaks": "/usr/local/bin/bp_pairwise_kaks", + "bp_parse_hmmsearch.pl": "/usr/local/bin/bp_parse_hmmsearch.pl", + "bp_process_gadfly": "/usr/local/bin/bp_process_gadfly", + "bp_process_sgd": "/usr/local/bin/bp_process_sgd", + "bp_revtrans-motif": "/usr/local/bin/bp_revtrans-motif", + "bp_search2alnblocks": "/usr/local/bin/bp_search2alnblocks", + "bp_search2gff": "/usr/local/bin/bp_search2gff", + "bp_search2table": "/usr/local/bin/bp_search2table", + "bp_search2tribe": "/usr/local/bin/bp_search2tribe", + "bp_seq_length": "/usr/local/bin/bp_seq_length", + "bp_seqconvert": "/usr/local/bin/bp_seqconvert", + "bp_seqcut": "/usr/local/bin/bp_seqcut", + "bp_seqpart": "/usr/local/bin/bp_seqpart", + "bp_seqret": "/usr/local/bin/bp_seqret", + "bp_seqretsplit": "/usr/local/bin/bp_seqretsplit", + "bp_split_seq": "/usr/local/bin/bp_split_seq", + "bp_sreformat": "/usr/local/bin/bp_sreformat", + "bp_taxid4species": "/usr/local/bin/bp_taxid4species", + "bp_taxonomy2tree": "/usr/local/bin/bp_taxonomy2tree", + "bp_translate_seq": "/usr/local/bin/bp_translate_seq", + "bp_tree2pag": "/usr/local/bin/bp_tree2pag", + "bp_unflatten_seq": "/usr/local/bin/bp_unflatten_seq", + "bunzip2": "/usr/local/bin/bunzip2", + "bwa": "/usr/local/bin/bwa", + "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", + "chi2": "/usr/local/bin/chi2", + "chrom_sizes.pl": "/usr/local/bin/chrom_sizes.pl", + "cit2pmid": "/usr/local/bin/cit2pmid", + "cleanup-blastdb-volumes.py": "/usr/local/bin/cleanup-blastdb-volumes.py", + "clear": "/usr/local/bin/clear", + "clustalo": "/usr/local/bin/clustalo", + "clustalw": "/usr/local/bin/clustalw", + "clustalw2": "/usr/local/bin/clustalw2", + "codeml": "/usr/local/bin/codeml", + "combine-uid-lists": "/usr/local/bin/combine-uid-lists", + "compile_et": "/usr/local/bin/compile_et", + "config_data": "/usr/local/bin/config_data", + "convert2blastmask": "/usr/local/bin/convert2blastmask", + "copymat": "/usr/local/bin/copymat", + "corelist": "/usr/local/bin/corelist", + "cpan": "/usr/local/bin/cpan", + "csv2xml": "/usr/local/bin/csv2xml", + "ct2db": "/usr/local/bin/ct2db", + "curl": "/usr/local/bin/curl", + "curl-config": "/usr/local/bin/curl-config", + "dataformat": "/usr/local/bin/dataformat", + "datasets": "/usr/local/bin/datasets", + "datatool": "/usr/local/bin/datatool", + "db_archive": "/usr/local/bin/db_archive", + "db_checkpoint": "/usr/local/bin/db_checkpoint", + "db_convert": "/usr/local/bin/db_convert", + "db_deadlock": "/usr/local/bin/db_deadlock", + "db_dump": "/usr/local/bin/db_dump", + "db_hotbackup": "/usr/local/bin/db_hotbackup", + "db_load": "/usr/local/bin/db_load", + "db_log_verify": "/usr/local/bin/db_log_verify", + "db_printlog": "/usr/local/bin/db_printlog", + "db_recover": "/usr/local/bin/db_recover", + "db_replicate": "/usr/local/bin/db_replicate", + "db_stat": "/usr/local/bin/db_stat", + "db_tuner": "/usr/local/bin/db_tuner", + "db_upgrade": "/usr/local/bin/db_upgrade", + "db_verify": "/usr/local/bin/db_verify", + "deltablast": "/usr/local/bin/deltablast", + "difference-uid-lists": "/usr/local/bin/difference-uid-lists", + "disambiguate-nucleotides": "/usr/local/bin/disambiguate-nucleotides", + "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", + "einsi": "/usr/local/bin/einsi", + "elink": "/usr/local/bin/elink", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "env_parallel": "/usr/local/bin/env_parallel", + "env_parallel.ash": "/usr/local/bin/env_parallel.ash", + "env_parallel.bash": "/usr/local/bin/env_parallel.bash", + "env_parallel.csh": "/usr/local/bin/env_parallel.csh", + "env_parallel.dash": "/usr/local/bin/env_parallel.dash", + "env_parallel.fish": "/usr/local/bin/env_parallel.fish", + "env_parallel.ksh": "/usr/local/bin/env_parallel.ksh", + "env_parallel.mksh": "/usr/local/bin/env_parallel.mksh", + "env_parallel.pdksh": "/usr/local/bin/env_parallel.pdksh", + "env_parallel.sh": "/usr/local/bin/env_parallel.sh", + "env_parallel.tcsh": "/usr/local/bin/env_parallel.tcsh", + "env_parallel.zsh": "/usr/local/bin/env_parallel.zsh", + "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", + "evolver": "/usr/local/bin/evolver", + "exclude-uid-lists": "/usr/local/bin/exclude-uid-lists", + "expand-current": "/usr/local/bin/expand-current", + "export2sam.pl": "/usr/local/bin/export2sam.pl", + "f2py": "/usr/local/bin/f2py", + "fasta-sanitize.pl": "/usr/local/bin/fasta-sanitize.pl", + "fastacmd": "/usr/local/bin/fastacmd", + "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", + "fftns": "/usr/local/bin/fftns", + "fftnsi": "/usr/local/bin/fftnsi", + "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", + "formatdb": "/usr/local/bin/formatdb", + "formatrpsdb": "/usr/local/bin/formatrpsdb", + "fuse-ranges": "/usr/local/bin/fuse-ranges", + "fuse-segments": "/usr/local/bin/fuse-segments", + "gawk": "/usr/local/bin/gawk", + "gawk-5.3.0": "/usr/local/bin/gawk-5.3.0", + "gawkbug": "/usr/local/bin/gawkbug", + "gbf2fsa": "/usr/local/bin/gbf2fsa", + "gbf2ref": "/usr/local/bin/gbf2ref", + "gbf2xml": "/usr/local/bin/gbf2xml", + "gene2range": "/usr/local/bin/gene2range", + "genomeCoverageBed.pl": "/usr/local/bin/genomeCoverageBed.pl", + "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", + "ginsi": "/usr/local/bin/ginsi", + "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", + "htsfile": "/usr/local/bin/htsfile", + "idle3": "/usr/local/bin/idle3", + "idle3.10": "/usr/local/bin/idle3.10", + "idn2": "/usr/local/bin/idn2", + "impala": "/usr/local/bin/impala", + "infinitesites": "/usr/local/bin/infinitesites", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "ini2xml": "/usr/local/bin/ini2xml", + "instmodsh": "/usr/local/bin/instmodsh", + "interpolate_sam.pl": "/usr/local/bin/interpolate_sam.pl", + "intersect-uid-lists": "/usr/local/bin/intersect-uid-lists", + "join-into-groups-of": "/usr/local/bin/join-into-groups-of", + "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", + "kinwalker": "/usr/local/bin/kinwalker", + "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", + "linsi": "/usr/local/bin/linsi", + "lwp-download": "/usr/local/bin/lwp-download", + "lwp-dump": "/usr/local/bin/lwp-dump", + "lwp-mirror": "/usr/local/bin/lwp-mirror", + "lwp-request": "/usr/local/bin/lwp-request", + "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", + "mafft": "/usr/local/bin/mafft", + "mafft-distance": "/usr/local/bin/mafft-distance", + "mafft-einsi": "/usr/local/bin/mafft-einsi", + "mafft-fftns": "/usr/local/bin/mafft-fftns", + "mafft-fftnsi": "/usr/local/bin/mafft-fftnsi", + "mafft-ginsi": "/usr/local/bin/mafft-ginsi", + "mafft-homologs.rb": "/usr/local/bin/mafft-homologs.rb", + "mafft-linsi": "/usr/local/bin/mafft-linsi", + "mafft-nwns": "/usr/local/bin/mafft-nwns", + "mafft-nwnsi": "/usr/local/bin/mafft-nwnsi", + "mafft-profile": "/usr/local/bin/mafft-profile", + "mafft-qinsi": "/usr/local/bin/mafft-qinsi", + "mafft-sparsecore.rb": "/usr/local/bin/mafft-sparsecore.rb", + "mafft-xinsi": "/usr/local/bin/mafft-xinsi", + "make_pscores.pl": "/usr/local/bin/make_pscores.pl", + "makeblastdb": "/usr/local/bin/makeblastdb", + "makemat": "/usr/local/bin/makemat", + "makembindex": "/usr/local/bin/makembindex", + "makeprofiledb": "/usr/local/bin/makeprofiledb", + "maq2sam-long": "/usr/local/bin/maq2sam-long", + "maq2sam-short": "/usr/local/bin/maq2sam-short", + "mcmctree": "/usr/local/bin/mcmctree", + "md5fa": "/usr/local/bin/md5fa", + "md5sum-lite": "/usr/local/bin/md5sum-lite", + "megablast": "/usr/local/bin/megablast", + "mlst": "/usr/local/bin/mlst", + "mlst-ST_mini_genomes": "/usr/local/bin/mlst-ST_mini_genomes", + "mlst-consistency_checker": "/usr/local/bin/mlst-consistency_checker", + "mlst-download_pub_mlst": "/usr/local/bin/mlst-download_pub_mlst", + "mlst-make_blast_db": "/usr/local/bin/mlst-make_blast_db", + "mlst-show_seqs": "/usr/local/bin/mlst-show_seqs", + "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", + "muscle": "/usr/local/bin/muscle", + "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", + "niceload": "/usr/local/bin/niceload", + "novo2sam.pl": "/usr/local/bin/novo2sam.pl", + "nquire": "/usr/local/bin/nquire", + "nwns": "/usr/local/bin/nwns", + "nwnsi": "/usr/local/bin/nwnsi", + "openssl": "/usr/local/bin/openssl", + "pamp": "/usr/local/bin/pamp", + "parallel": "/usr/local/bin/parallel", + "parcat": "/usr/local/bin/parcat", + "parset": "/usr/local/bin/parset", + "parsort": "/usr/local/bin/parsort", + "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", + "phrase-search": "/usr/local/bin/phrase-search", + "piconv": "/usr/local/bin/piconv", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pl2pm": "/usr/local/bin/pl2pm", + "plot-ampliconstats": "/usr/local/bin/plot-ampliconstats", + "plot-bamstats": "/usr/local/bin/plot-bamstats", + "pma2apa": "/usr/local/bin/pma2apa", + "pma2pme": "/usr/local/bin/pma2pme", + "pmc2bioc": "/usr/local/bin/pmc2bioc", + "pmc2info": "/usr/local/bin/pmc2info", + "poa": "/usr/local/bin/poa", + "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", + "popt": "/usr/local/bin/popt", + "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", + "psl2sam.pl": "/usr/local/bin/psl2sam.pl", + "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", + "pydoc3.10": "/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", + "qualfa2fq.pl": "/usr/local/bin/qualfa2fq.pl", + "quote-grouped-elements": "/usr/local/bin/quote-grouped-elements", + "rchive": "/usr/local/bin/rchive", + "rchive.Linux": "/usr/local/bin/rchive.Linux", + "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", + "sam2vcf.pl": "/usr/local/bin/sam2vcf.pl", + "samtools": "/usr/local/bin/samtools", + "samtools.pl": "/usr/local/bin/samtools.pl", + "sclient": "/usr/local/bin/sclient", + "scn2xml": "/usr/local/bin/scn2xml", + "seedtop": "/usr/local/bin/seedtop", + "segmasker": "/usr/local/bin/segmasker", + "sem": "/usr/local/bin/sem", + "seq_cache_populate.pl": "/usr/local/bin/seq_cache_populate.pl", + "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", + "soap2sam.pl": "/usr/local/bin/soap2sam.pl", + "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", + "sql": "/usr/local/bin/sql", + "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", + "t_coffee": "/usr/local/bin/t_coffee", + "tabix": "/usr/local/bin/tabix", + "tabs": "/usr/local/bin/tabs", + "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", + "toe": "/usr/local/bin/toe", + "toml2xml": "/usr/local/bin/toml2xml", + "tput": "/usr/local/bin/tput", + "transmute": "/usr/local/bin/transmute", + "transmute.Linux": "/usr/local/bin/transmute.Linux", + "tset": "/usr/local/bin/tset", + "uniq-table": "/usr/local/bin/uniq-table", + "unitig-caller": "/usr/local/bin/unitig-caller", + "unlzma": "/usr/local/bin/unlzma", + "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", + "wgsim": "/usr/local/bin/wgsim", + "wgsim_eval.pl": "/usr/local/bin/wgsim_eval.pl", + "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", + "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", + "xa2multi.pl": "/usr/local/bin/xa2multi.pl", + "xgettext": "/usr/local/bin/xgettext", + "xml2fsa": "/usr/local/bin/xml2fsa", + "xml2json": "/usr/local/bin/xml2json", + "xml2tbl": "/usr/local/bin/xml2tbl", + "xmlwf": "/usr/local/bin/xmlwf", + "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", + "yn00": "/usr/local/bin/yn00", + "zipdetails": "/usr/local/bin/zipdetails", + "zoom2sam.pl": "/usr/local/bin/zoom2sam.pl", + "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/g/gapseq:1.2--h9ee0642_0.json b/quay.io/biocontainers/g/gapseq:1.2--h9ee0642_0.json new file mode 100644 index 0000000..4b6d712 --- /dev/null +++ b/quay.io/biocontainers/g/gapseq:1.2--h9ee0642_0.json @@ -0,0 +1,720 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.12": "/usr/local/bin/2to3-3.12", + "R": "/usr/local/bin/R", + "Rscript": "/usr/local/bin/Rscript", + "accn-at-a-time": "/usr/local/bin/accn-at-a-time", + "activate-global-python-argcomplete": "/usr/local/bin/activate-global-python-argcomplete", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "align-columns": "/usr/local/bin/align-columns", + "alimask": "/usr/local/bin/alimask", + "amino-acid-composition": "/usr/local/bin/amino-acid-composition", + "annotateBed": "/usr/local/bin/annotateBed", + "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", + "args2slice": "/usr/local/bin/args2slice", + "asn2ref": "/usr/local/bin/asn2ref", + "asn2xml": "/usr/local/bin/asn2xml", + "autopoint": "/usr/local/bin/autopoint", + "awk": "/usr/local/bin/awk", + "b2sum": "/usr/local/bin/b2sum", + "bamToBed": "/usr/local/bin/bamToBed", + "bamToFastq": "/usr/local/bin/bamToFastq", + "barrnap": "/usr/local/bin/barrnap", + "base32": "/usr/local/bin/base32", + "base64": "/usr/local/bin/base64", + "basename": "/usr/local/bin/basename", + "basenc": "/usr/local/bin/basenc", + "bc": "/usr/local/bin/bc", + "bed12ToBed6": "/usr/local/bin/bed12ToBed6", + "bedToBam": "/usr/local/bin/bedToBam", + "bedToIgv": "/usr/local/bin/bedToIgv", + "bedpeToBam": "/usr/local/bin/bedpeToBam", + "bedtools": "/usr/local/bin/bedtools", + "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", + "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", + "cairo-trace": "/usr/local/bin/cairo-trace", + "captoinfo": "/usr/local/bin/captoinfo", + "cat": "/usr/local/bin/cat", + "chcon": "/usr/local/bin/chcon", + "chgrp": "/usr/local/bin/chgrp", + "chmod": "/usr/local/bin/chmod", + "chown": "/usr/local/bin/chown", + "chroot": "/usr/local/bin/chroot", + "cit2pmid": "/usr/local/bin/cit2pmid", + "cjpeg": "/usr/local/bin/cjpeg", + "cksum": "/usr/local/bin/cksum", + "cleanup-blastdb-volumes.py": "/usr/local/bin/cleanup-blastdb-volumes.py", + "clear": "/usr/local/bin/clear", + "closestBed": "/usr/local/bin/closestBed", + "clusterBed": "/usr/local/bin/clusterBed", + "combine-uid-lists": "/usr/local/bin/combine-uid-lists", + "comm": "/usr/local/bin/comm", + "compile_et": "/usr/local/bin/compile_et", + "complementBed": "/usr/local/bin/complementBed", + "convert2blastmask": "/usr/local/bin/convert2blastmask", + "corelist": "/usr/local/bin/corelist", + "coverageBed": "/usr/local/bin/coverageBed", + "cp": "/usr/local/bin/cp", + "cpan": "/usr/local/bin/cpan", + "csplit": "/usr/local/bin/csplit", + "csv2xml": "/usr/local/bin/csv2xml", + "curl": "/usr/local/bin/curl", + "curl-config": "/usr/local/bin/curl-config", + "cut": "/usr/local/bin/cut", + "datatool": "/usr/local/bin/datatool", + "date": "/usr/local/bin/date", + "dc": "/usr/local/bin/dc", + "dd": "/usr/local/bin/dd", + "deltablast": "/usr/local/bin/deltablast", + "derb": "/usr/local/bin/derb", + "df": "/usr/local/bin/df", + "difference-uid-lists": "/usr/local/bin/difference-uid-lists", + "dir": "/usr/local/bin/dir", + "dircolors": "/usr/local/bin/dircolors", + "dirname": "/usr/local/bin/dirname", + "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", + "du": "/usr/local/bin/du", + "dustmasker": "/usr/local/bin/dustmasker", + "easel": "/usr/local/bin/easel", + "echo": "/usr/local/bin/echo", + "ecommon.sh": "/usr/local/bin/ecommon.sh", + "efetch": "/usr/local/bin/efetch", + "efilter": "/usr/local/bin/efilter", + "egrep": "/usr/local/bin/egrep", + "einfo": "/usr/local/bin/einfo", + "elink": "/usr/local/bin/elink", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "env": "/usr/local/bin/env", + "env_parallel": "/usr/local/bin/env_parallel", + "env_parallel.ash": "/usr/local/bin/env_parallel.ash", + "env_parallel.bash": "/usr/local/bin/env_parallel.bash", + "env_parallel.csh": "/usr/local/bin/env_parallel.csh", + "env_parallel.dash": "/usr/local/bin/env_parallel.dash", + "env_parallel.fish": "/usr/local/bin/env_parallel.fish", + "env_parallel.ksh": "/usr/local/bin/env_parallel.ksh", + "env_parallel.mksh": "/usr/local/bin/env_parallel.mksh", + "env_parallel.pdksh": "/usr/local/bin/env_parallel.pdksh", + "env_parallel.sh": "/usr/local/bin/env_parallel.sh", + "env_parallel.tcsh": "/usr/local/bin/env_parallel.tcsh", + "env_parallel.zsh": "/usr/local/bin/env_parallel.zsh", + "envsubst": "/usr/local/bin/envsubst", + "epost": "/usr/local/bin/epost", + "esample": "/usr/local/bin/esample", + "esd2esi": "/usr/local/bin/esd2esi", + "esearch": "/usr/local/bin/esearch", + "esl-afetch": "/usr/local/bin/esl-afetch", + "esl-alimanip": "/usr/local/bin/esl-alimanip", + "esl-alimap": "/usr/local/bin/esl-alimap", + "esl-alimask": "/usr/local/bin/esl-alimask", + "esl-alimerge": "/usr/local/bin/esl-alimerge", + "esl-alipid": "/usr/local/bin/esl-alipid", + "esl-alirev": "/usr/local/bin/esl-alirev", + "esl-alistat": "/usr/local/bin/esl-alistat", + "esl-compalign": "/usr/local/bin/esl-compalign", + "esl-compstruct": "/usr/local/bin/esl-compstruct", + "esl-construct": "/usr/local/bin/esl-construct", + "esl-histplot": "/usr/local/bin/esl-histplot", + "esl-mask": "/usr/local/bin/esl-mask", + "esl-mixdchlet": "/usr/local/bin/esl-mixdchlet", + "esl-reformat": "/usr/local/bin/esl-reformat", + "esl-selectn": "/usr/local/bin/esl-selectn", + "esl-seqrange": "/usr/local/bin/esl-seqrange", + "esl-seqstat": "/usr/local/bin/esl-seqstat", + "esl-sfetch": "/usr/local/bin/esl-sfetch", + "esl-shuffle": "/usr/local/bin/esl-shuffle", + "esl-ssdraw": "/usr/local/bin/esl-ssdraw", + "esl-translate": "/usr/local/bin/esl-translate", + "esl-weight": "/usr/local/bin/esl-weight", + "esummary": "/usr/local/bin/esummary", + "exclude-uid-lists": "/usr/local/bin/exclude-uid-lists", + "exonerate": "/usr/local/bin/exonerate", + "exonerate-server": "/usr/local/bin/exonerate-server", + "expand": "/usr/local/bin/expand", + "expand-current": "/usr/local/bin/expand-current", + "expandCols": "/usr/local/bin/expandCols", + "expr": "/usr/local/bin/expr", + "factor": "/usr/local/bin/factor", + "false": "/usr/local/bin/false", + "fasta2esd": "/usr/local/bin/fasta2esd", + "fastaFromBed": "/usr/local/bin/fastaFromBed", + "fastaannotatecdna": "/usr/local/bin/fastaannotatecdna", + "fastachecksum": "/usr/local/bin/fastachecksum", + "fastaclean": "/usr/local/bin/fastaclean", + "fastaclip": "/usr/local/bin/fastaclip", + "fastacomposition": "/usr/local/bin/fastacomposition", + "fastadiff": "/usr/local/bin/fastadiff", + "fastaexplode": "/usr/local/bin/fastaexplode", + "fastafetch": "/usr/local/bin/fastafetch", + "fastahardmask": "/usr/local/bin/fastahardmask", + "fastaindex": "/usr/local/bin/fastaindex", + "fastalength": "/usr/local/bin/fastalength", + "fastanrdb": "/usr/local/bin/fastanrdb", + "fastaoverlap": "/usr/local/bin/fastaoverlap", + "fastareformat": "/usr/local/bin/fastareformat", + "fastaremove": "/usr/local/bin/fastaremove", + "fastarevcomp": "/usr/local/bin/fastarevcomp", + "fastasoftmask": "/usr/local/bin/fastasoftmask", + "fastasort": "/usr/local/bin/fastasort", + "fastasplit": "/usr/local/bin/fastasplit", + "fastasubseq": "/usr/local/bin/fastasubseq", + "fastatranslate": "/usr/local/bin/fastatranslate", + "fastavalidcds": "/usr/local/bin/fastavalidcds", + "fax2ps": "/usr/local/bin/fax2ps", + "fax2tiff": "/usr/local/bin/fax2tiff", + "fc-cache": "/usr/local/bin/fc-cache", + "fc-cat": "/usr/local/bin/fc-cat", + "fc-conflist": "/usr/local/bin/fc-conflist", + "fc-list": "/usr/local/bin/fc-list", + "fc-match": "/usr/local/bin/fc-match", + "fc-pattern": "/usr/local/bin/fc-pattern", + "fc-query": "/usr/local/bin/fc-query", + "fc-scan": "/usr/local/bin/fc-scan", + "fc-validate": "/usr/local/bin/fc-validate", + "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", + "fgrep": "/usr/local/bin/fgrep", + "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", + "flankBed": "/usr/local/bin/flankBed", + "fmt": "/usr/local/bin/fmt", + "fold": "/usr/local/bin/fold", + "freetype-config": "/usr/local/bin/freetype-config", + "fribidi": "/usr/local/bin/fribidi", + "fuse-ranges": "/usr/local/bin/fuse-ranges", + "fuse-segments": "/usr/local/bin/fuse-segments", + "gapplication": "/usr/local/bin/gapplication", + "gapseq": "/usr/local/bin/gapseq", + "gawk": "/usr/local/bin/gawk", + "gawk-5.3.0": "/usr/local/bin/gawk-5.3.0", + "gawkbug": "/usr/local/bin/gawkbug", + "gbf2fsa": "/usr/local/bin/gbf2fsa", + "gbf2ref": "/usr/local/bin/gbf2ref", + "gbf2xml": "/usr/local/bin/gbf2xml", + "gdbus": "/usr/local/bin/gdbus", + "gdbus-codegen": "/usr/local/bin/gdbus-codegen", + "genbrk": "/usr/local/bin/genbrk", + "gencfu": "/usr/local/bin/gencfu", + "gencnval": "/usr/local/bin/gencnval", + "gendict": "/usr/local/bin/gendict", + "gene2range": "/usr/local/bin/gene2range", + "genomeCoverageBed": "/usr/local/bin/genomeCoverageBed", + "genrb": "/usr/local/bin/genrb", + "getOverlap": "/usr/local/bin/getOverlap", + "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", + "gio": "/usr/local/bin/gio", + "gio-querymodules": "/usr/local/bin/gio-querymodules", + "git": "/usr/local/bin/git", + "git-cvsserver": "/usr/local/bin/git-cvsserver", + "git-receive-pack": "/usr/local/bin/git-receive-pack", + "git-shell": "/usr/local/bin/git-shell", + "git-upload-archive": "/usr/local/bin/git-upload-archive", + "git-upload-pack": "/usr/local/bin/git-upload-pack", + "gitk": "/usr/local/bin/gitk", + "glib-compile-resources": "/usr/local/bin/glib-compile-resources", + "glib-compile-schemas": "/usr/local/bin/glib-compile-schemas", + "glib-genmarshal": "/usr/local/bin/glib-genmarshal", + "glib-gettextize": "/usr/local/bin/glib-gettextize", + "glib-mkenums": "/usr/local/bin/glib-mkenums", + "glpsol": "/usr/local/bin/glpsol", + "gm2ranges": "/usr/local/bin/gm2ranges", + "gm2segs": "/usr/local/bin/gm2segs", + "gobject-query": "/usr/local/bin/gobject-query", + "grep": "/usr/local/bin/grep", + "gresource": "/usr/local/bin/gresource", + "groupBy": "/usr/local/bin/groupBy", + "groups": "/usr/local/bin/groups", + "gsettings": "/usr/local/bin/gsettings", + "gsl-config": "/usr/local/bin/gsl-config", + "gsl-histogram": "/usr/local/bin/gsl-histogram", + "gsl-randist": "/usr/local/bin/gsl-randist", + "gss-client": "/usr/local/bin/gss-client", + "gtester": "/usr/local/bin/gtester", + "gtester-report": "/usr/local/bin/gtester-report", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "hb-info": "/usr/local/bin/hb-info", + "hb-ot-shape-closure": "/usr/local/bin/hb-ot-shape-closure", + "hb-shape": "/usr/local/bin/hb-shape", + "hb-subset": "/usr/local/bin/hb-subset", + "hb-view": "/usr/local/bin/hb-view", + "head": "/usr/local/bin/head", + "hgvs2spdi": "/usr/local/bin/hgvs2spdi", + "hmmalign": "/usr/local/bin/hmmalign", + "hmmbuild": "/usr/local/bin/hmmbuild", + "hmmconvert": "/usr/local/bin/hmmconvert", + "hmmemit": "/usr/local/bin/hmmemit", + "hmmfetch": "/usr/local/bin/hmmfetch", + "hmmlogo": "/usr/local/bin/hmmlogo", + "hmmpgmd": "/usr/local/bin/hmmpgmd", + "hmmpgmd_shard": "/usr/local/bin/hmmpgmd_shard", + "hmmpress": "/usr/local/bin/hmmpress", + "hmmscan": "/usr/local/bin/hmmscan", + "hmmsearch": "/usr/local/bin/hmmsearch", + "hmmsim": "/usr/local/bin/hmmsim", + "hmmstat": "/usr/local/bin/hmmstat", + "hostid": "/usr/local/bin/hostid", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "id": "/usr/local/bin/id", + "idle3": "/usr/local/bin/idle3", + "idle3.12": "/usr/local/bin/idle3.12", + "idn2": "/usr/local/bin/idn2", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "ini2xml": "/usr/local/bin/ini2xml", + "install": "/usr/local/bin/install", + "installBiocDataPackage.sh": "/usr/local/bin/installBiocDataPackage.sh", + "install_archived_sybilSBML.sh": "/usr/local/bin/install_archived_sybilSBML.sh", + "instmodsh": "/usr/local/bin/instmodsh", + "intersect-uid-lists": "/usr/local/bin/intersect-uid-lists", + "intersectBed": "/usr/local/bin/intersectBed", + "ipcress": "/usr/local/bin/ipcress", + "jackhmmer": "/usr/local/bin/jackhmmer", + "join": "/usr/local/bin/join", + "join-into-groups-of": "/usr/local/bin/join-into-groups-of", + "jpegtran": "/usr/local/bin/jpegtran", + "jq": "/usr/local/bin/jq", + "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", + "kill": "/usr/local/bin/kill", + "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", + "link": "/usr/local/bin/link", + "linksBed": "/usr/local/bin/linksBed", + "ln": "/usr/local/bin/ln", + "logname": "/usr/local/bin/logname", + "ls": "/usr/local/bin/ls", + "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": "/usr/local/bin/make", + "makeblastdb": "/usr/local/bin/makeblastdb", + "makeconv": "/usr/local/bin/makeconv", + "makehmmerdb": "/usr/local/bin/makehmmerdb", + "makembindex": "/usr/local/bin/makembindex", + "makeprofiledb": "/usr/local/bin/makeprofiledb", + "mapBed": "/usr/local/bin/mapBed", + "maskFastaFromBed": "/usr/local/bin/maskFastaFromBed", + "md5sum": "/usr/local/bin/md5sum", + "mergeBed": "/usr/local/bin/mergeBed", + "mkdir": "/usr/local/bin/mkdir", + "mkfifo": "/usr/local/bin/mkfifo", + "mknod": "/usr/local/bin/mknod", + "mktemp": "/usr/local/bin/mktemp", + "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", + "multiBamCov": "/usr/local/bin/multiBamCov", + "multiIntersectBed": "/usr/local/bin/multiIntersectBed", + "mv": "/usr/local/bin/mv", + "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", + "nhmmer": "/usr/local/bin/nhmmer", + "nhmmscan": "/usr/local/bin/nhmmscan", + "nice": "/usr/local/bin/nice", + "niceload": "/usr/local/bin/niceload", + "nl": "/usr/local/bin/nl", + "nohup": "/usr/local/bin/nohup", + "nproc": "/usr/local/bin/nproc", + "nquire": "/usr/local/bin/nquire", + "nucBed": "/usr/local/bin/nucBed", + "numfmt": "/usr/local/bin/numfmt", + "od": "/usr/local/bin/od", + "onig-config": "/usr/local/bin/onig-config", + "openssl": "/usr/local/bin/openssl", + "pairToBed": "/usr/local/bin/pairToBed", + "pairToPair": "/usr/local/bin/pairToPair", + "pal2rgb": "/usr/local/bin/pal2rgb", + "pango-list": "/usr/local/bin/pango-list", + "pango-segmentation": "/usr/local/bin/pango-segmentation", + "pango-view": "/usr/local/bin/pango-view", + "parallel": "/usr/local/bin/parallel", + "parcat": "/usr/local/bin/parcat", + "parset": "/usr/local/bin/parset", + "parsort": "/usr/local/bin/parsort", + "paste": "/usr/local/bin/paste", + "pathchk": "/usr/local/bin/pathchk", + "pcre-config": "/usr/local/bin/pcre-config", + "pcre2-config": "/usr/local/bin/pcre2-config", + "pcre2_jit_test": "/usr/local/bin/pcre2_jit_test", + "pcre2grep": "/usr/local/bin/pcre2grep", + "pcre2test": "/usr/local/bin/pcre2test", + "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", + "phmmer": "/usr/local/bin/phmmer", + "phrase-search": "/usr/local/bin/phrase-search", + "piconv": "/usr/local/bin/piconv", + "pinky": "/usr/local/bin/pinky", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pkgdata": "/usr/local/bin/pkgdata", + "pl2pm": "/usr/local/bin/pl2pm", + "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", + "ppm2tiff": "/usr/local/bin/ppm2tiff", + "pr": "/usr/local/bin/pr", + "print-columns": "/usr/local/bin/print-columns", + "printenv": "/usr/local/bin/printenv", + "printf": "/usr/local/bin/printf", + "project_tree_builder": "/usr/local/bin/project_tree_builder", + "prove": "/usr/local/bin/prove", + "psiblast": "/usr/local/bin/psiblast", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "ptx": "/usr/local/bin/ptx", + "pwd": "/usr/local/bin/pwd", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.12": "/usr/local/bin/pydoc3.12", + "python": "/usr/local/bin/python", + "python-argcomplete-check-easy-install-script": "/usr/local/bin/python-argcomplete-check-easy-install-script", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.12": "/usr/local/bin/python3.12", + "python3.12-config": "/usr/local/bin/python3.12-config", + "quote-grouped-elements": "/usr/local/bin/quote-grouped-elements", + "randomBed": "/usr/local/bin/randomBed", + "raw2tiff": "/usr/local/bin/raw2tiff", + "rchive": "/usr/local/bin/rchive", + "rchive.Linux": "/usr/local/bin/rchive.Linux", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "readlink": "/usr/local/bin/readlink", + "realpath": "/usr/local/bin/realpath", + "recode-sr-latin": "/usr/local/bin/recode-sr-latin", + "ref2pmid": "/usr/local/bin/ref2pmid", + "refseq-nm-cds": "/usr/local/bin/refseq-nm-cds", + "register-python-argcomplete": "/usr/local/bin/register-python-argcomplete", + "reorder-columns": "/usr/local/bin/reorder-columns", + "reset": "/usr/local/bin/reset", + "rm": "/usr/local/bin/rm", + "rmdir": "/usr/local/bin/rmdir", + "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", + "runcon": "/usr/local/bin/runcon", + "scalar": "/usr/local/bin/scalar", + "sclient": "/usr/local/bin/sclient", + "scn2xml": "/usr/local/bin/scn2xml", + "sed": "/usr/local/bin/sed", + "segmasker": "/usr/local/bin/segmasker", + "sem": "/usr/local/bin/sem", + "seq": "/usr/local/bin/seq", + "sha1sum": "/usr/local/bin/sha1sum", + "sha224sum": "/usr/local/bin/sha224sum", + "sha256sum": "/usr/local/bin/sha256sum", + "sha384sum": "/usr/local/bin/sha384sum", + "sha512sum": "/usr/local/bin/sha512sum", + "shasum": "/usr/local/bin/shasum", + "shiftBed": "/usr/local/bin/shiftBed", + "shred": "/usr/local/bin/shred", + "shuf": "/usr/local/bin/shuf", + "shuffleBed": "/usr/local/bin/shuffleBed", + "sim_client": "/usr/local/bin/sim_client", + "skip-if-file-exists": "/usr/local/bin/skip-if-file-exists", + "sleep": "/usr/local/bin/sleep", + "slopBed": "/usr/local/bin/slopBed", + "snp2hgvs": "/usr/local/bin/snp2hgvs", + "snp2tbl": "/usr/local/bin/snp2tbl", + "sort": "/usr/local/bin/sort", + "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", + "sortBed": "/usr/local/bin/sortBed", + "spdi2tbl": "/usr/local/bin/spdi2tbl", + "splain": "/usr/local/bin/splain", + "split": "/usr/local/bin/split", + "split-at-intron": "/usr/local/bin/split-at-intron", + "sql": "/usr/local/bin/sql", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "stat": "/usr/local/bin/stat", + "stdbuf": "/usr/local/bin/stdbuf", + "stream-local": "/usr/local/bin/stream-local", + "stream-pubmed": "/usr/local/bin/stream-pubmed", + "streamzip": "/usr/local/bin/streamzip", + "stty": "/usr/local/bin/stty", + "subtractBed": "/usr/local/bin/subtractBed", + "sum": "/usr/local/bin/sum", + "sync": "/usr/local/bin/sync", + "tabs": "/usr/local/bin/tabs", + "tac": "/usr/local/bin/tac", + "tagBam": "/usr/local/bin/tagBam", + "tail": "/usr/local/bin/tail", + "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": 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"/usr/local/bin/toe", + "toml2xml": "/usr/local/bin/toml2xml", + "tomlq": "/usr/local/bin/tomlq", + "touch": "/usr/local/bin/touch", + "tput": "/usr/local/bin/tput", + "tr": "/usr/local/bin/tr", + "transmute": "/usr/local/bin/transmute", + "transmute.Linux": "/usr/local/bin/transmute.Linux", + "true": "/usr/local/bin/true", + "truncate": "/usr/local/bin/truncate", + "tset": "/usr/local/bin/tset", + "tsort": "/usr/local/bin/tsort", + "tty": "/usr/local/bin/tty", + "uname": "/usr/local/bin/uname", + "unexpand": "/usr/local/bin/unexpand", + "unionBedGraphs": "/usr/local/bin/unionBedGraphs", + "uniq": "/usr/local/bin/uniq", + "uniq-table": "/usr/local/bin/uniq-table", + "unlink": "/usr/local/bin/unlink", + "unlzma": "/usr/local/bin/unlzma", + "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", + "update_sequences.sh": 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/dev/null +++ b/quay.io/biocontainers/g/get_orfs:1.0.0--hdcf5f25_0.json @@ -0,0 +1,4 @@ +{ + "get_orfs": "/usr/local/bin/get_orfs", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/h/handyreadgenotyper:0.1.13--pyhdfd78af_0.json b/quay.io/biocontainers/h/handyreadgenotyper:0.1.13--pyhdfd78af_0.json new file mode 100644 index 0000000..288dfd8 --- /dev/null +++ b/quay.io/biocontainers/h/handyreadgenotyper:0.1.13--pyhdfd78af_0.json @@ -0,0 +1,151 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.8": "/usr/local/bin/2to3-3.8", + "ace2sam": "/usr/local/bin/ace2sam", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "annot-tsv": "/usr/local/bin/annot-tsv", + "bgzip": "/usr/local/bin/bgzip", + "blast2sam.pl": "/usr/local/bin/blast2sam.pl", + "bowtie2sam.pl": "/usr/local/bin/bowtie2sam.pl", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": 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"/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", + "zoom2sam.pl": "/usr/local/bin/zoom2sam.pl", + "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/m/mgikit:0.1.5--h4c94732_0.json b/quay.io/biocontainers/m/mgikit:0.1.5--h4c94732_0.json new file mode 100644 index 0000000..192cf06 --- /dev/null +++ b/quay.io/biocontainers/m/mgikit:0.1.5--h4c94732_0.json @@ -0,0 +1,4 @@ +{ + "mgikit": "/usr/local/bin/mgikit", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/m/mmseqs2-server:8.c4b9644--he881be0_0.json b/quay.io/biocontainers/m/mmseqs2-server:8.c4b9644--he881be0_0.json new file mode 100644 index 0000000..87bc75d --- /dev/null +++ b/quay.io/biocontainers/m/mmseqs2-server:8.c4b9644--he881be0_0.json @@ -0,0 +1,130 @@ +{ + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "aria2c": "/usr/local/bin/aria2c", + "autopoint": "/usr/local/bin/autopoint", + "awk": "/usr/local/bin/awk", + "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", + "corelist": "/usr/local/bin/corelist", + "cpan": "/usr/local/bin/cpan", + "derb": "/usr/local/bin/derb", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "envsubst": "/usr/local/bin/envsubst", + "foldseek": "/usr/local/bin/foldseek", + "gawk": "/usr/local/bin/gawk", + "gawk-5.3.0": "/usr/local/bin/gawk-5.3.0", + "gawkbug": "/usr/local/bin/gawkbug", + "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", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "idn2": "/usr/local/bin/idn2", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "instmodsh": "/usr/local/bin/instmodsh", + "json_pp": "/usr/local/bin/json_pp", + "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", + "makeconv": "/usr/local/bin/makeconv", + "mmseqs": "/usr/local/bin/mmseqs", + "mmseqs-server": "/usr/local/bin/mmseqs-server", + "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", + "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", + "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", + "prove": "/usr/local/bin/prove", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "recode-sr-latin": "/usr/local/bin/recode-sr-latin", + "reset": "/usr/local/bin/reset", + "shasum": "/usr/local/bin/shasum", + "splain": "/usr/local/bin/splain", + "streamzip": "/usr/local/bin/streamzip", + "tabs": "/usr/local/bin/tabs", + "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", + "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", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/r/rnavirhost:1.0.5--pyh7cba7a3_0.json b/quay.io/biocontainers/r/rnavirhost:1.0.5--pyh7cba7a3_0.json new file mode 100644 index 0000000..d8e5a78 --- /dev/null +++ b/quay.io/biocontainers/r/rnavirhost:1.0.5--pyh7cba7a3_0.json @@ -0,0 +1,306 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.12": "/usr/local/bin/2to3-3.12", + "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", + "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", + "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", + "cit2pmid": "/usr/local/bin/cit2pmid", + "cleanup-blastdb-volumes.py": "/usr/local/bin/cleanup-blastdb-volumes.py", + "clear": "/usr/local/bin/clear", + "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", + "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", + "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", + "idle3.12": "/usr/local/bin/idle3.12", + "idn2": "/usr/local/bin/idn2", + "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", + "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", + "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", + "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", + "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", + "phrase-search": "/usr/local/bin/phrase-search", + "piconv": "/usr/local/bin/piconv", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pl2pm": "/usr/local/bin/pl2pm", + "pma2apa": "/usr/local/bin/pma2apa", + "pma2pme": "/usr/local/bin/pma2pme", + "pmc2bioc": "/usr/local/bin/pmc2bioc", + "pmc2info": "/usr/local/bin/pmc2info", + "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", + "prodigal": "/usr/local/bin/prodigal", + "project_tree_builder": "/usr/local/bin/project_tree_builder", + "prove": "/usr/local/bin/prove", + "psiblast": "/usr/local/bin/psiblast", + "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", + "pydoc3.12": "/usr/local/bin/pydoc3.12", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.12": "/usr/local/bin/python3.12", + "python3.12-config": "/usr/local/bin/python3.12-config", + "quote-grouped-elements": "/usr/local/bin/quote-grouped-elements", + "rchive": "/usr/local/bin/rchive", + "rchive.Linux": "/usr/local/bin/rchive.Linux", + "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", + "rnavirhost": "/usr/local/bin/rnavirhost", + "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", + "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", + "toe": "/usr/local/bin/toe", + "toml2xml": "/usr/local/bin/toml2xml", + "tput": "/usr/local/bin/tput", + "transmute": "/usr/local/bin/transmute", + "transmute.Linux": "/usr/local/bin/transmute.Linux", + "tset": "/usr/local/bin/tset", + "uniq-table": "/usr/local/bin/uniq-table", + "unlzma": "/usr/local/bin/unlzma", + "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", + "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", + "xgboost": "/usr/local/bin/xgboost", + "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/s/shigapass:1.5.0--hdfd78af_0.json b/quay.io/biocontainers/s/shigapass:1.5.0--hdfd78af_0.json new file mode 100644 index 0000000..c9d1022 --- /dev/null +++ b/quay.io/biocontainers/s/shigapass:1.5.0--hdfd78af_0.json @@ -0,0 +1,257 @@ +{ + "ShigaPass.sh": "/usr/local/bin/ShigaPass.sh", + "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", + "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", + "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", + "cit2pmid": "/usr/local/bin/cit2pmid", + "cleanup-blastdb-volumes.py": "/usr/local/bin/cleanup-blastdb-volumes.py", + "clear": "/usr/local/bin/clear", + "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", + "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", + "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", + "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", + "idn2": "/usr/local/bin/idn2", + "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", + "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", + "libnetcfg": "/usr/local/bin/libnetcfg", + "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", + "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", + "phrase-search": "/usr/local/bin/phrase-search", + "piconv": "/usr/local/bin/piconv", + "pl2pm": "/usr/local/bin/pl2pm", + "pma2apa": "/usr/local/bin/pma2apa", + "pma2pme": "/usr/local/bin/pma2pme", + "pmc2bioc": "/usr/local/bin/pmc2bioc", + "pmc2info": "/usr/local/bin/pmc2info", + "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", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "quote-grouped-elements": "/usr/local/bin/quote-grouped-elements", + "rchive": "/usr/local/bin/rchive", + "rchive.Linux": "/usr/local/bin/rchive.Linux", + "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", + "stream-local": "/usr/local/bin/stream-local", + "stream-pubmed": "/usr/local/bin/stream-pubmed", + "streamzip": "/usr/local/bin/streamzip", + "tabs": "/usr/local/bin/tabs", + "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", + "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", + "toe": "/usr/local/bin/toe", + "toml2xml": "/usr/local/bin/toml2xml", + "tput": "/usr/local/bin/tput", + "transmute": "/usr/local/bin/transmute", + "transmute.Linux": "/usr/local/bin/transmute.Linux", + "tset": "/usr/local/bin/tset", + "uniq-table": "/usr/local/bin/uniq-table", + "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", + "windowmasker": "/usr/local/bin/windowmasker", + "windowmasker_2.2.22_adapter.py": "/usr/local/bin/windowmasker_2.2.22_adapter.py", + "word-at-a-time": "/usr/local/bin/word-at-a-time", + "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", + "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/s/sneakernet-qc:0.25.0--pl5321hdfd78af_0.json b/quay.io/biocontainers/s/sneakernet-qc:0.25.0--pl5321hdfd78af_0.json new file mode 100644 index 0000000..2a543ab --- /dev/null +++ b/quay.io/biocontainers/s/sneakernet-qc:0.25.0--pl5321hdfd78af_0.json @@ -0,0 +1,892 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.10": "/usr/local/bin/2to3-3.10", + "AnalyseDists": "/usr/local/bin/AnalyseDists", + "AnalyseSeqs": "/usr/local/bin/AnalyseSeqs", + "Kinfold": "/usr/local/bin/Kinfold", + "RNA2Dfold": "/usr/local/bin/RNA2Dfold", + "RNALalifold": "/usr/local/bin/RNALalifold", + "RNALfold": "/usr/local/bin/RNALfold", + "RNAPKplex": "/usr/local/bin/RNAPKplex", + "RNAaliduplex": "/usr/local/bin/RNAaliduplex", + "RNAalifold": "/usr/local/bin/RNAalifold", + "RNAcofold": "/usr/local/bin/RNAcofold", + "RNAdistance": "/usr/local/bin/RNAdistance", + "RNAdos": "/usr/local/bin/RNAdos", + "RNAduplex": "/usr/local/bin/RNAduplex", + "RNAeval": "/usr/local/bin/RNAeval", + "RNAfold": "/usr/local/bin/RNAfold", + "RNAforester": "/usr/local/bin/RNAforester", + "RNAheat": "/usr/local/bin/RNAheat", + "RNAinverse": "/usr/local/bin/RNAinverse", + "RNAlocmin": "/usr/local/bin/RNAlocmin", + "RNAmultifold": "/usr/local/bin/RNAmultifold", + "RNApaln": "/usr/local/bin/RNApaln", + "RNAparconv": "/usr/local/bin/RNAparconv", + "RNApdist": "/usr/local/bin/RNApdist", + "RNAplex": "/usr/local/bin/RNAplex", + "RNAplfold": "/usr/local/bin/RNAplfold", + "RNAplot": "/usr/local/bin/RNAplot", + "RNApvmin": "/usr/local/bin/RNApvmin", + "RNAsnoop": "/usr/local/bin/RNAsnoop", + "RNAsubopt": "/usr/local/bin/RNAsubopt", + "RNAup": "/usr/local/bin/RNAup", + "SalmID.py": "/usr/local/bin/SalmID.py", + "SneakerNet.checkdeps.pl": "/usr/local/bin/SneakerNet.checkdeps.pl", + "SneakerNet.ionTorrent.ro.pl": "/usr/local/bin/SneakerNet.ionTorrent.ro.pl", + "SneakerNet.pl": "/usr/local/bin/SneakerNet.pl", + "SneakerNet.roRun.pl": "/usr/local/bin/SneakerNet.roRun.pl", + "SneakerNetPlugins.pl": "/usr/local/bin/SneakerNetPlugins.pl", + "TMalign": "/usr/local/bin/TMalign", + "accn-at-a-time": "/usr/local/bin/accn-at-a-time", + "ace2sam": "/usr/local/bin/ace2sam", + "addReadMetrics.pl": "/usr/local/bin/addReadMetrics.pl", + "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", + "annot-tsv": "/usr/local/bin/annot-tsv", + "annotate": "/usr/local/bin/annotate", + "annotateBed": "/usr/local/bin/annotateBed", + "any2fasta": "/usr/local/bin/any2fasta", + "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", + "args2slice": "/usr/local/bin/args2slice", + "aserver": "/usr/local/bin/aserver", + "asn2ref": "/usr/local/bin/asn2ref", + "asn2xml": "/usr/local/bin/asn2xml", + "assembleAll.pl": "/usr/local/bin/assembleAll.pl", + "autopoint": "/usr/local/bin/autopoint", + "awk": "/usr/local/bin/awk", + "b2ct": "/usr/local/bin/b2ct", + "bamToBed": "/usr/local/bin/bamToBed", + "bamToFastq": "/usr/local/bin/bamToFastq", + "bamToGBrowse.pl": "/usr/local/bin/bamToGBrowse.pl", + "baseBalance.pl": "/usr/local/bin/baseBalance.pl", + "baseml": "/usr/local/bin/baseml", + "basemlg": "/usr/local/bin/basemlg", + "bdf2gdfont.pl": "/usr/local/bin/bdf2gdfont.pl", + "bdftogd": "/usr/local/bin/bdftogd", + "bed12ToBed6": "/usr/local/bin/bed12ToBed6", + "bedToBam": "/usr/local/bin/bedToBam", + "bedToIgv": "/usr/local/bin/bedToIgv", + "bedpeToBam": "/usr/local/bin/bedpeToBam", + "bedtools": 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"/usr/local/bin/gsl-histogram", + "gsl-randist": "/usr/local/bin/gsl-randist", + "gss-client": "/usr/local/bin/gss-client", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "hb-info": "/usr/local/bin/hb-info", + "hb-ot-shape-closure": "/usr/local/bin/hb-ot-shape-closure", + "hb-shape": "/usr/local/bin/hb-shape", + "hb-subset": "/usr/local/bin/hb-subset", + "hb-view": "/usr/local/bin/hb-view", + "hgvs2spdi": "/usr/local/bin/hgvs2spdi", + "htsfile": "/usr/local/bin/htsfile", + "humanfriendly": "/usr/local/bin/humanfriendly", + "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": 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"/usr/local/bin/kmc_tools", + "kmercounter": "/usr/local/bin/kmercounter", + "kpasswd": "/usr/local/bin/kpasswd", + "kraken": "/usr/local/bin/kraken", + "kraken-build": "/usr/local/bin/kraken-build", + "kraken-filter": "/usr/local/bin/kraken-filter", + "kraken-mpa-report": "/usr/local/bin/kraken-mpa-report", + "kraken-report": "/usr/local/bin/kraken-report", + "kraken-translate": "/usr/local/bin/kraken-translate", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktClassifyBLAST": "/usr/local/bin/ktClassifyBLAST", + "ktClassifyHits": "/usr/local/bin/ktClassifyHits", + "ktGetContigMagnitudes": "/usr/local/bin/ktGetContigMagnitudes", + "ktGetLCA": "/usr/local/bin/ktGetLCA", + "ktGetLibPath": "/usr/local/bin/ktGetLibPath", + "ktGetTaxIDFromAcc": "/usr/local/bin/ktGetTaxIDFromAcc", + "ktGetTaxInfo": "/usr/local/bin/ktGetTaxInfo", + "ktImportBLAST": "/usr/local/bin/ktImportBLAST", + "ktImportDiskUsage": 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+ "megahit_core_popcnt": "/usr/local/bin/megahit_core_popcnt", + "megahit_toolkit": "/usr/local/bin/megahit_toolkit", + "mergeBed": "/usr/local/bin/mergeBed", + "metaquast": "/usr/local/bin/metaquast", + "metaquast.py": "/usr/local/bin/metaquast.py", + "metaspades.py": "/usr/local/bin/metaspades.py", + "minimap2": "/usr/local/bin/minimap2", + "mlst": "/usr/local/bin/mlst", + "mlst-ST_mini_genomes": "/usr/local/bin/mlst-ST_mini_genomes", + "mlst-consistency_checker": "/usr/local/bin/mlst-consistency_checker", + "mlst-download_pub_mlst": "/usr/local/bin/mlst-download_pub_mlst", + "mlst-make_blast_db": "/usr/local/bin/mlst-make_blast_db", + "mlst-show_seqs": "/usr/local/bin/mlst-show_seqs", + "mobsuiteRepresentativeFasta.pl": "/usr/local/bin/mobsuiteRepresentativeFasta.pl", + "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": 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"spades-corrector-core": "/usr/local/bin/spades-corrector-core", + "spades-gbuilder": "/usr/local/bin/spades-gbuilder", + "spades-gmapper": "/usr/local/bin/spades-gmapper", + "spades-gsimplifier": "/usr/local/bin/spades-gsimplifier", + "spades-hammer": "/usr/local/bin/spades-hammer", + "spades-ionhammer": "/usr/local/bin/spades-ionhammer", + "spades-kmer-estimating": "/usr/local/bin/spades-kmer-estimating", + "spades-kmercount": "/usr/local/bin/spades-kmercount", + "spades-read-filter": "/usr/local/bin/spades-read-filter", + "spades-truseq-scfcorrection": "/usr/local/bin/spades-truseq-scfcorrection", + "spades.py": "/usr/local/bin/spades.py", + "spades_init.py": "/usr/local/bin/spades_init.py", + "spaligner": "/usr/local/bin/spaligner", + "spdi2tbl": "/usr/local/bin/spdi2tbl", + "splain": "/usr/local/bin/splain", + "split-at-intron": "/usr/local/bin/split-at-intron", + "sql": "/usr/local/bin/sql", + "sqlite3": "/usr/local/bin/sqlite3", + "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", + "subtractBed": "/usr/local/bin/subtractBed", + "t_coffee": "/usr/local/bin/t_coffee", + "tabix": "/usr/local/bin/tabix", + "tabs": "/usr/local/bin/tabs", + "tagBam": "/usr/local/bin/tagBam", + "tar": "/usr/local/bin/tar", + "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.modules": "/usr/local/bin/test.modules", + "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", + "tqdm": "/usr/local/bin/tqdm", + "trainGlimmerHMM": "/usr/local/bin/trainGlimmerHMM", + "transferFilesToRemoteComputers.pl": "/usr/local/bin/transferFilesToRemoteComputers.pl", + "transicc": "/usr/local/bin/transicc", + "transmute": "/usr/local/bin/transmute", + "transmute.Linux": "/usr/local/bin/transmute.Linux", + "trimmomatic": "/usr/local/bin/trimmomatic", + "truspades.py": "/usr/local/bin/truspades.py", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "unionBedGraphs": "/usr/local/bin/unionBedGraphs", + "uniq-table": "/usr/local/bin/uniq-table", + "unlz4": "/usr/local/bin/unlz4", + "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", + "validateTaxonomy.pl": "/usr/local/bin/validateTaxonomy.pl", + "velvetg": "/usr/local/bin/velvetg", + "velveth": "/usr/local/bin/velveth", + "webpinfo": "/usr/local/bin/webpinfo", + "webpmux": "/usr/local/bin/webpmux", + "webpng": "/usr/local/bin/webpng", + "wget": "/usr/local/bin/wget", + "wgsim": "/usr/local/bin/wgsim", + "wgsim_eval.pl": "/usr/local/bin/wgsim_eval.pl", + "wheel": "/usr/local/bin/wheel", + "windowBed": "/usr/local/bin/windowBed", + "windowMaker": "/usr/local/bin/windowMaker", + "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", + "xa2multi.pl": "/usr/local/bin/xa2multi.pl", + "xgettext": "/usr/local/bin/xgettext", + "xml2-config": "/usr/local/bin/xml2-config", + "xml2fsa": "/usr/local/bin/xml2fsa", + "xml2json": "/usr/local/bin/xml2json", + "xml2tbl": "/usr/local/bin/xml2tbl", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xmlwf": "/usr/local/bin/xmlwf", + "xsubpp": "/usr/local/bin/xsubpp", + "xtract": "/usr/local/bin/xtract", + "xtract.Linux": "/usr/local/bin/xtract.Linux", + "xxh128sum": "/usr/local/bin/xxh128sum", + "xxh32sum": "/usr/local/bin/xxh32sum", + "xxh64sum": "/usr/local/bin/xxh64sum", + "xxhsum": "/usr/local/bin/xxhsum", + "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", + "yn00": "/usr/local/bin/yn00", + "zipdetails": "/usr/local/bin/zipdetails", + "zoom2sam.pl": "/usr/local/bin/zoom2sam.pl", + "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/sspace_basic:2.1.1--hdfd78af_0.json b/quay.io/biocontainers/s/sspace_basic:2.1.1--hdfd78af_0.json new file mode 100644 index 0000000..dc56357 --- /dev/null +++ b/quay.io/biocontainers/s/sspace_basic:2.1.1--hdfd78af_0.json @@ -0,0 +1,165 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.10": "/usr/local/bin/2to3-3.10", + "ExtendOrFormatContigs.pl": "/usr/local/bin/ExtendOrFormatContigs.pl", + "ExtendOrFormatContigs.pl.bak": "/usr/local/bin/ExtendOrFormatContigs.pl.bak", + "PairingAndScaffolding.pl": "/usr/local/bin/PairingAndScaffolding.pl", + "PairingAndScaffolding.pl.bak": "/usr/local/bin/PairingAndScaffolding.pl.bak", + "SSPACE_Basic.pl": "/usr/local/bin/SSPACE_Basic.pl", + "SSPACE_Basic.pl.bak": "/usr/local/bin/SSPACE_Basic.pl.bak", + "TQS.py": "/usr/local/bin/TQS.py", + "TQS.readme": "/usr/local/bin/TQS.readme", + "TQSexport.py": "/usr/local/bin/TQSexport.py", + "TQSfastq.py": "/usr/local/bin/TQSfastq.py", + "bowtie": "/usr/local/bin/bowtie", + "bowtie-align-l": "/usr/local/bin/bowtie-align-l", + "bowtie-align-s": "/usr/local/bin/bowtie-align-s", + "bowtie-build": "/usr/local/bin/bowtie-build", + "bowtie-build-l": "/usr/local/bin/bowtie-build-l", + "bowtie-build-s": "/usr/local/bin/bowtie-build-s", + "bowtie-inspect": "/usr/local/bin/bowtie-inspect", + "bowtie-inspect-l": "/usr/local/bin/bowtie-inspect-l", + "bowtie-inspect-s": "/usr/local/bin/bowtie-inspect-s", + "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", + "corelist": "/usr/local/bin/corelist", + "cpan": "/usr/local/bin/cpan", + "derb": "/usr/local/bin/derb", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "estimate_insert_size.pl": "/usr/local/bin/estimate_insert_size.pl", + "estimate_insert_size.pl.bak": "/usr/local/bin/estimate_insert_size.pl.bak", + "fq_all2std.pl": "/usr/local/bin/fq_all2std.pl", + "fq_all2std.pl.bak": "/usr/local/bin/fq_all2std.pl.bak", + "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", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "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": "/usr/local/bin/idle3.10", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "instmodsh": "/usr/local/bin/instmodsh", + "json_pp": "/usr/local/bin/json_pp", + "libnetcfg": "/usr/local/bin/libnetcfg", + "lstopo": "/usr/local/bin/lstopo", + "lstopo-no-graphics": "/usr/local/bin/lstopo-no-graphics", + "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", + "makeconv": "/usr/local/bin/makeconv", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "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", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "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", + "prove": "/usr/local/bin/prove", + "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", + "pydoc3.10": "/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", + "qseq2fasta.pl": "/usr/local/bin/qseq2fasta.pl", + "qseq2fasta.pl.bak": "/usr/local/bin/qseq2fasta.pl.bak", + "qseq2fastq.pl": "/usr/local/bin/qseq2fastq.pl", + "qseq2fastq.pl.bak": "/usr/local/bin/qseq2fastq.pl.bak", + "readLibFiles.pl": "/usr/local/bin/readLibFiles.pl", + "readLibFiles.pl.bak": "/usr/local/bin/readLibFiles.pl.bak", + "reset": "/usr/local/bin/reset", + "sam_bam2tab.pl": "/usr/local/bin/sam_bam2tab.pl", + "sam_bam2tab.pl.bak": "/usr/local/bin/sam_bam2tab.pl.bak", + "shasum": "/usr/local/bin/shasum", + "splain": "/usr/local/bin/splain", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "sspace_basic": "/usr/local/bin/sspace_basic", + "streamzip": "/usr/local/bin/streamzip", + "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", + "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", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file