From 7d064fc78f5ee0ec0214a8a1ea4809fc9b828e5b Mon Sep 17 00:00:00 2001 From: github-actions Date: Thu, 31 Oct 2024 00:59:57 +0000 Subject: [PATCH] Automated deployment with updated cache 2024-10-31 --- counts.json | 1236 +++++++++-------- .../a/ampd-up:1.0.0--pyhdfd78af_0.json | 93 ++ .../c/cell2cell:0.7.4--py38h4ac6f70_0.json | 208 +++ .../c/coptr:1.1.4--pyhdfd78af_1.json | 195 +++ .../c/corneto:1.0.0a0--pyhdfd78af_0.json | 74 + ...eepchopper-cli:1.2.5--py310h77ce02f_0.json | 74 + .../d/doubletdetection:4.2--pyhdfd78af_0.json | 205 +++ .../j/jarvis3:3.7--h031d066_1.json | 8 + .../l/libgff:2.0.0--hdcf5f25_1.json | 1 + .../p/phenograph:1.5.7--pyhdfd78af_0.json | 80 ++ .../p/pyscenic:0.12.1--pyhdfd78af_0.json | 245 ++++ .../s/sopa:1.1.5--pyhdfd78af_0.json | 360 +++++ .../s/stxtyper:1.0.25--hdcf5f25_0.json | 259 ++++ 13 files changed, 2428 insertions(+), 610 deletions(-) create mode 100644 quay.io/biocontainers/a/ampd-up:1.0.0--pyhdfd78af_0.json create mode 100644 quay.io/biocontainers/c/cell2cell:0.7.4--py38h4ac6f70_0.json create mode 100644 quay.io/biocontainers/c/coptr:1.1.4--pyhdfd78af_1.json create mode 100644 quay.io/biocontainers/c/corneto:1.0.0a0--pyhdfd78af_0.json create mode 100644 quay.io/biocontainers/d/deepchopper-cli:1.2.5--py310h77ce02f_0.json create mode 100644 quay.io/biocontainers/d/doubletdetection:4.2--pyhdfd78af_0.json create mode 100644 quay.io/biocontainers/j/jarvis3:3.7--h031d066_1.json create mode 100644 quay.io/biocontainers/l/libgff:2.0.0--hdcf5f25_1.json create mode 100644 quay.io/biocontainers/p/phenograph:1.5.7--pyhdfd78af_0.json create mode 100644 quay.io/biocontainers/p/pyscenic:0.12.1--pyhdfd78af_0.json create mode 100644 quay.io/biocontainers/s/sopa:1.1.5--pyhdfd78af_0.json create mode 100644 quay.io/biocontainers/s/stxtyper:1.0.25--hdcf5f25_0.json diff --git a/counts.json b/counts.json index a64848a..fc4a3ec 100644 --- a/counts.json +++ b/counts.json @@ -2326,15 +2326,15 @@ "2csfastq_1csfastq": 1, "2ft": 2, "2ndscore": 1, - "2to3": 3802, - "2to3-3.10": 830, - "2to3-3.11": 281, - "2to3-3.12": 286, + "2to3": 3811, + "2to3-3.10": 831, + "2to3-3.11": 283, + "2to3-3.12": 290, "2to3-3.4": 6, "2to3-3.5": 103, - "2to3-3.6": 343, + "2to3-3.6": 344, "2to3-3.7": 383, - "2to3-3.8": 577, + "2to3-3.8": 578, "2to3-3.9": 660, "3EdgeTests": 1, "3_1_filter_mapQ_for_sam.pl": 1, @@ -2364,6 +2364,7 @@ "AMOScmp": 2, "AMOScmp-shortReads": 2, "AMOScmp-shortReads-alignmentTrimmed": 2, + "AMPd-Up": 1, "AMPlify": 1, "AMUSED": 2, "AMUSED-KS": 2, @@ -2769,7 +2770,7 @@ "Corrector_HA": 1, "CountUnmatchedSampleIndices": 1, "CoverageOfEachTrans": 1, - "CreateDOMDocument": 52, + "CreateDOMDocument": 53, "CreateGermlines.py": 2, "CreateIntervalsFiles": 1, "CrossMap.py": 3, @@ -2823,8 +2824,8 @@ "DNA2StdRegion": 1, "DNAMarkMaker": 1, "DNN_models.py": 1, - "DOMCount": 52, - "DOMPrint": 52, + "DOMCount": 53, + "DOMPrint": 53, "DRAM-setup.py": 1, "DRAM-v.py": 1, "DRAM.py": 1, @@ -2916,7 +2917,7 @@ "EnsembleScripts_sipros_peptides_assembling": 1, "EnsembleScripts_sipros_prepare_protein_database": 1, "EnsembleScripts_sipros_psm_tabulating": 1, - "EnumVal": 52, + "EnumVal": 53, "Epifany": 1, "Epsilon-NB.py": 1, "ErrorCorrection": 1, @@ -3287,6 +3288,9 @@ "J01415.2.gb": 1, "JAMM.sh": 1, "JARVIS": 1, + "JARVIS3": 1, + "JARVIS3.sh": 1, + "JARVIS3.sh.bak": 1, "JCcirc": 1, "JCcirc.pl": 1, "Jaeger": 1, @@ -3294,8 +3298,8 @@ "Joiner": 2, "JolyTree.sh": 1, "Juicebox_KR_normalization.sh": 1, - "JxrDecApp": 27, - "JxrEncApp": 27, + "JxrDecApp": 28, + "JxrEncApp": 28, "KAligner": 17, "KEGGCharter_prokaryotic_maps.txt": 2, "KO_database.keg": 1, @@ -3515,7 +3519,7 @@ "MaxQuantTaskCore.dll": 1, "MaxQuantTaskCore.runtimeconfig.json": 1, "Mayu.pl": 2, - "MemParse": 52, + "MemParse": 53, "MentaLiST.jl": 2, "MergeContigs": 17, "MergeContigs.py": 1, @@ -3763,14 +3767,14 @@ "PM-select-taxa": 1, "PM-split-seq": 1, "PM-update-taxa": 1, - "PParse": 52, + "PParse": 53, "PREFACE": 1, "PRScs.py": 1, "PReFerSim": 1, "PSCM_to_PSEM": 1, "PSCM_to_PSEM.cpp": 1, "PSMFeatureExtractor": 2, - "PSVIWriter": 52, + "PSVIWriter": 53, "PStrain.py": 1, "PStrain_m2.py": 1, "PTMProphetParser": 2, @@ -4244,7 +4248,7 @@ "RearrangementCheck.py": 1, "RecombinationSummary.r": 1, "Red": 2, - "Redirect": 52, + "Redirect": 53, "ReduceGtf": 1, "RefMapOpt.sh": 2, "ReferenceOpt.sh": 2, @@ -4298,19 +4302,19 @@ "SAMstats": 1, "SAMstatsParallel": 1, "SASpector": 1, - "SAX2Count": 52, - "SAX2Print": 52, - "SAXCount": 52, - "SAXPrint": 52, + "SAX2Count": 53, + "SAX2Print": 53, + "SAXCount": 53, + "SAXPrint": 53, "SCALOP": 1, "SCFtoCTG": 1, - "SCMPrint": 52, + "SCMPrint": 53, "SCNIC_analysis.py": 1, "SEACR_1.3.R": 1, "SEACR_1.3.sh": 1, "SELAM": 1, "SELAM_STATS": 1, - "SEnumVal": 52, + "SEnumVal": 53, "SGA-ICE.py": 1, "SHAPEIT5_ligate": 1, "SHAPEIT5_phase_common": 1, @@ -4511,7 +4515,7 @@ "StatisticReadsOnDNAsContam": 1, "StatisticSingle.py": 2, "Statistics.pm": 5, - "StdInParse": 52, + "StdInParse": 53, "StereoGene": 1, "StoatyDive.py": 1, "Stockholm.pm": 3, @@ -4525,7 +4529,7 @@ "SvPrep": 1, "SvmTheoreticalSpectrumGeneratorTrainer": 2, "SvtAv1DecApp": 12, - "SvtAv1EncApp": 18, + "SvtAv1EncApp": 19, "Sweave": 1, "SweepFinder2": 1, "SymmetryTester": 3, @@ -4730,11 +4734,13 @@ "XFDR": 2, "XGBoost.dll": 1, "XGBoostLib.dll": 1, - "XInclude": 52, + "XInclude": 53, "XMLValidator": 2, "XPressPeptideParser": 2, "XPressProteinRatioParser": 2, "XS": 1, + "XScoreC": 1, + "XScoreD": 1, "XTandemAdapter": 2, "XXmotif": 5, "Xcalcmem.sh": 13, @@ -5096,7 +5102,7 @@ "acc2locus": 2, "acc2tax": 1, "accession_retrieve": 1, - "accn-at-a-time": 284, + "accn-at-a-time": 285, "accurate_bkp.py": 1, "acdc": 28, "acdc-filter-fasta-by-name.awk": 1, @@ -5208,7 +5214,7 @@ "addtit.pl": 2, "adf_checker.pl": 1, "adhocfilelist": 1, - "adig": 4612, + "adig": 4618, "adjustPeakFile.pl": 5, "adjustRedunGroupFile.pl": 5, "adjustScanRankerScoreByGroup": 2, @@ -5325,7 +5331,7 @@ "agrvate": 1, "agtsampleinforw.dll": 2, "ahmm-s": 1, - "ahost": 4612, + "ahost": 4618, "airr-tools": 5, "akita_data.py": 1, "akita_data_read.py": 1, @@ -5369,7 +5375,7 @@ "align-cache.2.11.0": 10, "align-cache.3": 2, "align-cache.3.0.0": 2, - "align-columns": 227, + "align-columns": 228, "align-ema.smk": 1, "align-families.py": 1, "align-info": 23, @@ -5499,7 +5505,7 @@ "amdgpu-arch": 1, "ame": 13, "amgr": 1, - "amino-acid-composition": 315, + "amino-acid-composition": 316, "aminoextract": 2, "amk_ccc": 2, "amk_fft2": 2, @@ -5831,8 +5837,8 @@ "anvi-upgrade": 2, "any2fasta": 22, "aodp": 1, - "aomdec": 26, - "aomenc": 26, + "aomdec": 27, + "aomenc": 27, "api_binding_site": 1, "apirst2html.py": 1, "aplanat": 2, @@ -5849,7 +5855,7 @@ "appletviewer": 117, "apply_mdae": 1, "apply_to_db.py": 1, - "applygeo": 38, + "applygeo": 39, "applyvariants.sh": 30, "appspam": 1, "apptainer": 1, @@ -5934,15 +5940,16 @@ "arb_wetc": 2, "arb_who": 2, "arborator": 1, + "arboreto_with_multiprocessing.py": 1, "arcasHLA": 1, "archer": 1, "architeuthis": 1, - "archive-ncbinlp": 38, - "archive-nihocc": 38, - "archive-nmcds": 38, - "archive-pmc": 38, - "archive-pubmed": 314, - "archive-taxonomy": 38, + "archive-ncbinlp": 39, + "archive-nihocc": 39, + "archive-nmcds": 39, + "archive-pmc": 39, + "archive-pubmed": 315, + "archive-taxonomy": 39, "archive_directory.py": 2, "archosv": 2, "archspec": 11, @@ -5953,7 +5960,7 @@ "argnorm": 1, "argparse2tool": 1, "argparse2tool_check_path": 1, - "args2slice": 38, + "args2slice": 39, "args_oap": 1, "aria2c": 28, "ariba": 3, @@ -6030,8 +6037,8 @@ "asn2ff": 1, "asn2gb": 2, "asn2idx": 1, - "asn2ref": 38, - "asn2xml": 228, + "asn2ref": 39, + "asn2xml": 229, "asndhuff": 1, "asntool": 1, "asp-cp": 87, @@ -6137,7 +6144,7 @@ "autometa-taxonomy-majority-vote": 2, "autometa-unclustered-recruitment": 2, "autometa-update-databases": 2, - "autopoint": 5319, + "autopoint": 5320, "autoreconf.bak": 10, "autoscan.bak": 10, "autoupdate.bak": 10, @@ -6740,7 +6747,7 @@ "beta_diversity.py": 4, "beta_diversity_through_plots.py": 1, "beta_significance.py": 1, - "between-two-genes": 315, + "between-two-genes": 316, "bf.sh": 1, "bfc": 1, "bfconvert": 1, @@ -6958,7 +6965,7 @@ "blast_check_pair.pl": 1, "blast_filter.pl": 1, "blast_format_unit_test": 5, - "blast_formatter": 349, + "blast_formatter": 350, "blast_names_mapping.tsv": 1, "blast_outfmt6_replace_trans_id_w_gene_symbol.pl": 1, "blast_report": 21, @@ -6973,12 +6980,12 @@ "blastbesties": 1, "blastcl3": 1, "blastclust": 38, - "blastdb_aliastool": 349, + "blastdb_aliastool": 350, "blastdb_convert": 21, "blastdb_format_unit_test": 5, "blastdb_path": 21, - "blastdbcheck": 349, - "blastdbcmd": 349, + "blastdbcheck": 350, + "blastdbcmd": 350, "blastdbcp": 55, "blastdiag_unit_test": 5, "blastengine_unit_test": 5, @@ -6987,13 +6994,13 @@ "blastfilter_unit_test": 5, "blasthits_unit_test": 5, "blastinput_unit_test": 5, - "blastn": 349, - "blastn_vdb": 62, + "blastn": 350, + "blastn_vdb": 63, "blastoptions_unit_test": 5, - "blastp": 349, + "blastp": 350, "blastpgp": 38, "blastsetup_unit_test": 5, - "blastx": 349, + "blastx": 350, "blastzWrapper": 1, "blat": 19, "blat2gbrowse.pl": 15, @@ -7017,8 +7024,8 @@ "blossom5": 1, "blossom_randGraph.py": 1, "blosum62.fas": 2, - "blst2gm": 38, - "blst2tkns": 227, + "blst2gm": 39, + "blst2tkns": 228, "bmaToLinks.pl": 1, "bmfilter": 4, "bmge": 1, @@ -7036,7 +7043,7 @@ "bogusness": 3, "bohra": 1, "boink": 1, - "bokeh": 72, + "bokeh": 74, "bold2utax.py": 1, "bold_identification": 1, "bolt": 2, @@ -7062,15 +7069,15 @@ "bowtie-inspect": 41, "bowtie-inspect-l": 36, "bowtie-inspect-s": 36, - "bowtie2": 115, - "bowtie2-align-l": 115, - "bowtie2-align-s": 115, - "bowtie2-build": 115, - "bowtie2-build-l": 115, - "bowtie2-build-s": 115, - "bowtie2-inspect": 115, - "bowtie2-inspect-l": 115, - "bowtie2-inspect-s": 115, + "bowtie2": 116, + "bowtie2-align-l": 116, + "bowtie2-align-s": 116, + "bowtie2-build": 116, + "bowtie2-build-l": 116, + "bowtie2-build-s": 116, + "bowtie2-inspect": 116, + "bowtie2-inspect-l": 116, + "bowtie2-inspect-s": 116, "bowtie2_stuff.py": 2, "bowtie2sam.pl": 533, "bowtie_PE_separate_then_join.pl": 1, @@ -7239,7 +7246,7 @@ "broad_utils.py": 1, "brockman_pipeline": 1, "brooklyn_plot": 1, - "brotli": 462, + "brotli": 466, "browse": 18, "bs_call": 2, "bs_seeker2-align.py": 1, @@ -7247,14 +7254,14 @@ "bs_seeker2-call_methylation.py": 1, "bsalign": 1, "bsb4": 1, - "bsdcat": 38, - "bsdcpio": 38, - "bsdtar": 38, - "bsdunzip": 8, + "bsdcat": 39, + "bsdcpio": 39, + "bsdtar": 39, + "bsdunzip": 9, "bseqc2": 4, "bseqc2mbiasplot.R": 4, "bsmap": 5, - "bsmp2info": 18, + "bsmp2info": 19, "bsp2sam.py": 1, "bsrate": 1, "bsseeker2bismark.pl": 1, @@ -7344,7 +7351,7 @@ "bundlelinks": 2, "bundler": 19, "bunwarpj": 4, - "bunzip2": 6797, + "bunzip2": 6806, "burden_test_vase": 1, "burst_linux_DB12": 1, "burst_linux_DB15": 1, @@ -7398,16 +7405,16 @@ "bxStats.py": 1, "bxcl_seqqc": 1, "bxtools": 1, - "bzcat": 6797, - "bzcmp": 6797, - "bzdiff": 6797, - "bzegrep": 6797, - "bzfgrep": 6797, - "bzgrep": 6797, - "bzip2": 6797, - "bzip2recover": 6797, - "bzless": 6797, - "bzmore": 6797, + "bzcat": 6806, + "bzcmp": 6806, + "bzdiff": 6806, + "bzegrep": 6806, + "bzfgrep": 6806, + "bzgrep": 6806, + "bzip2": 6807, + "bzip2recover": 6806, + "bzless": 6806, + "bzmore": 6806, "c++": 5, "c++filt": 8, "c-index-test": 8, @@ -7424,7 +7431,7 @@ "cPecanLibTests": 1, "cPecanModifyHmm": 1, "cPecanRealign": 1, - "c_rehash": 7942, + "c_rehash": 7952, "ca2ace.pl": 3, "ca2ctg": 2, "ca2mates": 2, @@ -7605,7 +7612,7 @@ "capnpc-capnp": 58, "capnpc-cython": 1, "capri_eval": 1, - "captoinfo": 7874, + "captoinfo": 7884, "captus_assembly": 1, "caqc.pl": 3, "caqc_help.ini": 3, @@ -7696,7 +7703,7 @@ "cbc": 110, "cbi": 1, "cblaster": 1, - "cbrunsli": 27, + "cbrunsli": 28, "cc": 5, "cc.bin": 2, "ccache-swig": 13, @@ -7722,7 +7729,7 @@ "ccs-kinetics-bystrandify": 3, "ccs_dir": 1, "ccsmeth": 1, - "cct": 42, + "cct": 43, "cctk": 1, "cd-hit": 50, "cd-hit-2d": 50, @@ -7942,7 +7949,7 @@ "checkqc-ws": 1, "checkstrand.sh": 1, "checksub": 1, - "checksum-profile": 3, + "checksum-profile": 5, "checktrans": 27, "checkv": 3, "cheetah": 10, @@ -8050,10 +8057,10 @@ "circulocov": 1, "cirdna": 27, "cirtap": 1, - "cit2pmid": 38, + "cit2pmid": 39, "civicpy": 1, "cjk-gs-integrate": 1, - "cjpeg": 5844, + "cjpeg": 5849, "ckeygen": 1, "cksum": 85, "claMLST": 1, @@ -8160,11 +8167,11 @@ "cleanmap.awk": 1, "cleanme.pl": 1, "cleanpp.sh": 3, - "cleanup-blastdb-volumes.py": 276, + "cleanup-blastdb-volumes.py": 277, "cleanup-coverage.py": 2, "cleanup-stale-gcp-resources.py": 1, "cleanup.py": 1, - "clear": 7874, + "clear": 7884, "clearCNV": 1, "clearcut": 1, "cleric": 1, @@ -8435,7 +8442,7 @@ "combine": 4, "combine-assembled-files.sh": 1, "combine-subexons": 1, - "combine-uid-lists": 38, + "combine-uid-lists": 39, "combineAndAnnotateReferences.pl": 1, "combineFile": 2, "combineFragandDBGraph_fastg.py": 1, @@ -8541,7 +8548,7 @@ "compileSpliceCands": 13, "compile_STARE_Linux.sh": 1, "compile_STARE_macOS.sh": 1, - "compile_et": 5903, + "compile_et": 5909, "compiled_table.py": 1, "compleasm": 1, "complementBed": 280, @@ -8718,11 +8725,11 @@ "conv-template": 17, "convbkmk": 1, "convert": 77, - "convert-caffe2-to-onnx": 53, + "convert-caffe2-to-onnx": 55, "convert-ccds-to-bed": 3, "convert-fasta-to-v2.pl": 3, "convert-mirdeep2-fasta.py": 1, - "convert-onnx-to-caffe2": 53, + "convert-onnx-to-caffe2": 55, "convert-readcount-file.py": 1, "convert-regions": 2, "convert-sam-for-rsem": 1, @@ -8730,7 +8737,7 @@ "convert2bed-float128": 15, "convert2bed-megarow": 15, "convert2bed-typical": 15, - "convert2blastmask": 349, + "convert2blastmask": 350, "convert2snns": 2, "convertCoordinates.pl": 5, "convertFastaQualToFastQ.rb": 1, @@ -8837,6 +8844,7 @@ "coords2clnt.py": 1, "coords2fa": 2, "copernicusmarine": 1, + "coptr": 1, "copyConfigTemplate": 1, "copy_accesion.py": 1, "copy_bismark_files_for_release.pl": 2, @@ -8852,7 +8860,7 @@ "core_diversity_analyses.py": 1, "core_methods.py": 1, "core_overlap_plot.py": 1, - "corelist": 1740, + "corelist": 1742, "corepack": 12, "coreprocess.pl": 3, "coresnpfilter": 1, @@ -8960,7 +8968,7 @@ "cp2k_run": 1, "cp2k_shell.ssmp": 1, "cpack": 11, - "cpan": 1740, + "cpan": 1742, "cpancover": 6, "cpanm": 245, "cpat.py": 1, @@ -9131,7 +9139,7 @@ "cryptogenotyper": 1, "cs": 3, "cs2bs_assembly": 1, - "cs2cs": 45, + "cs2cs": 46, "csb-bfit": 1, "csb-bfite": 1, "csb-buildhmm": 1, @@ -9154,12 +9162,13 @@ "cstacks": 1, "cstag": 1, "cstranslate": 4, - "csv-import": 71, + "csv-import": 73, "csv2kml": 1, + "csv2loom": 1, "csv2rdf": 34, "csv2tsv": 1, "csv2xlsx": 1, - "csv2xml": 227, + "csv2xml": 228, "csvExtractBorders": 1, "csvFrags2text": 1, "csv_to_tsv": 1, @@ -9207,8 +9216,8 @@ "curate_spatial_data": 1, "curate_universe": 1, "curesim": 2, - "curl": 5149, - "curl-config": 6007, + "curl": 5150, + "curl-config": 6013, "curlywhirly": 1, "curve_keygen": 72, "cusp": 27, @@ -9326,16 +9335,16 @@ "dash-generate-components": 13, "dash-update-components": 5, "dashing": 8, - "dask": 24, + "dask": 26, "dask scheduler": 1, "dask ssh": 1, "dask worker": 1, "dask-mpi": 4, "dask-remote": 5, - "dask-scheduler": 49, - "dask-ssh": 49, + "dask-scheduler": 51, + "dask-ssh": 51, "dask-submit": 5, - "dask-worker": 49, + "dask-worker": 51, "dask_utils.py": 1, "data.py": 1, "data_classes.py": 1, @@ -9363,13 +9372,13 @@ "dataset_manager.py": 1, "datasets": 3, "datasets-cli": 4, - "datashader": 2, - "datatool": 349, + "datashader": 3, + "datatool": 350, "datavzrd": 2, "date": 85, "datma.py": 1, "datma_seq.py": 1, - "dav1d": 19, + "dav1d": 20, "davix-cp": 1, "davix-get": 1, "davix-http": 1, @@ -9382,6 +9391,7 @@ "davix-unit-tests": 1, "dawg": 1, "dazcon": 4, + "db2feather": 1, "db2files": 2, "db2hgs": 2, "db2microsyntree": 2, @@ -9424,7 +9434,7 @@ "dbkit_create.py": 1, "dbkit_extract.py": 1, "dbkit_merge.py": 1, - "dbrunsli": 27, + "dbrunsli": 28, "dbscan": 1, "dbsnp_iit": 12, "dbtell": 27, @@ -9573,6 +9583,7 @@ "deeparg": 1, "deepbgc": 1, "deepbinner": 1, + "deepchopper-chop": 1, "deepdirect": 1, "deeplc": 4, "deeplc-gui": 4, @@ -9608,7 +9619,7 @@ "deltaBS.pl": 1, "delta_filter_wrapper.py": 5, "delta_unit_test": 5, - "deltablast": 349, + "deltablast": 350, "deltapd": 1, "demes": 5, "demesdraw": 1, @@ -9659,7 +9670,7 @@ "depth_calc.py": 1, "depth_estim_from_vcf.sh": 1, "depythontex": 1, - "derb": 5919, + "derb": 5922, "derep_stuff.py": 2, "deripcal": 1, "derna": 1, @@ -9748,7 +9759,7 @@ "diff_iso_usage": 1, "diff_motif": 1, "diffacto": 1, - "difference-uid-lists": 38, + "difference-uid-lists": 39, "difference_from_first_TSS_script_mordor.r": 1, "difference_from_first_TSS_script_mordor_chrom_wide.r": 1, "differentialBindingAffinity_multipleSNPs": 1, @@ -9788,7 +9799,7 @@ "dirmngr-client": 2, "dirname": 85, "dirseq": 2, - "disambiguate-nucleotides": 227, + "disambiguate-nucleotides": 228, "disco": 18, "disco.cfg": 1, "disco_2.cfg": 1, @@ -9829,7 +9840,7 @@ "django-admin": 4, "django-admin.py": 3, "django-admin.pyc": 1, - "djpeg": 5844, + "djpeg": 5849, "dkfzbiasfilter.py": 1, "dkfzbiasfilter_summarize.py": 1, "dlcoal_to_dlcpar": 1, @@ -9942,15 +9953,15 @@ "download-db.sh": 9, "download-dfam.py": 1, "download-entities.pl": 2, - "download-ncbi-data": 300, + "download-ncbi-data": 301, "download-ncbi-genomes": 1, - "download-ncbi-software": 227, + "download-ncbi-software": 228, "download-ncbi-taxa.sh": 1, "download-ncbi-taxmaps": 1, "download-ncbi-taxonomy": 1, - "download-pmc": 38, - "download-pubmed": 314, - "download-sequence": 314, + "download-pmc": 39, + "download-pubmed": 315, + "download-sequence": 315, "download-spatypes.sh": 1, "download-srr-files": 3, "download-taxonomy.sh": 1, @@ -10052,7 +10063,7 @@ "drtext": 27, "drttest": 1, "drugbank": 1, - "ds2pme": 38, + "ds2pme": 39, "dsCompareCurves": 1, "dsComputeBEDDensity": 1, "dsComputeGCCoverage": 1, @@ -10190,7 +10201,7 @@ "dupre": 1, "dupsifter": 1, "dust": 13, - "dustmasker": 349, + "dustmasker": 350, "dv_call_variants.py": 1, "dv_make_examples.py": 1, "dv_postprocess_variants.py": 1, @@ -10279,7 +10290,7 @@ "ecodbtaxstat": 1, "ecofind": 1, "ecogrep": 1, - "ecommon.sh": 227, + "ecommon.sh": 228, "econtact": 88, "ecotag": 1, "ecotaxspecificity": 1, @@ -10315,9 +10326,9 @@ "edonr256-hash": 9, "edonr512-hash": 9, "eel": 1, - "efetch": 315, + "efetch": 316, "effectivet3": 1, - "efilter": 315, + "efilter": 316, "efishent": 1, "efn": 1, "efn2": 6, @@ -10333,7 +10344,7 @@ "eigenstrat_database_tools": 1, "eigenstrat_rename_snps": 1, "eigenstrat_snp_coverage": 1, - "einfo": 315, + "einfo": 316, "einsi": 113, "einverted": 27, "eject": 13, @@ -10350,11 +10361,11 @@ "elandresult2bed": 1, "elastic-blast": 1, "elasticluster": 1, - "elasticurl": 63, - "elasticurl_cpp": 63, - "elastipubsub": 63, - "elastipubsub5": 52, - "elastishadow": 3, + "elasticurl": 65, + "elasticurl_cpp": 65, + "elastipubsub": 65, + "elastipubsub5": 54, + "elastishadow": 5, "elb-cost.py": 1, "elbadmin": 29, "elector": 1, @@ -10363,7 +10374,7 @@ "elfedit": 8, "elgato_report.py": 1, "eliminateBadSuperReadsUsingList": 1, - "elink": 315, + "elink": 316, "elm2meme": 13, "elprep": 1, "elsize": 6, @@ -10400,8 +10411,8 @@ "enano": 1, "enasearch": 1, "enc": 1, - "enc2xs": 1740, - "encguess": 1740, + "enc2xs": 1742, + "encguess": 1742, "encode2var": 1, "encode_dir": 1, "encode_exclude_loci": 1, @@ -10450,7 +10461,7 @@ "environment.yml": 1, "envpath": 3, "envset.cmd": 1, - "envsubst": 5319, + "envsubst": 5320, "eoulsan.sh": 1, "epa-ng": 4, "epestfind": 27, @@ -10466,7 +10477,7 @@ "epimuller-define": 1, "epimuller-draw": 1, "epimuller-parse": 1, - "epost": 315, + "epost": 316, "eprimer3": 27, "eprimer32": 27, "eproxy": 88, @@ -10502,11 +10513,11 @@ "errorEstimate": 6, "error_corrected2frg": 1, "ervdetective": 1, - "esample": 300, + "esample": 301, "esbuild": 1, "esd2esi": 12, "esdcompat": 12, - "esearch": 315, + "esearch": 316, "esh": 1, "esimsa": 1, "eskrim": 1, @@ -10568,7 +10579,7 @@ "estscan": 1, "estwise": 3, "estwisedb": 3, - "esummary": 315, + "esummary": 316, "esvee": 1, "etandem": 27, "ete": 2, @@ -10628,7 +10639,7 @@ "excise_precursors.pl": 1, "excise_precursors_iterative_final.pl": 1, "excl_seqs": 2, - "exclude-uid-lists": 300, + "exclude-uid-lists": 301, "exclude_N": 1, "exclude_loci": 1, "exclude_loci_backup": 1, @@ -10654,7 +10665,7 @@ "expam": 1, "expam_limit": 1, "expand": 85, - "expand-current": 300, + "expand-current": 301, "expandCols": 280, "expand_fastq": 1, "expand_links.pl": 7, @@ -10839,15 +10850,15 @@ "ezez4makefile_v4.pl": 1, "ezez4qsub_vx1.pl": 1, "ezez_vx1.pl": 1, - "f2py": 2157, + "f2py": 2165, "f2py2": 136, "f2py2.7": 136, - "f2py3": 1598, + "f2py3": 1601, "f2py3.10": 446, - "f2py3.11": 110, - "f2py3.6": 127, + "f2py3.11": 111, + "f2py3.6": 128, "f2py3.7": 257, - "f2py3.8": 246, + "f2py3.8": 247, "f2py3.9": 412, "f4ratio": 2, "f5c": 1, @@ -11008,12 +11019,12 @@ "fastaToCA": 3, "fastaToRead": 1, "fasta_base_content.py": 2, - "fasta_check": 11, + "fasta_check": 12, "fasta_clipping_histogram.pl": 8, "fasta_concatenate": 1, "fasta_diff": 1, "fasta_exclude_motif": 1, - "fasta_extract": 9, + "fasta_extract": 10, "fasta_filter.py": 2, "fasta_formatter": 8, "fasta_generate_regions.py": 28, @@ -11304,8 +11315,8 @@ "fasxl": 2, "fathom": 2, "favites_lite.py": 1, - "fax2ps": 5316, - "fax2tiff": 5316, + "fax2ps": 5321, + "fax2tiff": 5321, "fba": 1, "fc": 1, "fc-cache": 5378, @@ -11397,12 +11408,12 @@ "fermi2.pl": 2, "fetch": 4, "fetch-extras": 73, - "fetch-local": 38, - "fetch-nmcds": 38, - "fetch-pmc": 38, - "fetch-pubmed": 314, + "fetch-local": 39, + "fetch-nmcds": 39, + "fetch-pmc": 39, + "fetch-pubmed": 315, "fetch-tax.pl": 1, - "fetch-taxonomy": 38, + "fetch-taxonomy": 39, "fetchChromSizes": 5, "fetchEnaLibraryFastqs.sh": 1, "fetchFastq.sh": 1, @@ -11482,18 +11493,18 @@ "filter-alignments.py": 1, "filter-bam": 2, "filter-bam-by-ids": 3, - "filter-columns": 215, - "filter-genbank": 38, + "filter-columns": 216, + "filter-genbank": 39, "filter-gff": 1, "filter-nonunique-peptide-matches": 2, "filter-positions.pl": 1, "filter-ppx.pl": 15, - "filter-record": 38, + "filter-record": 39, "filter-sort": 1, "filter-stage-1.prl": 5, "filter-stage-2.prl": 5, "filter-stats.pl": 1, - "filter-stop-words": 315, + "filter-stop-words": 316, "filter-stoptags.py": 7, "filter-sync-by-gtf.pl": 1, "filter-table": 12, @@ -11673,7 +11684,7 @@ "find-all-symbols": 2, "find-compounds.pl": 2, "find-duplicate-reads": 2, - "find-in-gene": 227, + "find-in-gene": 228, "find-knots.py": 7, "find-mango-assembly.sh": 1, "find-mango-home": 1, @@ -11826,7 +11837,7 @@ "flagstats-quickbam": 1, "flaimapper": 1, "flair": 1, - "flake8": 4, + "flake8": 5, "flankBed": 280, "flanker": 1, "flapjack": 1, @@ -11897,7 +11908,7 @@ "font-awesome-to-png": 2, "font2c": 3, "fontinst": 1, - "fonttools": 436, + "fonttools": 440, "fop": 1, "forceOneClusterPerPairMem.py": 1, "forest.py": 1, @@ -11989,7 +12000,7 @@ "freec": 1, "freec2bed.pl": 1, "freec2circos.pl": 1, - "freetype-config": 5907, + "freetype-config": 5912, "freeze_graph": 25, "freq2group.pl": 5, "frequency.py": 1, @@ -12024,7 +12035,7 @@ "from_unionbed_to_ratio_per_window_CC0": 1, "fs": 1, "fsa": 1, - "fsa2xml": 18, + "fsa2xml": 19, "fsc": 1, "fsc.bat": 1, "fseq": 1, @@ -12139,8 +12150,8 @@ "funr": 1, "funzip": 25, "fuse": 1, - "fuse-ranges": 227, - "fuse-segments": 215, + "fuse-ranges": 228, + "fuse-segments": 216, "fuse.sh": 31, "fusion-bloom": 1, "fusion-bloom.makefile": 1, @@ -12148,7 +12159,7 @@ "fusion_report": 1, "fusioncatcher-to-CG": 2, "fusionsam2junc_filteranchor_newfmt": 1, - "futurize": 247, + "futurize": 248, "fuzznuc": 27, "fuzzpro": 27, "fuzztran": 27, @@ -12425,10 +12436,10 @@ "gb2fasta": 1, "gbSmallDNA2gff.pl": 15, "gbase": 2, - "gbf2fsa": 38, - "gbf2info": 18, - "gbf2ref": 38, - "gbf2xml": 314, + "gbf2fsa": 39, + "gbf2info": 19, + "gbf2ref": 39, + "gbf2xml": 315, "gbf2xml.bak": 1, "gbfalncut": 2, "gbfcut": 2, @@ -12480,7 +12491,7 @@ "gd2copypal": 243, "gd2togif": 243, "gd2topng": 243, - "gdal-config": 39, + "gdal-config": 40, "gdal2tiles": 1, "gdal2tiles.py": 6, "gdal2xyz": 1, @@ -12489,16 +12500,16 @@ "gdal_calc": 1, "gdal_calc.dox": 1, "gdal_calc.py": 6, - "gdal_contour": 39, - "gdal_create": 32, + "gdal_contour": 40, + "gdal_create": 33, "gdal_edit": 1, "gdal_edit.dox": 1, "gdal_edit.py": 6, "gdal_fillnodata": 1, "gdal_fillnodata.dox": 1, "gdal_fillnodata.py": 6, - "gdal_footprint": 4, - "gdal_grid": 39, + "gdal_footprint": 5, + "gdal_grid": 40, "gdal_merge": 1, "gdal_merge.py": 6, "gdal_pansharpen": 1, @@ -12509,39 +12520,39 @@ "gdal_proximity": 1, "gdal_proximity.dox": 1, "gdal_proximity.py": 6, - "gdal_rasterize": 39, + "gdal_rasterize": 40, "gdal_retile": 1, "gdal_retile.py": 6, "gdal_sieve": 1, "gdal_sieve.dox": 1, "gdal_sieve.py": 6, - "gdal_translate": 39, - "gdal_viewshed": 33, - "gdaladdo": 39, + "gdal_translate": 40, + "gdal_viewshed": 34, + "gdaladdo": 40, "gdalattachpct": 1, "gdalattachpct.py": 2, - "gdalbuildvrt": 39, + "gdalbuildvrt": 40, "gdalchksum.py": 4, "gdalcompare": 1, "gdalcompare.dox": 1, "gdalcompare.py": 6, - "gdaldem": 39, - "gdalenhance": 39, + "gdaldem": 40, + "gdalenhance": 40, "gdalident.py": 4, "gdalimport.py": 4, - "gdalinfo": 39, - "gdallocationinfo": 39, - "gdalmanage": 39, - "gdalmdiminfo": 33, - "gdalmdimtranslate": 33, + "gdalinfo": 40, + "gdallocationinfo": 40, + "gdalmanage": 40, + "gdalmdiminfo": 34, + "gdalmdimtranslate": 34, "gdalmove": 1, "gdalmove.dox": 1, "gdalmove.py": 6, "gdalserver": 7, - "gdalsrsinfo": 39, - "gdaltindex": 39, - "gdaltransform": 39, - "gdalwarp": 39, + "gdalsrsinfo": 40, + "gdaltindex": 40, + "gdaltransform": 40, + "gdalwarp": 40, "gdbm_dump": 25, "gdbm_load": 25, "gdbmtool": 25, @@ -12603,20 +12614,20 @@ "genbank_to": 1, "genblastG": 1, "genbox": 1, - "genbrk": 5919, - "gencfu": 5919, + "genbrk": 5922, + "gencfu": 5922, "genclust": 1, - "gencnval": 5919, + "gencnval": 5922, "gencode_extract_relevant_gtf_exons.pl": 1, "gencode_singleton_unit_test": 5, "genconf": 1, "gencore": 1, "gencove": 1, "gendb": 13, - "gendict": 5919, + "gendict": 5922, "gendist": 10, "gene2protein.db3": 2, - "gene2range": 215, + "gene2range": 216, "gene2xml": 1, "geneAssociationZscore.py": 1, "geneBody_coverage.py": 3, @@ -12781,7 +12792,7 @@ "genotyphi.py": 1, "genpcz": 2, "genpept2gsi.pl": 2, - "genrb": 5919, + "genrb": 5922, "genreflex": 3, "genremdinputs.py": 6, "genrestr": 4, @@ -12792,14 +12803,14 @@ "geo2fasta.pl": 1, "geo2fastq": 2, "geoDL": 1, - "geod": 45, + "geod": 46, "geofetch": 1, "geoff": 2, "geomap": 1, "geomet": 1, - "geos-config": 67, - "geosop": 49, - "geotifcp": 38, + "geos-config": 68, + "geosop": 50, + "geotifcp": 39, "gepard": 1, "gepardcmd": 1, "gerpcol": 1, @@ -12936,7 +12947,7 @@ "get_general_stats.pl": 1, "get_genes_table.pl": 3, "get_genomes_info.py": 1, - "get_gprof": 14, + "get_gprof": 15, "get_homologues-est.pl": 1, "get_homologues.pl": 1, "get_homology.pl": 1, @@ -12950,7 +12961,7 @@ "get_mirdeep2_precursors.pl": 1, "get_mnv": 1, "get_mpilup_from_id_list.py": 2, - "get_objgraph": 64, + "get_objgraph": 65, "get_objgraph.py": 1, "get_obsolete_term_id_vs_def_in_go.pl": 1, "get_obsolete_term_id_vs_name_in_go.pl": 1, @@ -12986,7 +12997,7 @@ "get_sequence_type": 1, "get_sequences_for_meme.py": 1, "get_simple_cycs.py": 1, - "get_species_taxids.sh": 314, + "get_species_taxids.sh": 315, "get_species_taxids.sh.bak": 300, "get_standard_headers": 1, "get_stats_summary.pl": 1, @@ -13060,9 +13071,9 @@ "getscu": 1, "getsize": 13, "getsnvfreq_by_interval": 1, - "gettext": 5319, - "gettext.sh": 5319, - "gettextize": 5319, + "gettext": 5320, + "gettext.sh": 5320, + "gettextize": 5320, "getu0.X86_64.LINUX": 1, "getu0.X86_64.SUNOS": 1, "getuniqgenomealign": 1, @@ -13142,7 +13153,7 @@ "gffutils-cli": 34, "gfinisher": 1, "gflags2man.py": 3, - "gflags_completions.sh": 80, + "gflags_completions.sh": 82, "gfmix": 1, "gfmix.yaml": 1, "gfmix_mammal.smk": 1, @@ -13175,17 +13186,17 @@ "gi2ancestors.sh": 31, "gi2taxid.sh": 31, "gid-taxid": 1, - "gie": 42, - "gif2h5": 566, + "gie": 43, + "gif2h5": 570, "gif2hdf": 127, - "gif2rgb": 775, + "gif2rgb": 776, "gif2tiff": 189, "gif2webp": 357, - "gifbuild": 775, - "gifclrmp": 775, + "gifbuild": 776, + "gifclrmp": 776, "gifecho": 39, "giffilter": 25, - "giffix": 775, + "giffix": 776, "gifinto": 39, "gifmaker.py": 20, "gifrop": 1, @@ -13196,9 +13207,9 @@ "gifrop_pannotate.R": 1, "gifrop_plots.R": 1, "gifsponge": 25, - "giftext": 775, + "giftext": 776, "giftogd2": 243, - "giftool": 775, + "giftool": 776, "gigrnd.py": 1, "gil2bin": 1, "gimbleprep": 1, @@ -13251,11 +13262,11 @@ "glnexus_cli": 1, "glob_res.pl": 1, "global.json": 1, - "glpsol": 250, + "glpsol": 252, "glsearch36": 7, "gm": 2, - "gm2ranges": 38, - "gm2segs": 38, + "gm2ranges": 39, + "gm2segs": 39, "gmap": 14, "gmap.nosimd": 9, "gmap.sse42": 12, @@ -13283,6 +13294,7 @@ "gmk_ub2": 2, "gml2gv": 203, "gmsc-mapper": 1, + "gmt2regions": 1, "gmtkDMLPtrain": 4, "gmtkDTindex": 4, "gmtkEMtrain": 4, @@ -13321,8 +13333,8 @@ "gnali": 1, "gnali_get_data": 1, "gndiff": 1, - "gnmanalyse": 38, - "gnmmanage": 38, + "gnmanalyse": 39, + "gnmmanage": 39, "gnos_pull.pl": 3, "gnparser": 1, "gnuplot": 24, @@ -13555,13 +13567,13 @@ "grouperThreads2.32": 1, "groups": 85, "grow-readbank": 2, - "grpc_cpp_plugin": 162, - "grpc_csharp_plugin": 162, - "grpc_node_plugin": 162, - "grpc_objective_c_plugin": 162, - "grpc_php_plugin": 162, - "grpc_python_plugin": 162, - "grpc_ruby_plugin": 162, + "grpc_cpp_plugin": 164, + "grpc_csharp_plugin": 164, + "grpc_node_plugin": 164, + "grpc_objective_c_plugin": 164, + "grpc_php_plugin": 164, + "grpc_python_plugin": 164, + "grpc_ruby_plugin": 164, "gs": 106, "gsbj": 106, "gscat": 2, @@ -13570,7 +13582,7 @@ "gsdj500": 106, "gsea": 1, "gsea-cli": 1, - "gseapy": 4, + "gseapy": 5, "gsettings": 1665, "gsf": 1, "gsf-office-thumbnailer": 1, @@ -13589,7 +13601,7 @@ "gsnapl.sse42": 12, "gsnd": 106, "gsort": 5, - "gss-client": 5903, + "gss-client": 5909, "gss-server": 2, "gst-completion-helper": 1, "gst-device-monitor-1.0": 241, @@ -13813,40 +13825,40 @@ "h264dec": 11, "h264enc": 11, "h2load": 3929, - "h2ph": 1740, - "h2xs": 1740, + "h2ph": 1742, + "h2xs": 1742, "h4_ncdump": 127, "h4_ncgen": 127, "h4cc": 127, "h4redeploy": 127, - "h52gif": 566, - "h5c++": 566, - "h5cc": 571, - "h5clear": 550, - "h5copy": 566, - "h5debug": 566, - "h5delete": 106, - "h5diff": 566, - "h5dump": 568, - "h5fc": 553, - "h5format_convert": 550, + "h52gif": 570, + "h5c++": 570, + "h5cc": 575, + "h5clear": 554, + "h5copy": 570, + "h5debug": 570, + "h5delete": 110, + "h5diff": 570, + "h5dump": 572, + "h5fc": 557, + "h5format_convert": 554, "h5fuse": 1, - "h5fuse.sh": 73, - "h5import": 566, - "h5jam": 566, - "h5ls": 566, - "h5mkgrp": 566, + "h5fuse.sh": 77, + "h5import": 570, + "h5jam": 570, + "h5ls": 570, + "h5mkgrp": 570, "h5pcc": 3, "h5perf": 3, - "h5perf_serial": 566, + "h5perf_serial": 570, "h5pfc": 3, - "h5redeploy": 566, - "h5repack": 566, - "h5repart": 566, - "h5stat": 566, - "h5tools_test_utils": 53, - "h5unjam": 566, - "h5watch": 550, + "h5redeploy": 570, + "h5repack": 570, + "h5repart": 570, + "h5stat": 570, + "h5tools_test_utils": 57, + "h5unjam": 570, + "h5watch": 554, "hAMRoaster": 1, "h_num": 1, "haarz.x": 1, @@ -14051,7 +14063,7 @@ "hg2hg_net": 1, "hgGcPercent": 3, "hgvs-shell": 1, - "hgvs2spdi": 227, + "hgvs2spdi": 228, "hhalign": 4, "hhalign_omp": 4, "hhblits": 4, @@ -14373,21 +14385,21 @@ "humann_unpack_pathways": 1, "humid": 1, "hv-pipeline.py": 1, - "hwloc-annotate": 87, + "hwloc-annotate": 92, "hwloc-assembler": 2, "hwloc-assembler-remote": 2, - "hwloc-bind": 87, - "hwloc-calc": 87, - "hwloc-compress-dir": 87, - "hwloc-diff": 87, + "hwloc-bind": 92, + "hwloc-calc": 92, + "hwloc-compress-dir": 92, + "hwloc-diff": 92, "hwloc-distances": 2, - "hwloc-distrib": 87, - "hwloc-gather-cpuid": 85, - "hwloc-gather-topology": 87, - "hwloc-info": 87, - "hwloc-ls": 87, - "hwloc-patch": 87, - "hwloc-ps": 87, + "hwloc-distrib": 92, + "hwloc-gather-cpuid": 90, + "hwloc-gather-topology": 92, + "hwloc-info": 92, + "hwloc-ls": 92, + "hwloc-patch": 92, + "hwloc-ps": 92, "hyb_analyze": 1, "hyb_check": 1, "hyb_eval": 1, @@ -14455,9 +14467,9 @@ "ichar": 1, "icon-font-to-png": 2, "iconv": 5462, - "icu-config": 5919, - "icuexportdata": 2131, - "icuinfo": 5919, + "icu-config": 5922, + "icuexportdata": 2134, + "icuinfo": 5922, "id": 85, "id_conserved_regions.pl": 1, "idba": 10, @@ -14490,21 +14502,21 @@ "idfetch": 1, "idiag-socket-details": 14, "idle": 334, - "idle3": 3477, - "idle3.10": 830, - "idle3.11": 281, - "idle3.12": 286, + "idle3": 3486, + "idle3.10": 831, + "idle3.11": 283, + "idle3.12": 290, "idle3.13": 8, "idle3.4": 6, "idle3.5": 103, - "idle3.6": 343, + "idle3.6": 344, "idle3.7": 383, - "idle3.8": 577, + "idle3.8": 578, "idle3.9": 660, "idlj": 117, "idmatrix.sh": 31, "idn": 31, - "idn2": 293, + "idn2": 294, "idpAssemble": 2, "idpQonvert": 2, "idpQuery": 2, @@ -14571,7 +14583,7 @@ "igor": 1, "igor-compute_pgen": 1, "igphyml": 1, - "igraph": 52, + "igraph": 54, "igraph_extract_clusters.R": 1, "igv": 1, "igv_hidpi": 1, @@ -14610,9 +14622,9 @@ "illumiprocessor": 2, "ilp-rrrmt": 1, "im2deep": 1, - "imagecodecs": 27, - "imageio_download_bin": 29, - "imageio_remove_bin": 29, + "imagecodecs": 28, + "imageio_download_bin": 30, + "imageio_remove_bin": 30, "imagespread": 5, "imagetops": 1, "imc": 2, @@ -14714,12 +14726,12 @@ "infoalign": 27, "infoassembly": 27, "infobase": 27, - "infocmp": 7874, + "infocmp": 7884, "inforesidue": 27, "informant.py": 1, "infoseq": 27, - "infotocap": 7874, - "ini2xml": 38, + "infotocap": 7884, + "ini2xml": 39, "init_Trinotate_sqlite_db.pl": 1, "init_db.sh": 1, "initdb": 48, @@ -14780,7 +14792,7 @@ "installpackages.R": 1, "installvst": 16, "instance_events": 29, - "instmodsh": 1740, + "instmodsh": 1742, "int_seqs_to_char_strings.py": 60, "intake": 1, "intake-server": 1, @@ -14815,7 +14827,7 @@ "interprophet.rb": 1, "interproscan.sh": 1, "intersect": 5, - "intersect-uid-lists": 313, + "intersect-uid-lists": 314, "intersectBed": 280, "intersectFiles.py": 2, "intersectGenomicSets.py": 1, @@ -14837,11 +14849,12 @@ "intron_exon_reads.pyc": 1, "inv": 2, "invert-pubmed": 1, + "invertdb": 1, "invertkey.sh": 31, - "invgeod": 40, + "invgeod": 41, "invoke": 2, "involucro": 2, - "invproj": 40, + "invproj": 41, "io.pl": 1, "io_demo": 29, "io_functions.py": 1, @@ -14891,9 +14904,9 @@ "iptest2": 7, "iptest3": 46, "ipyrad": 1, - "ipython": 102, + "ipython": 103, "ipython2": 7, - "ipython3": 95, + "ipython3": 96, "ipython3.10": 1, "ipython3.9": 4, "iqkm": 1, @@ -14954,7 +14967,7 @@ "isql": 1, "iss": 2, "isutf8": 3, - "isympy": 39, + "isympy": 40, "it.cpython-36m-x86_64-linux-gnu.so": 1, "it.so": 1, "iterate": 2, @@ -15111,7 +15124,7 @@ "jobTreeStatus": 2, "jobTreeTest_Dependencies.py": 1, "join": 85, - "join-into-groups-of": 315, + "join-into-groups-of": 316, "join-long-chromosomes": 3, "join.pl": 1, "join.pl.bak": 1, @@ -15132,11 +15145,11 @@ "joingenes": 16, "joint-indels": 1, "joint-parsimony": 1, - "jp.py": 105, + "jp.py": 106, "jpackage": 134, "jpeg2hdf": 127, - "jpegtran": 5844, - "jpgicc": 1048, + "jpegtran": 5849, + "jpgicc": 1053, "jpredapi": 1, "jps": 554, "jq": 310, @@ -15148,12 +15161,12 @@ "jsearch": 1, "jshell": 445, "json2gff": 1, - "json2xml": 227, + "json2xml": 228, "json_collect_data_source.py": 1, - "json_pp": 1740, - "json_xs": 373, + "json_pp": 1742, + "json_xs": 374, "jsondiff": 9, - "jsonl2xml": 38, + "jsonl2xml": 39, "jsonpatch": 9, "jsonpath.py": 1, "jsonpath_ng": 1, @@ -15209,17 +15222,17 @@ "jupyter-troubleshoot": 157, "jupyter-trust": 150, "just-first-key": 20, - "just-top-hits": 18, + "just-top-hits": 19, "just_blast_test.pl": 1, "jwebserver": 50, - "k5srvutil": 5903, + "k5srvutil": 5909, "k8": 170, "k8-Linux": 1, "k_means": 1, "k_means_coefficient": 1, "k_neighbors": 1, "k_neighbors_coefficient": 1, - "kadmin": 5903, + "kadmin": 5909, "kadmin.local": 2, "kadmind": 2, "kaiju": 4, @@ -15314,7 +15327,7 @@ "kdbmeta.3.0.3": 1, "kdbmeta.3.1.0": 1, "kdbmeta.3.1.1": 1, - "kdestroy": 5903, + "kdestroy": 5909, "kea-config": 38, "keep-header": 1, "keep-ribo-periodic": 1, @@ -15325,7 +15338,7 @@ "keggcharter.py": 1, "keggpathway_map.py": 1, "keyFreq": 1, - "keyctl": 2532, + "keyctl": 2538, "keygen": 1, "keyring": 10, "keytool": 554, @@ -15356,7 +15369,7 @@ "kinSimRiboswitch": 1, "king": 1, "kingfisher": 1, - "kinit": 5903, + "kinit": 5909, "kinship-read": 1, "kinshipDecompose": 1, "kinwalker": 56, @@ -15369,7 +15382,7 @@ "kitsch": 10, "kitsune": 1, "kleborate": 1, - "klist": 5903, + "klist": 5909, "kma": 19, "kma_index": 19, "kma_shm": 19, @@ -15459,7 +15472,7 @@ "kp1mer_to_kmer.py": 1, "kp2np.py": 1, "kpal": 2, - "kpasswd": 5903, + "kpasswd": 5909, "kpileup.py": 1, "kprop": 2, "kpropd": 2, @@ -15506,7 +15519,7 @@ "krakenuniq-report": 1, "krakenuniq-translate": 1, "krakmeopen": 1, - "krb5-config": 5903, + "krb5-config": 5909, "krb5-send-pr": 2, "krb5kdc": 2, "kreport2krona.py": 3, @@ -15522,9 +15535,9 @@ "kseq_split": 1, "ksnp": 1, "kssd": 1, - "ksu": 5903, + "ksu": 5909, "ksw": 1, - "kswitch": 5903, + "kswitch": 5909, "ktClassifyBLAST": 17, "ktClassifyHits": 13, "ktGetContigMagnitudes": 17, @@ -15555,12 +15568,12 @@ "ktserver": 2, "kttimedmgr": 2, "kttimedtest": 2, - "ktutil": 5903, + "ktutil": 5909, "ktutilmgr": 2, "ktutilserv": 2, "ktutiltest": 2, "kubectl": 1, - "kvno": 5903, + "kvno": 5909, "kwip": 2, "kwip-stats": 2, "l4p-tmpl": 32, @@ -15683,7 +15696,7 @@ "lefse_plot_features.py": 1, "lefse_plot_res.py": 1, "lefse_run.py": 1, - "legacy_blast.pl": 349, + "legacy_blast.pl": 350, "legsta": 1, "lemon-0.x-to-1.x.sh": 4, "lemur": 1, @@ -15718,8 +15731,8 @@ "libclair3.cpython-36m-x86_64-linux-gnu.so": 1, "libclair3.o": 1, "libclair3.so": 1, - "libdeflate-gunzip": 4219, - "libdeflate-gzip": 4219, + "libdeflate-gunzip": 4224, + "libdeflate-gzip": 4224, "libdrawgram.so": 5, "libdrawtree.so": 5, "libfile.pl": 1, @@ -15728,9 +15741,9 @@ "libiomp5md.dll": 1, "liblist.pl": 1, "liblist.pl.bak": 1, - "libnetcfg": 1740, - "libpng-config": 5963, - "libpng16-config": 5963, + "libnetcfg": 1742, + "libpng-config": 5968, + "libpng16-config": 5968, "libpypy-c.so": 1, "libpypy-c.so.debug": 1, "libpypy3-c.so.debug": 3, @@ -15790,7 +15803,7 @@ "link_ssv.py": 1, "linkage2allegro": 1, "linkhsp_unit_test": 5, - "linkicc": 1048, + "linkicc": 1053, "linknets": 2, "links2sql.pl": 7, "linksBed": 280, @@ -15820,7 +15833,7 @@ "list_of_files": 1, "listbib": 1, "listcontigreads": 2, - "listgeo": 38, + "listgeo": 39, "listings-ext.sh": 1, "listor": 27, "livekraken": 1, @@ -16007,7 +16020,7 @@ "longstitch": 1, "look": 13, "lookup_table": 1, - "loompy": 10, + "loompy": 11, "lorax": 1, "lordec-build-SR-graph": 2, "lordec-correct": 2, @@ -16064,12 +16077,12 @@ "lsirq": 8, "lslocks": 13, "lslogins": 13, - "lsm2bin": 27, + "lsm2bin": 28, "lsmem": 13, "lsns": 13, "lss3": 29, - "lstopo": 87, - "lstopo-no-graphics": 87, + "lstopo": 92, + "lstopo-no-graphics": 92, "ltqnorm.pl": 1, "ltqnorm.pl.bak": 1, "ltr_finder": 3, @@ -16107,21 +16120,21 @@ "lwp-request": 200, "lyner": 1, "lz-ani": 1, - "lz4": 3543, + "lz4": 3545, "lz4_decompress": 2, - "lz4c": 3542, - "lz4cat": 3542, - "lzcat": 7699, - "lzcmp": 7699, - "lzdiff": 7699, - "lzegrep": 7699, - "lzfgrep": 7699, - "lzgrep": 7699, - "lzless": 7699, - "lzma": 7699, - "lzmadec": 7699, - "lzmainfo": 7699, - "lzmore": 7699, + "lz4c": 3544, + "lz4cat": 3544, + "lzcat": 7708, + "lzcmp": 7708, + "lzdiff": 7708, + "lzegrep": 7708, + "lzfgrep": 7708, + "lzgrep": 7708, + "lzless": 7708, + "lzma": 7708, + "lzmadec": 7708, + "lzmainfo": 7708, + "lzmore": 7708, "lzop_build_offset_table.py": 60, "m-party": 1, "m-tx": 1, @@ -16432,27 +16445,27 @@ "makeagp2.awk": 1, "makeagp_full.awk": 1, "makeagp_full2.awk": 1, - "makeblastdb": 351, + "makeblastdb": 352, "makecert": 16, "makechimeras.sh": 31, "makeclusterdb": 5, "makecontaminatedgenomes.sh": 31, - "makeconv": 5919, + "makeconv": 5922, "makedtx": 1, "makefasta.awk": 1, - "makegeo": 38, + "makegeo": 39, "makeglossaries": 1, "makeglossaries-lite": 1, "makehmmerdb": 189, "makeidx.pl": 4, "makemat": 38, - "makembindex": 349, + "makembindex": 350, "makenucseq": 27, "makepBAM_genome.sh": 1, "makepBAM_transcriptome.sh": 1, "makeplot.pl": 3, "makepolymers.sh": 31, - "makeprofiledb": 349, + "makeprofiledb": 350, "makeprotseq": 27, "maker": 1, "maker2chado": 1, @@ -16572,7 +16585,7 @@ "mark_partial_genes.py": 2, "mark_productivity": 1, "mark_prophage_features.py": 2, - "markdown-it": 70, + "markdown-it": 71, "markdown_py": 125, "markdups": 1, "markermagu": 1, @@ -17320,7 +17333,7 @@ "minibusco": 1, "minidot": 13, "minigraph": 3, - "minigzip": 4, + "minigzip": 5, "minimap": 1, "minimap-lite": 1, "minimap2": 173, @@ -17351,7 +17364,7 @@ "minirmd": 1, "miniterm.py": 1, "miniwdl": 2, - "minizip": 4, + "minizip": 5, "minnow": 1, "minority_freq": 1, "mintie": 1, @@ -17635,9 +17648,9 @@ "mprof-report": 16, "mptopdf": 1, "mpxstats": 1, - "mqtt5_app": 52, - "mqtt5_canary": 52, - "mqtt5canary": 52, + "mqtt5_app": 54, + "mqtt5_canary": 54, + "mqtt5canary": 54, "mquad": 1, "mrcfile-header": 3, "mrcfile-validate": 3, @@ -17679,24 +17692,24 @@ "mseqtools": 1, "msformatter": 1, "msfragger": 2, - "msgattrib": 5319, - "msgcat": 5319, - "msgcmp": 5319, - "msgcomm": 5319, - "msgconv": 5319, - "msgen": 5319, - "msgexec": 5319, + "msgattrib": 5320, + "msgcat": 5320, + "msgcmp": 5320, + "msgcomm": 5320, + "msgconv": 5320, + "msgen": 5320, + "msgexec": 5320, "msgf2pin": 1, "msgf_plus": 3, - "msgfilter": 5319, - "msgfmt": 5319, + "msgfilter": 5320, + "msgfmt": 5320, "msgfplus_search.rb": 1, - "msggrep": 5319, - "msginit": 5319, - "msgmerge": 5319, + "msggrep": 5320, + "msginit": 5320, + "msgmerge": 5320, "msgserv": 1, - "msgunfmt": 5319, - "msguniq": 5319, + "msgunfmt": 5320, + "msguniq": 5320, "msi": 1, "msi_cluster2reads": 1, "msi_clustr2map.pl": 1, @@ -17959,7 +17972,7 @@ "nasm": 1, "nasp": 1, "native2ascii": 112, - "natsort": 166, + "natsort": 169, "nb-classify": 1, "nb-train": 1, "nbmodel_stan2.py": 1, @@ -18001,14 +18014,14 @@ "ncrf_to_bed": 2, "ncrf_to_bed.py": 2, "ncurses5-config": 565, - "ncurses6-config": 7167, + "ncurses6-config": 7177, "ncursesw5-config": 703, - "ncursesw6-config": 7168, + "ncursesw6-config": 7178, "ndg_httpclient": 2, "ndisasm": 1, "ndmetis": 60, "ndx2resttop": 3, - "nearblack": 39, + "nearblack": 40, "neato": 203, "nebulizer": 1, "necat": 1, @@ -18098,7 +18111,7 @@ "nf-test": 1, "nfe-umbrella-slice": 6, "ngd": 12, - "ngettext": 5319, + "ngettext": 5320, "ngg_barabasi_albert": 2, "ngg_barbell": 2, "ngg_complete": 2, @@ -18108,9 +18121,9 @@ "ngg_newman_watts_strogatz": 2, "ngg_path": 2, "ngg_ring_lattice": 2, - "nghttp": 4559, - "nghttpd": 4559, - "nghttpx": 4559, + "nghttp": 4565, + "nghttpd": 4565, + "nghttpx": 4565, "ngless": 2, "ngless-wrapped": 1, "nglview": 2, @@ -18145,7 +18158,7 @@ "ngsngs": 1, "ngsplotdb.py": 5, "ngsutils": 1, - "nhance.sh": 38, + "nhance.sh": 39, "nhmmer": 189, "nhmmscan": 189, "nib-conform": 2, @@ -18170,7 +18183,7 @@ "nimblegen2adf.pl": 1, "nimnexus": 1, "ninety_five_percent.py": 1, - "ninja": 35, + "ninja": 36, "njTree.R": 1, "nl": 85, "nl-addr-add": 14, @@ -18253,7 +18266,7 @@ "normalize_multicov.pl": 1, "normalize_oneD.R": 1, "normalize_table.py": 1, - "normalizer": 509, + "normalizer": 512, "normandcorrectwrapper.sh": 1, "nose2": 1, "nose2-2.7": 1, @@ -18295,7 +18308,7 @@ "nproc": 85, "npth-config": 2, "npx": 16, - "nquire": 315, + "nquire": 316, "nquire.bak": 1, "nrForwardSplicedReads.pl": 1, "nr_ORFs_gff3.pl": 5, @@ -18357,11 +18370,11 @@ "nullarbor.pl": 1, "nulltype_module.py": 1, "numCI": 4, - "numba": 160, + "numba": 164, "number-lines": 1, "numfmt": 85, "numlines": 1, - "numpy-config": 64, + "numpy-config": 67, "nunit-console": 10, "nunit-console2": 10, "nunit-console4": 10, @@ -18567,14 +18580,14 @@ "offset_finder.py": 2, "ofm2opl": 1, "ofstd_tests": 1, - "ogr2ogr": 39, + "ogr2ogr": 40, "ogr_layer_algebra": 1, "ogr_layer_algebra.py": 2, - "ogrinfo": 39, - "ogrlineref": 39, + "ogrinfo": 40, + "ogrlineref": 40, "ogrmerge": 1, "ogrmerge.py": 5, - "ogrtindex": 39, + "ogrtindex": 40, "ogs_check": 1, "ogs_merge": 1, "oid2name": 47, @@ -18594,7 +18607,7 @@ "omamer": 2, "omark": 1, "ome2name": 2, - "ome_zarr": 2, + "ome_zarr": 3, "omero": 5, "omero.bat": 3, "omfonts": 1, @@ -18646,12 +18659,12 @@ "openslide-quickhash1sum": 2, "openslide-show-properties": 2, "openslide-write-png": 2, - "openssl": 7942, + "openssl": 7952, "opentargets_validator": 1, "operation.py": 1, - "opj_compress": 689, - "opj_decompress": 689, - "opj_dump": 689, + "opj_compress": 694, + "opj_decompress": 694, + "opj_dump": 694, "opl2ofm": 1, "opsin": 1, "opt": 6, @@ -18670,11 +18683,11 @@ "orator": 1, "orbd": 117, "orc-bugreport": 14, - "orc-contents": 76, - "orc-memory": 71, - "orc-metadata": 76, - "orc-scan": 71, - "orc-statistics": 76, + "orc-contents": 78, + "orc-memory": 73, + "orc-metadata": 78, + "orc-scan": 73, + "orc-statistics": 78, "orca-server": 1, "orcc": 14, "order.smk": 1, @@ -18891,7 +18904,7 @@ "pairtools": 3, "pairwise_comparison": 1, "pal2nal.pl": 9, - "pal2rgb": 5316, + "pal2rgb": 5321, "pal_finder": 1, "paladin": 2, "palindrome": 27, @@ -19100,7 +19113,7 @@ "pass": 1, "paste": 85, "pasteseq": 27, - "pasteurize": 247, + "pasteurize": 248, "pastml": 1, "pastrami.py": 1, "pasty": 1, @@ -19196,11 +19209,11 @@ "pcoaPlot.py": 2, "pcor": 1, "pcre-config": 4952, - "pcre2-config": 3763, + "pcre2-config": 3764, "pcre2_jit_test": 3685, - "pcre2grep": 3763, + "pcre2grep": 3764, "pcre2posix_test": 113, - "pcre2test": 3763, + "pcre2test": 3764, "pcregrep": 4952, "pcretest": 4952, "pct2rgb": 1, @@ -19407,7 +19420,7 @@ "perf": 1, "perfect-square": 2, "perform_controls.pl": 1, - "perl": 1740, + "perl": 1742, "perl-doc": 2, "perl-reversion": 9, "perl5.22.0": 55, @@ -19415,12 +19428,12 @@ "perl5.26.2": 369, "perl5.30.3": 5, "perl5.32.0": 64, - "perl5.32.1": 1247, - "perlbug": 1740, - "perldoc": 1740, - "perlivp": 1740, + "perl5.32.1": 1249, + "perlbug": 1742, + "perldoc": 1742, + "perlivp": 1742, "perltex": 1, - "perlthanks": 1740, + "perlthanks": 1742, "permuteGPAT++": 32, "permuteSmooth": 32, "permute_structure.pl": 1, @@ -19578,7 +19591,7 @@ "phonopy-vasp-born": 1, "phonopy-vasp-efe": 1, "photo": 2, - "phrase-search": 313, + "phrase-search": 314, "phsolverserver": 3, "phy2nex": 1, "phykit": 1, @@ -19777,7 +19790,7 @@ "pickle_cat.py": 1, "pickorientation.awk": 1, "pickout": 1, - "piconv": 1740, + "piconv": 1742, "picopore": 1, "picopore-realtime": 1, "picopore-rename": 1, @@ -19816,10 +19829,10 @@ "pints_caller": 1, "pints_normalizer": 1, "pints_visualizer": 1, - "pip": 3811, + "pip": 3820, "pip2": 1, "pip2.7": 1, - "pip3": 2734, + "pip3": 2743, "pipdeptree": 1, "pipelign": 1, "pipeline.py": 3, @@ -19972,13 +19985,13 @@ "pkfix-helper": 1, "pkg-config": 78, "pkg-config.bin": 78, - "pkgdata": 5919, + "pkgdata": 5922, "pkginfo": 10, "pkill": 1, "pktogf": 1, "pktype": 1, "pl2bat.pl": 6, - "pl2pm": 1740, + "pl2pm": 1742, "plaScope.sh": 1, "plac_runner.py": 70, "place_orient1.smk": 1, @@ -20149,11 +20162,11 @@ "pm4ngs-rnaseq-demo": 1, "pm4ngs-server": 1, "pm_which": 2, - "pma2apa": 38, - "pma2pme": 38, + "pma2apa": 39, + "pma2pme": 39, "pmap": 1, - "pmc2bioc": 38, - "pmc2info": 38, + "pmc2bioc": 39, + "pmc2info": 39, "pmd": 1, "pmdtools": 1, "pmemd_mdrun": 1, @@ -20179,22 +20192,22 @@ "pmxmutate": 1, "pn2pdf": 1, "pneumo-typer": 1, - "png-fix-itxt": 5963, + "png-fix-itxt": 5968, "pngcp": 89, - "pngfix": 5963, + "pngfix": 5968, "pngtogd": 243, "pngtogd2": 243, "pnps-gen": 1, "poa": 24, "pocheck": 1, "poclcc": 3, - "pod2html": 1740, - "pod2man": 1740, - "pod2text": 1740, - "pod2usage": 1740, + "pod2html": 1742, + "pod2man": 1742, + "pod2text": 1742, + "pod2usage": 1742, "pod5": 1, "pod_cover": 12, - "podchecker": 1740, + "podchecker": 1742, "podselect": 438, "poetry": 6, "pointwise_datasets_concatenator.py": 1, @@ -20302,7 +20315,7 @@ "ppi2html": 2, "pplacer": 22, "ppltotf": 1, - "ppm2tiff": 5316, + "ppm2tiff": 5321, "pprodigal": 2, "pprof": 2, "pprof-symbolize": 1, @@ -20438,7 +20451,7 @@ "prinseq-graphs-noPCA.pl": 3, "prinseq-graphs.pl": 3, "prinseq-lite.pl": 3, - "print-columns": 227, + "print-columns": 228, "print.pl": 1, "printIcounts": 1, "printScaff": 2, @@ -20531,14 +20544,14 @@ "progressbar": 4, "progressiveMauve": 7, "progressiveMauveStatic": 4, - "proj": 45, + "proj": 46, "project.sh": 1, "project.sh.orig": 1, "projectAndStrip": 4, "projectFeatures": 3, - "project_tree_builder": 349, - "projinfo": 41, - "projsync": 38, + "project_tree_builder": 350, + "projinfo": 42, + "projsync": 39, "prokka": 24, "prokka-abricate_to_fasta_db": 19, "prokka-annotation-refupdate.py": 1, @@ -20646,7 +20659,7 @@ "protmapper": 1, "protobuf-net.dll": 2, "protobuf-net.xml": 2, - "protoc": 285, + "protoc": 288, "protoc-23.1.0": 1, "protoc-23.3.0": 4, "protoc-23.4.0": 6, @@ -20655,7 +20668,7 @@ "protoc-25.1.0": 5, "protoc-25.2.0": 2, "protoc-25.3.0": 30, - "protoc-27.5.0": 1, + "protoc-27.5.0": 3, "protoc-gen-grpclib_python": 1, "protoc-gen-mypy": 1, "protoc-gen-mypy_grpc": 1, @@ -20683,7 +20696,7 @@ "protxml_to_table.rb": 1, "prov-compare": 9, "prov-convert": 9, - "prove": 1740, + "prove": 1742, "provean": 1, "provean.sh": 1, "provis": 1, @@ -20728,10 +20741,10 @@ "psiCalculator.py": 1, "psiPerGene.py": 1, "psibl2seq_unit_test": 5, - "psiblast": 349, + "psiblast": 350, "psiblast_iteration_unit_test": 5, "psiblast_unit_test": 5, - "psicc": 1048, + "psicc": 1053, "psiclass": 1, "psiphi": 27, "psirc": 1, @@ -20789,9 +20802,9 @@ "pt2to3": 75, "ptGAUL.sh": 1, "ptangle": 1, - "ptar": 1740, - "ptardiff": 1740, - "ptargrep": 1740, + "ptar": 1742, + "ptardiff": 1742, + "ptargrep": 1742, "ptdump": 75, "ptest": 1, "ptex": 1, @@ -20957,31 +20970,31 @@ "pycc": 104, "pyclone-vi": 1, "pycoQC": 1, - "pycodestyle": 6, + "pycodestyle": 7, "pycomo": 1, "pycompleter": 1, "pycompleter2": 1, "pycompleter2.7": 1, "pycov3": 1, "pycrust": 6, - "pyct": 2, + "pyct": 3, "pyctv.py": 1, "pyctv_taxonomy.py": 1, "pydamage": 1, "pydemult": 1, "pydicom": 1, "pydna_repeatfinder": 1, - "pydoc": 3810, - "pydoc3": 3477, - "pydoc3.10": 830, - "pydoc3.11": 281, - "pydoc3.12": 286, + "pydoc": 3819, + "pydoc3": 3486, + "pydoc3.10": 831, + "pydoc3.11": 283, + "pydoc3.12": 290, "pydoc3.13": 8, "pydoc3.4": 6, "pydoc3.5": 103, - "pydoc3.6": 343, + "pydoc3.6": 344, "pydoc3.7": 383, - "pydoc3.8": 577, + "pydoc3.8": 578, "pydoc3.9": 660, "pydownsampler": 1, "pyega3": 1, @@ -20992,18 +21005,18 @@ "pyfba": 1, "pyfiglet": 9, "pyfish": 1, - "pyflakes": 5, + "pyflakes": 6, "pyflyte": 1, "pyflyte-execute": 1, "pyflyte-fast-execute": 1, "pyflyte-map-execute": 1, - "pyftmerge": 436, - "pyftsubset": 436, + "pyftmerge": 440, + "pyftsubset": 440, "pygal_gen.py": 2, "pygcap": 1, "pygenetic_code": 1, "pygmentex": 1, - "pygmentize": 274, + "pygmentize": 276, "pygmes": 1, "pygrun": 1, "pygtail": 2, @@ -21046,7 +21059,7 @@ "pypolca": 1, "pypore_batch_csv.py": 1, "pyppeteer-install": 3, - "pyproj": 3, + "pyproj": 4, "pyproject-build": 2, "pypublish": 1, "pypy": 6, @@ -21083,6 +21096,7 @@ "pyrsa-verify": 158, "pysamstats": 4, "pysassc": 1, + "pyscenic": 1, "pyscss": 3, "pyseer": 2, "pysemver": 6, @@ -21105,7 +21119,7 @@ "pytest": 151, "pytest-benchmark": 1, "pythia8-config": 1, - "python": 3811, + "python": 3820, "python-argcomplete-check-easy-install-script": 347, "python-argcomplete-tcsh": 191, "python-build": 2, @@ -21116,15 +21130,15 @@ "python2.5-config": 1, "python2.7": 333, "python2.7-config": 316, - "python3": 3478, - "python3-config": 3477, - "python3.1": 1405, - "python3.10": 830, - "python3.10-config": 830, - "python3.11": 281, - "python3.11-config": 281, - "python3.12": 286, - "python3.12-config": 286, + "python3": 3487, + "python3-config": 3486, + "python3.1": 1412, + "python3.10": 831, + "python3.10-config": 831, + "python3.11": 283, + "python3.11-config": 283, + "python3.12": 290, + "python3.12-config": 290, "python3.13": 8, "python3.13-config": 8, "python3.4": 6, @@ -21135,16 +21149,16 @@ "python3.5-config": 103, "python3.5m": 103, "python3.5m-config": 103, - "python3.6": 343, - "python3.6-config": 343, - "python3.6m": 343, - "python3.6m-config": 343, + "python3.6": 344, + "python3.6-config": 344, + "python3.6m": 344, + "python3.6m-config": 344, "python3.7": 384, "python3.7-config": 383, "python3.7m": 383, "python3.7m-config": 383, - "python3.8": 577, - "python3.8-config": 577, + "python3.8": 578, + "python3.8-config": 578, "python3.9": 660, "python3.9-config": 660, "pythonsh": 2, @@ -21156,10 +21170,10 @@ "pyuic4": 8, "pyuic5": 221, "pyutilib_test_driver": 3, - "pyvenv": 835, + "pyvenv": 836, "pyvenv-3.4": 6, "pyvenv-3.5": 103, - "pyvenv-3.6": 343, + "pyvenv-3.6": 344, "pyvenv-3.7": 383, "pywgsim": 2, "pywxrc": 6, @@ -21183,7 +21197,7 @@ "qcli_make_script": 3, "qcollectiongenerator": 257, "qcollectiongenerator-qt4": 3, - "qconvex": 42, + "qconvex": 45, "qcp": 2, "qcreporter.py": 1, "qcs": 2, @@ -21198,7 +21212,7 @@ "qdbusviewer6": 1, "qdbusxml2cpp": 255, "qdbusxml2cpp-qt4": 3, - "qdelaunay": 42, + "qdelaunay": 45, "qdistancefieldgenerator": 141, "qdistancefieldgenerator6": 1, "qdoc": 229, @@ -21209,13 +21223,13 @@ "qfy.py": 1, "qgltf": 189, "qgrs": 1, - "qhalf": 42, + "qhalf": 45, "qhelpconverter": 116, "qhelpconverter-qt4": 3, "qhelpgenerator": 257, "qhelpgenerator-qt4": 3, "qhery": 1, - "qhull": 42, + "qhull": 45, "qiime2lefse.py": 1, "qiimeToMaaslin.py": 1, "qiskit-xyz2pdb": 1, @@ -21348,7 +21362,7 @@ "quorum_create_database": 4, "quorum_error_correct_reads": 4, "quota_Anchor": 1, - "quote-grouped-elements": 38, + "quote-grouped-elements": 39, "qv_to_bqv.py": 60, "qvality": 1, "qvalue": 13, @@ -21357,7 +21371,7 @@ "qvinaw": 1, "qvinaw_split": 1, "qvkgen": 141, - "qvoronoi": 42, + "qvoronoi": 45, "qwebengine_convert_dict": 141, "r-seurat-scripts-post-install-tests.bats": 2, "r-seurat-scripts-post-install-tests.sh": 2, @@ -21467,9 +21481,9 @@ "rasusa": 5, "ratewig.pl": 5, "ratt": 2, - "rav1e": 11, + "rav1e": 12, "raven": 4, - "raw2tiff": 5316, + "raw2tiff": 5321, "raw_n50": 10, "raw_n50.o": 10, "raw_vcf_parse.py": 1, @@ -21497,7 +21511,7 @@ "rbhtfinder": 1, "rblist": 2, "rbmoegrid": 2, - "rbox": 42, + "rbox": 45, "rbpbench": 1, "rbrms": 1, "rbs": 9, @@ -21519,8 +21533,8 @@ "rcexplain.3.1.0": 1, "rcexplain.3.1.1": 1, "rcf": 1, - "rchive": 314, - "rchive.Linux": 314, + "rchive": 315, + "rchive.Linux": 315, "rchive.go": 14, "rcl": 3, "rcl-dot-resmap.pl": 3, @@ -21537,7 +21551,7 @@ "rdfgraphisomorphism": 34, "rdfpipe": 34, "rdfs2dot": 34, - "rdjpgcom": 5844, + "rdjpgcom": 5849, "rdkit2fps": 1, "rdma_client": 25, "rdma_server": 25, @@ -21637,7 +21651,7 @@ "recgraph": 1, "reciprocal_blast_local": 1, "reciprocal_blast_local.py": 1, - "recode-sr-latin": 5319, + "recode-sr-latin": 5320, "recode_dir": 1, "recode_dir_legacy": 1, "recoder": 27, @@ -21686,7 +21700,7 @@ "ref-variation.3.0.3": 1, "ref-variation.3.1.0": 1, "ref-variation.3.1.1": 1, - "ref2pmid": 38, + "ref2pmid": 39, "refFinder": 1, "ref_map.pl": 1, "ref_seqs_from_bam": 1, @@ -21726,7 +21740,7 @@ "refresh-versioned": 1, "refseq-download": 1, "refseq-extract": 1, - "refseq-nm-cds": 38, + "refseq-nm-cds": 39, "refseq_masher": 1, "refseqget": 27, "refseqsplit.py": 2, @@ -21940,7 +21954,7 @@ "renumberRMFiles.pl": 4, "renumber_structure": 1, "reorder": 1, - "reorder-columns": 315, + "reorder-columns": 316, "reorder-fasta": 3, "reorder.smk": 1, "reorient_sequences_by_id.py": 2, @@ -22006,7 +22020,7 @@ "rescue_fusion.py": 1, "reseq": 1, "reseq-prepare-names.py": 1, - "reset": 7874, + "reset": 7884, "resetFragLibrary": 2, "reset_array.pl": 1, "reset_experiment.pl": 1, @@ -22276,9 +22290,9 @@ "rpkmforgenes.py": 1, "rppr": 17, "rps_unit_test": 5, - "rpsblast": 358, - "rpsbproc": 276, - "rpstblastn": 349, + "rpsblast": 359, + "rpsbproc": 277, + "rpstblastn": 350, "rpt_map": 1, "rqcfilter.sh": 31, "rqcfilter2.sh": 30, @@ -22380,7 +22394,7 @@ "run-htseq-workflow": 1, "run-mummer1": 45, "run-mummer3": 45, - "run-ncbi-converter": 314, + "run-ncbi-converter": 315, "run-ncbi-converter.bak": 1, "run-ntedit": 1, "run-polap-genes.R": 1, @@ -22595,7 +22609,7 @@ "run_vote.py": 1, "run_voteSpecies.py": 1, "run_vsclust_app.R": 1, - "run_with_lock": 339, + "run_with_lock": 340, "run_workflows.py": 1, "run_x_platform_fuzz_corpus": 38, "runabyss.py": 1, @@ -22624,7 +22638,7 @@ "runsge": 2, "runsge0": 1, "runshell": 1, - "runxlrd.py": 19, + "runxlrd.py": 20, "rust-demangler": 1, "rust-gdb": 1, "rust-gdbgui": 1, @@ -22924,7 +22938,7 @@ "scancel-range": 1, "scancel_range.py": 1, "scandeps.pl": 2, - "scanpy": 54, + "scanpy": 57, "scanpy-cli": 1, "scanpy-filter-cells": 1, "scanpy-filter-genes": 1, @@ -22997,7 +23011,7 @@ "scitokens-test-access": 1, "scitokens-verify": 1, "sclass.X86_64.LINUX": 1, - "sclient": 5903, + "sclient": 5909, "sclust_summary.sh": 1, "scluster": 3, "scmap-cli-post-install-tests.bats": 1, @@ -23016,7 +23030,7 @@ "scn-post-install-tests.sh": 1, "scn-predict.R": 1, "scn-train-model.R": 1, - "scn2xml": 38, + "scn2xml": 39, "scoary": 3, "scoary_GUI": 3, "scompare": 6, @@ -23137,7 +23151,7 @@ "segalign": 2, "segalign_repeat_masker": 2, "segemehl.x": 1, - "segmasker": 349, + "segmasker": 350, "segment-cnv": 1, "segment.py": 1, "segmentFst": 32, @@ -23434,7 +23448,7 @@ "sharq.3": 2, "sharq.3.0.0": 2, "shasta": 1, - "shasum": 1740, + "shasum": 1742, "shed-tools": 2, "shell_utils.py": 1, "shiboken2": 2, @@ -23531,7 +23545,7 @@ "sim-cover2": 2, "sim-shotgun": 2, "sim4db": 3, - "sim_client": 5903, + "sim_client": 5909, "sim_reads": 10, "sim_reads.o": 10, "sim_reads_tran": 10, @@ -23651,13 +23665,13 @@ "sketchy": 1, "skewer": 1, "skg_convert.py": 2, - "skip-if-file-exists": 284, + "skip-if-file-exists": 285, "skip_psl_self.awk": 2, "skip_psl_self_ss.awk": 2, "skip_selfmatches.py": 1, "skipredundant": 27, "skipseq": 27, - "skivi": 29, + "skivi": 30, "skmer": 1, "skopeo": 1, "skyline2isocor": 1, @@ -23804,8 +23818,8 @@ "snp-pileup": 2, "snp-pileup-quickbam": 1, "snp-sites": 13, - "snp2hgvs": 227, - "snp2tbl": 227, + "snp2hgvs": 228, + "snp2tbl": 228, "snpEff": 24, "snpEffAnnotate.py": 3, "snp_diversity.py": 1, @@ -23868,6 +23882,7 @@ "sonnet_sad_multi.py": 1, "sonnet_sat_bed.py": 1, "sonnet_sat_vcf.py": 1, + "sopa": 1, "soprano_submitter": 2, "sort": 85, "sort-bed": 15, @@ -23878,9 +23893,9 @@ "sort-last-maf": 1, "sort-snos": 2, "sort-snos.pl": 2, - "sort-table": 227, - "sort-uniq-count": 315, - "sort-uniq-count-rank": 315, + "sort-table": 228, + "sort-uniq-count": 316, + "sort-uniq-count-rank": 316, "sort2": 2, "sortBed": 280, "sortByRefAndCor.pl": 1, @@ -23910,7 +23925,7 @@ "sortsam": 1, "sourcepredict": 1, "sourmash": 12, - "sozip": 6, + "sozip": 7, "spaTyper": 1, "spacepharer": 1, "spacy": 1, @@ -23958,7 +23973,7 @@ "sparsetable_unittest": 1, "spatypes.txt": 1, "spdi2prod": 12, - "spdi2tbl": 227, + "spdi2tbl": 228, "specialk": 1, "species_abundance_cal.py": 1, "spectra-cluster-cli": 1, @@ -23981,7 +23996,7 @@ "sphinx-quickstart": 42, "spine.pl": 1, "spinner.py": 1, - "splain": 1740, + "splain": 1742, "splash": 2, "splice_site_summary.pl": 1, "spliceai": 1, @@ -23990,7 +24005,7 @@ "splinter.pl": 1, "splinter_scaffolds.pl": 1, "split": 85, - "split-at-intron": 227, + "split-at-intron": 228, "split-bed12-blocks": 3, "split-coverages.py": 1, "split-fasta": 1, @@ -24120,8 +24135,8 @@ "sql": 109, "sqlformat": 9, "sqlite.pl": 1, - "sqlite3": 2724, - "sqlite3_analyzer": 7264, + "sqlite3": 2726, + "sqlite3_analyzer": 7273, "sqlitebrowser": 1, "sqlmetal": 16, "sqlsharp": 16, @@ -24467,15 +24482,15 @@ "stranger": 1, "strawk": 1, "stream": 77, - "stream-local": 38, - "stream-pubmed": 313, + "stream-local": 39, + "stream-pubmed": 314, "stream_atac": 1, "stream_run_test": 1, "streamer_1d": 22, "streamlit": 6, "streamlit.cmd": 6, "streamsam.sh": 31, - "streamzip": 1311, + "streamzip": 1313, "streme": 6, "streme_xml_to_html": 6, "stress-ng": 1, @@ -24519,8 +24534,8 @@ "stubgen": 3, "stubmaker.pl": 57, "stubtest": 3, - "stx.prot": 1, - "stxtyper": 1, + "stx.prot": 2, + "stxtyper": 2, "sty2dtx": 1, "sub_then_run_mtgrasp.sh": 1, "subcontig": 1, @@ -24729,7 +24744,7 @@ "syri": 1, "syrupy.py": 1, "sysc": 1, - "systematic-mutations": 18, + "systematic-mutations": 19, "t1k-build.pl": 1, "t1k-merge.py": 1, "t1k-smartseq.pl": 1, @@ -24759,7 +24774,7 @@ "tableschema": 1, "tablet": 1, "tabnum2id": 1, - "tabs": 7874, + "tabs": 7884, "tabulate": 143, "tabulate.py": 1, "tabulator": 1, @@ -24921,11 +24936,11 @@ "tba": 1, "tbl2asn": 30, "tbl2asn-test": 13, - "tbl2prod": 215, - "tbl2xml": 227, - "tblastn": 349, - "tblastn_vdb": 62, - "tblastx": 349, + "tbl2prod": 216, + "tbl2xml": 228, + "tblastn": 350, + "tblastn_vdb": 63, + "tblastx": 350, "tblite": 1, "tbox-scan": 1, "tbpore": 1, @@ -24933,9 +24948,9 @@ "tbvcfreport": 1, "tcdemux": 1, "tcfinder": 1, - "tclsh": 7501, + "tclsh": 7510, "tclsh8.5": 473, - "tclsh8.6": 7264, + "tclsh8.6": 7273, "tcode": 27, "tcsh": 3, "td_bignet": 2, @@ -24974,12 +24989,12 @@ "test-download": 2, "test-download.3": 2, "test-download.3.0.0": 2, - "test-edirect": 284, - "test-eutils": 313, + "test-edirect": 285, + "test-eutils": 314, "test-gzip": 1, "test-merStream": 5, - "test-pmc-index": 38, - "test-pubmed-index": 313, + "test-pmc-index": 39, + "test-pubmed-index": 314, "test-read-write-cursor": 2, "test-read-write-cursor.3": 2, "test-read-write-cursor.3.0.0": 2, @@ -25033,10 +25048,11 @@ "test_install.bak": 1, "test_miso": 1, "test_musicc.py": 2, - "test_pcre": 110, + "test_pcre": 111, "test_proton.bam": 1, "test_proton.bam.bai": 1, "test_regexp": 1, + "test_stxtyper.sh": 1, "test_suite.py": 1, "test_table_equality": 3, "test_trtools.sh": 1, @@ -25138,7 +25154,7 @@ "tiara-test": 2, "tiberius": 1, "tiberius.py": 1, - "tic": 7874, + "tic": 7884, "tiddit": 1, "tides": 1, "tidk": 1, @@ -25146,23 +25162,23 @@ "tidygff3": 1, "tidyp": 66, "tie": 1, - "tiff2bw": 5316, - "tiff2fsspec": 22, - "tiff2pdf": 5316, - "tiff2ps": 5316, - "tiff2rgba": 5316, - "tiffcmp": 5316, - "tiffcomment": 24, - "tiffcp": 5590, - "tiffcrop": 5316, - "tiffdither": 5316, - "tiffdump": 5590, - "tifffile": 27, - "tiffinfo": 5590, - "tiffmedian": 5316, - "tiffset": 5590, - "tiffsplit": 5590, - "tificc": 1048, + "tiff2bw": 5321, + "tiff2fsspec": 23, + "tiff2pdf": 5321, + "tiff2ps": 5321, + "tiff2rgba": 5321, + "tiffcmp": 5321, + "tiffcomment": 25, + "tiffcp": 5595, + "tiffcrop": 5321, + "tiffdither": 5321, + "tiffdump": 5595, + "tifffile": 28, + "tiffinfo": 5595, + "tiffmedian": 5321, + "tiffset": 5595, + "tiffsplit": 5595, + "tificc": 1053, "tigStore": 3, "tiger-hash": 11, "tigge_check": 1, @@ -25196,7 +25212,7 @@ "timeout_decorator.py": 1, "timescorealn": 1, "timetree_inference.py": 1, - "timezone-dump": 71, + "timezone-dump": 73, "timsdata.dll": 2, "tin.py": 3, "ting": 1, @@ -25216,7 +25232,7 @@ "titan-gc-prepare.py": 1, "titan.py": 1, "titration": 2, - "tjbench": 463, + "tjbench": 468, "tkconch": 1, "tkpp": 1, "tksm": 1, @@ -25247,14 +25263,14 @@ "to_upper_case.pl.bak": 1, "toco": 80, "toco_from_protos": 80, - "toe": 7874, + "toe": 7884, "tohnsw": 1, "toil": 3, "toil-cwl-runner": 3, "toil-wdl-runner": 2, "tolkein": 1, "tombo": 2, - "toml2xml": 38, + "toml2xml": 39, "tomlq": 298, "tomsimilarity": 1, "tomtom": 13, @@ -25275,7 +25291,7 @@ "topology": 1, "tops-viterbi_decoding": 1, "topword.R": 1, - "torch_shm_manager": 12, + "torch_shm_manager": 13, "torchapp": 1, "torchapp-imageclassifier": 1, "torchbiggraph_config": 2, @@ -25287,7 +25303,7 @@ "torchbiggraph_import_from_tsv": 2, "torchbiggraph_partitionserver": 2, "torchbiggraph_train": 2, - "torchrun": 40, + "torchrun": 41, "touch": 85, "toulligqc": 1, "tox": 2, @@ -25300,8 +25316,8 @@ "tpp_hostname": 2, "tpp_models.pl": 2, "tpptray.bat": 2, - "tput": 7874, - "tqdm": 390, + "tput": 7884, + "tqdm": 394, "tr": 85, "tr-trimmer": 1, "trace_comment": 2, @@ -25375,7 +25391,7 @@ "transform_gfa.py": 1, "transformers-cli": 4, "transformseq": 13, - "transicc": 1048, + "transicc": 1053, "transit": 1, "transition_counter": 1, "transl": 1, @@ -25391,8 +25407,8 @@ "translate_reduced_reads.pl": 1, "translatorx": 1, "translatorx_vLocal.pl": 1, - "transmute": 313, - "transmute.Linux": 227, + "transmute": 314, + "transmute.Linux": 228, "transposcope": 1, "transpose.pl": 1, "transpose.pl.bak": 1, @@ -25531,7 +25547,7 @@ "tryptic.py": 1, "ts": 3, "tsebra.py": 3, - "tset": 7874, + "tset": 7884, "tskit": 7, "tsort": 85, "tsp": 2, @@ -25567,7 +25583,7 @@ "tth-hash": 11, "ttree": 66, "tts": 5, - "ttx": 436, + "ttx": 440, "tty": 85, "tune": 1, "turbocor": 1, @@ -25598,7 +25614,7 @@ "type_constellations.py": 2, "typeoutfileinfo": 1, "typeprof": 9, - "typer": 5, + "typer": 6, "tzselect": 45, "uLTRA": 1, "ubismap.py": 1, @@ -25655,7 +25671,7 @@ "undexar": 1, "undexqv": 1, "undexta": 3, - "undill": 64, + "undill": 65, "unexpand": 85, "unfazed": 1, "unfiltered_plot.R": 1, @@ -25683,7 +25699,7 @@ "uniprot_sprot_to_sqlite3.py": 2, "uniprot_support.py": 1, "uniq": 86, - "uniq-table": 215, + "uniq-table": 216, "uniqLine.pl": 1, "uniqPolishes": 3, "uniqscan": 1, @@ -25711,8 +25727,8 @@ "unix2dos": 2, "unix2mac": 2, "unlink": 85, - "unlz4": 3542, - "unlzma": 7699, + "unlz4": 3544, + "unlzma": 7708, "unmapped2anchors.py": 1, "unmerge": 1, "unmerge-paired-reads.sh": 2, @@ -25730,7 +25746,7 @@ "unstarch-typical": 15, "untangle": 2, "unweight_fasta.py": 1, - "unxz": 7924, + "unxz": 7933, "unzip": 32, "unzip.sh": 30, "unziphdf5": 1, @@ -25738,7 +25754,7 @@ "unzipont": 1, "unzipont_dir": 1, "unzipsfx": 25, - "unzstd": 5331, + "unzstd": 5337, "update-blastdb.py": 2, "update-serotypefinder-db": 1, "update-sort-bed-migrate-candidates": 15, @@ -25758,7 +25774,7 @@ "updateDeltaClr": 2, "updateLibSizes": 2, "update_alias.py": 1, - "update_blastdb.pl": 349, + "update_blastdb.pl": 350, "update_blastdb.pl.bak": 309, "update_database": 1, "update_info.py": 3, @@ -25812,7 +25828,7 @@ "utmpdump": 13, "utrgff2gbrowse.pl": 15, "utrrnaseq": 13, - "uuclient": 5903, + "uuclient": 5909, "uuid": 38, "uuid-config": 38, "uuidgen": 13, @@ -26510,7 +26526,7 @@ "wgMLST": 1, "wgatools": 1, "wgdi": 1, - "wget": 449, + "wget": 450, "wgetdir": 1, "wgmlst": 1, "wgs2ncbi": 1, @@ -26519,7 +26535,7 @@ "wham": 1, "whamg": 1, "whatshap": 14, - "wheel": 3800, + "wheel": 3809, "wheezy.template": 2, "whereis": 13, "which": 1, @@ -26558,15 +26574,15 @@ "window-acgt": 2, "windowBed": 280, "windowMaker": 280, - "windowmasker": 349, - "windowmasker_2.2.22_adapter.py": 349, + "windowmasker": 350, + "windowmasker_2.2.22_adapter.py": 350, "winextract": 1, "winnowmap": 3, "wiq.py": 1, "wisestork": 1, - "wish": 7501, + "wish": 7510, "wish8.5": 473, - "wish8.6": 7264, + "wish8.6": 7273, "wkhtmltoimage": 2, "wkhtmltopdf": 2, "wlmscpfs": 1, @@ -26576,7 +26592,7 @@ "woltka": 1, "womtool": 4, "wopl2ofm": 1, - "word-at-a-time": 315, + "word-at-a-time": 316, "word-square": 2, "word_enrich.pl": 1, "wordcloud_cli": 1, @@ -26617,7 +26633,7 @@ "write_tfrecord_species.py": 1, "writedb_entry": 1, "writedb_unit_test": 5, - "wrjpgcom": 5844, + "wrjpgcom": 5849, "ws": 2, "wsdl": 16, "wsdl2": 16, @@ -26683,7 +26699,7 @@ "x86_64-conda-linux-gnu-gfortran": 3363, "x86_64-conda-linux-gnu-gfortran.bin": 575, "x86_64-conda-linux-gnu-gprof": 3401, - "x86_64-conda-linux-gnu-ld": 5653, + "x86_64-conda-linux-gnu-ld": 5662, "x86_64-conda-linux-gnu-ld.bfd": 3401, "x86_64-conda-linux-gnu-ld.gold": 3401, "x86_64-conda-linux-gnu-nm": 3401, @@ -26719,7 +26735,7 @@ "x86_64-conda_cos6-linux-gnu-gfortran": 4132, "x86_64-conda_cos6-linux-gnu-gfortran.bin": 1344, "x86_64-conda_cos6-linux-gnu-gprof": 4168, - "x86_64-conda_cos6-linux-gnu-ld": 6487, + "x86_64-conda_cos6-linux-gnu-ld": 6496, "x86_64-conda_cos6-linux-gnu-ld.bfd": 4168, "x86_64-conda_cos6-linux-gnu-ld.gold": 4168, "x86_64-conda_cos6-linux-gnu-nm": 4168, @@ -26758,7 +26774,7 @@ "xgboost": 30, "xgboost.dll": 1, "xgboost.lib": 1, - "xgettext": 5319, + "xgettext": 5320, "xgui": 2, "xhmm": 1, "xinteract": 2, @@ -26772,23 +26788,23 @@ "xmfa2maf": 4, "xmfa2maf.pl": 1, "xml": 1, - "xml2-config": 5445, + "xml2-config": 5451, "xml2-config.bak": 34, "xml2dcm": 1, "xml2dsr": 1, - "xml2fsa": 227, - "xml2json": 227, - "xml2tbl": 300, + "xml2fsa": 228, + "xml2json": 228, + "xml2tbl": 301, "xml_grep": 64, "xml_merge": 64, "xml_pp": 64, "xml_spellcheck": 64, "xml_split": 64, "xml_to_bas.pl": 3, - "xmlcatalog": 5445, + "xmlcatalog": 5451, "xmlget": 23, "xmlindent": 1, - "xmllint": 5445, + "xmllint": 5451, "xmlpatterns": 255, "xmlpatterns-qt4": 3, "xmlpatternsvalidator": 255, @@ -26823,14 +26839,14 @@ "xrdsssadmin": 1, "xrootd": 1, "xrootd-config": 1, - "xrspatial": 2, + "xrspatial": 3, "xsd": 18, "xslt-config": 268, "xsltproc": 268, "xsltproc_lite": 7, "xstreme": 2, "xstreme_html_to_tsv": 2, - "xsubpp": 1740, + "xsubpp": 1742, "xsv": 1, "xtandem": 3, "xtb": 1, @@ -26838,8 +26854,8 @@ "xtea_hg19": 1, "xtea_long": 1, "xtermcolor": 2, - "xtract": 315, - "xtract.Linux": 227, + "xtract": 316, + "xtract.Linux": 228, "xtract.go": 15, "xtract.pl": 1, "xtractcol": 1, @@ -26853,16 +26869,16 @@ "xy-plot": 88, "xyalign": 1, "xyz_sfetch": 1, - "xz": 7924, - "xzcat": 7699, - "xzcmp": 7699, - "xzdec": 7699, - "xzdiff": 7699, - "xzegrep": 7699, - "xzfgrep": 7699, - "xzgrep": 7699, - "xzless": 7699, - "xzmore": 7699, + "xz": 7933, + "xzcat": 7708, + "xzcmp": 7708, + "xzdec": 7708, + "xzdiff": 7708, + "xzegrep": 7708, + "xzfgrep": 7708, + "xzgrep": 7708, + "xzless": 7708, + "xzmore": 7708, "y2racc": 7, "yacc": 4, "yacht": 1, @@ -26873,7 +26889,7 @@ "yak": 2, "yaml2gff.1.4.pl": 15, "yaml2obj": 4, - "yaml2xml": 38, + "yaml2xml": 39, "yamllint": 1, "yamlpp5-events": 4, "yamlpp5-highlight": 4, @@ -26917,7 +26933,7 @@ "zff2gff3.pl": 2, "zfgrep": 20, "zforce": 20, - "zfp": 27, + "zfp": 28, "zga": 1, "zgrep": 20, "zic": 45, @@ -26925,7 +26941,7 @@ "zipHomerResults.pl": 5, "zipcloak": 2, "zipcmp": 95, - "zipdetails": 1740, + "zipdetails": 1742, "zipgrep": 25, "zipinfo": 25, "zipmerge": 95, @@ -26941,8 +26957,8 @@ "zol": 2, "zoom": 1, "zoom2sam.pl": 533, - "zopfli": 27, - "zopflipng": 27, + "zopfli": 28, + "zopflipng": 28, "zorro": 1, "zorro_dist.pl": 1, "zpca-counts": 1, @@ -26950,10 +26966,10 @@ "zrun": 3, "zsh": 3, "zsh-5.8": 3, - "zstd": 5331, - "zstdcat": 5331, - "zstdgrep": 5129, - "zstdless": 5129, - "zstdmt": 5331, + "zstd": 5337, + "zstdcat": 5337, + "zstdgrep": 5135, + "zstdless": 5135, + "zstdmt": 5337, "ztr_dump": 2 } \ No newline at end of file diff --git a/quay.io/biocontainers/a/ampd-up:1.0.0--pyhdfd78af_0.json b/quay.io/biocontainers/a/ampd-up:1.0.0--pyhdfd78af_0.json new file mode 100644 index 0000000..e1df4fc --- /dev/null +++ b/quay.io/biocontainers/a/ampd-up:1.0.0--pyhdfd78af_0.json @@ -0,0 +1,93 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.6": "/usr/local/bin/2to3-3.6", + "AMPd-Up": "/usr/local/bin/AMPd-Up", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "clear": "/usr/local/bin/clear", + "convert-caffe2-to-onnx": "/usr/local/bin/convert-caffe2-to-onnx", + "convert-onnx-to-caffe2": "/usr/local/bin/convert-onnx-to-caffe2", + "f2py": "/usr/local/bin/f2py", + "f2py3": "/usr/local/bin/f2py3", + "f2py3.6": "/usr/local/bin/f2py3.6", + "futurize": "/usr/local/bin/futurize", + "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", + "idle3": "/usr/local/bin/idle3", + "idle3.6": "/usr/local/bin/idle3.6", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "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", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "ninja": "/usr/local/bin/ninja", + "openssl": "/usr/local/bin/openssl", + "pasteurize": "/usr/local/bin/pasteurize", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "protoc": "/usr/local/bin/protoc", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.6": "/usr/local/bin/pydoc3.6", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.6": "/usr/local/bin/python3.6", + "python3.6-config": "/usr/local/bin/python3.6-config", + "python3.6m": "/usr/local/bin/python3.6m", + "python3.6m-config": "/usr/local/bin/python3.6m-config", + "pyvenv": "/usr/local/bin/pyvenv", + "pyvenv-3.6": "/usr/local/bin/pyvenv-3.6", + "reset": "/usr/local/bin/reset", + "sqlite3": "/usr/local/bin/sqlite3", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tset": "/usr/local/bin/tset", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xml2-config": "/usr/local/bin/xml2-config", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore" +} \ No newline at end of file diff --git a/quay.io/biocontainers/c/cell2cell:0.7.4--py38h4ac6f70_0.json b/quay.io/biocontainers/c/cell2cell:0.7.4--py38h4ac6f70_0.json new file mode 100644 index 0000000..ebe9c3d --- /dev/null +++ b/quay.io/biocontainers/c/cell2cell:0.7.4--py38h4ac6f70_0.json @@ -0,0 +1,208 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.8": "/usr/local/bin/2to3-3.8", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "brotli": "/usr/local/bin/brotli", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "curl-config": "/usr/local/bin/curl-config", + "derb": "/usr/local/bin/derb", + "djpeg": "/usr/local/bin/djpeg", + "f2py": "/usr/local/bin/f2py", + "f2py3": "/usr/local/bin/f2py3", + "f2py3.8": "/usr/local/bin/f2py3.8", + "fax2ps": "/usr/local/bin/fax2ps", + "fax2tiff": "/usr/local/bin/fax2tiff", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "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", + "gif2h5": "/usr/local/bin/gif2h5", + "gseapy": "/usr/local/bin/gseapy", + "gss-client": "/usr/local/bin/gss-client", + "h52gif": "/usr/local/bin/h52gif", + "h5c++": "/usr/local/bin/h5c++", + "h5cc": "/usr/local/bin/h5cc", + "h5clear": "/usr/local/bin/h5clear", + "h5copy": "/usr/local/bin/h5copy", + "h5debug": "/usr/local/bin/h5debug", + "h5delete": "/usr/local/bin/h5delete", + "h5diff": "/usr/local/bin/h5diff", + "h5dump": "/usr/local/bin/h5dump", + "h5fc": "/usr/local/bin/h5fc", + "h5format_convert": "/usr/local/bin/h5format_convert", + "h5fuse.sh": "/usr/local/bin/h5fuse.sh", + "h5import": "/usr/local/bin/h5import", + "h5jam": "/usr/local/bin/h5jam", + "h5ls": "/usr/local/bin/h5ls", + "h5mkgrp": "/usr/local/bin/h5mkgrp", + "h5perf_serial": "/usr/local/bin/h5perf_serial", + "h5redeploy": "/usr/local/bin/h5redeploy", + "h5repack": "/usr/local/bin/h5repack", + "h5repart": "/usr/local/bin/h5repart", + "h5stat": "/usr/local/bin/h5stat", + "h5tools_test_utils": "/usr/local/bin/h5tools_test_utils", + "h5unjam": "/usr/local/bin/h5unjam", + "h5watch": "/usr/local/bin/h5watch", + "hwloc-annotate": "/usr/local/bin/hwloc-annotate", + "hwloc-bind": "/usr/local/bin/hwloc-bind", + "hwloc-calc": "/usr/local/bin/hwloc-calc", + "hwloc-compress-dir": "/usr/local/bin/hwloc-compress-dir", + "hwloc-diff": "/usr/local/bin/hwloc-diff", + "hwloc-distrib": "/usr/local/bin/hwloc-distrib", + "hwloc-gather-cpuid": "/usr/local/bin/hwloc-gather-cpuid", + "hwloc-gather-topology": "/usr/local/bin/hwloc-gather-topology", + "hwloc-info": "/usr/local/bin/hwloc-info", + "hwloc-ls": "/usr/local/bin/hwloc-ls", + "hwloc-patch": "/usr/local/bin/hwloc-patch", + "hwloc-ps": "/usr/local/bin/hwloc-ps", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "idle3": "/usr/local/bin/idle3", + "idle3.8": "/usr/local/bin/idle3.8", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "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", + "natsort": "/usr/local/bin/natsort", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "normalizer": "/usr/local/bin/normalizer", + "numba": "/usr/local/bin/numba", + "openssl": "/usr/local/bin/openssl", + "opj_compress": "/usr/local/bin/opj_compress", + "opj_decompress": "/usr/local/bin/opj_decompress", + "opj_dump": "/usr/local/bin/opj_dump", + "pal2rgb": "/usr/local/bin/pal2rgb", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pkgdata": "/usr/local/bin/pkgdata", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "ppm2tiff": "/usr/local/bin/ppm2tiff", + "psicc": "/usr/local/bin/psicc", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.8": "/usr/local/bin/pydoc3.8", + "pyftmerge": "/usr/local/bin/pyftmerge", + "pyftsubset": "/usr/local/bin/pyftsubset", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.8": "/usr/local/bin/python3.8", + "python3.8-config": "/usr/local/bin/python3.8-config", + "raw2tiff": "/usr/local/bin/raw2tiff", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "reset": "/usr/local/bin/reset", + "runxlrd.py": "/usr/local/bin/runxlrd.py", + "scanpy": "/usr/local/bin/scanpy", + "sclient": "/usr/local/bin/sclient", + "sim_client": "/usr/local/bin/sim_client", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "tiff2bw": "/usr/local/bin/tiff2bw", + "tiff2pdf": "/usr/local/bin/tiff2pdf", + "tiff2ps": "/usr/local/bin/tiff2ps", + "tiff2rgba": "/usr/local/bin/tiff2rgba", + "tiffcmp": "/usr/local/bin/tiffcmp", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffcrop": "/usr/local/bin/tiffcrop", + "tiffdither": "/usr/local/bin/tiffdither", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffmedian": "/usr/local/bin/tiffmedian", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tqdm": "/usr/local/bin/tqdm", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xml2-config": "/usr/local/bin/xml2-config", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/c/coptr:1.1.4--pyhdfd78af_1.json b/quay.io/biocontainers/c/coptr:1.1.4--pyhdfd78af_1.json new file mode 100644 index 0000000..c4aeedb --- /dev/null +++ b/quay.io/biocontainers/c/coptr:1.1.4--pyhdfd78af_1.json @@ -0,0 +1,195 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.12": "/usr/local/bin/2to3-3.12", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "bowtie2": "/usr/local/bin/bowtie2", + "bowtie2-align-l": "/usr/local/bin/bowtie2-align-l", + "bowtie2-align-s": "/usr/local/bin/bowtie2-align-s", + "bowtie2-build": "/usr/local/bin/bowtie2-build", + "bowtie2-build-l": "/usr/local/bin/bowtie2-build-l", + "bowtie2-build-s": "/usr/local/bin/bowtie2-build-s", + "bowtie2-inspect": "/usr/local/bin/bowtie2-inspect", + "bowtie2-inspect-l": "/usr/local/bin/bowtie2-inspect-l", + "bowtie2-inspect-s": "/usr/local/bin/bowtie2-inspect-s", + "brotli": "/usr/local/bin/brotli", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "coptr": "/usr/local/bin/coptr", + "corelist": "/usr/local/bin/corelist", + "cpan": "/usr/local/bin/cpan", + "curl-config": "/usr/local/bin/curl-config", + "djpeg": "/usr/local/bin/djpeg", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "f2py": "/usr/local/bin/f2py", + "fax2ps": "/usr/local/bin/fax2ps", + "fax2tiff": "/usr/local/bin/fax2tiff", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "gss-client": "/usr/local/bin/gss-client", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "idle3": "/usr/local/bin/idle3", + "idle3.12": "/usr/local/bin/idle3.12", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "instmodsh": "/usr/local/bin/instmodsh", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "json_pp": "/usr/local/bin/json_pp", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libnetcfg": "/usr/local/bin/libnetcfg", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "numpy-config": "/usr/local/bin/numpy-config", + "openssl": "/usr/local/bin/openssl", + "opj_compress": "/usr/local/bin/opj_compress", + "opj_decompress": "/usr/local/bin/opj_decompress", + "opj_dump": "/usr/local/bin/opj_dump", + "pal2rgb": "/usr/local/bin/pal2rgb", + "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", + "pl2pm": "/usr/local/bin/pl2pm", + "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", + "prove": "/usr/local/bin/prove", + "psicc": "/usr/local/bin/psicc", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.12": "/usr/local/bin/pydoc3.12", + "pyftmerge": "/usr/local/bin/pyftmerge", + "pyftsubset": "/usr/local/bin/pyftsubset", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.12": "/usr/local/bin/python3.12", + "python3.12-config": "/usr/local/bin/python3.12-config", + "qconvex": "/usr/local/bin/qconvex", + "qdelaunay": "/usr/local/bin/qdelaunay", + "qhalf": "/usr/local/bin/qhalf", + "qhull": "/usr/local/bin/qhull", + "qvoronoi": "/usr/local/bin/qvoronoi", + "raw2tiff": "/usr/local/bin/raw2tiff", + "rbox": "/usr/local/bin/rbox", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "reset": "/usr/local/bin/reset", + "sclient": "/usr/local/bin/sclient", + "shasum": "/usr/local/bin/shasum", + "sim_client": "/usr/local/bin/sim_client", + "splain": "/usr/local/bin/splain", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "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", + "tiff2bw": "/usr/local/bin/tiff2bw", + "tiff2pdf": "/usr/local/bin/tiff2pdf", + "tiff2ps": "/usr/local/bin/tiff2ps", + "tiff2rgba": "/usr/local/bin/tiff2rgba", + "tiffcmp": "/usr/local/bin/tiffcmp", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffcrop": "/usr/local/bin/tiffcrop", + "tiffdither": "/usr/local/bin/tiffdither", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffmedian": "/usr/local/bin/tiffmedian", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xsubpp": "/usr/local/bin/xsubpp", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zipdetails": "/usr/local/bin/zipdetails", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/c/corneto:1.0.0a0--pyhdfd78af_0.json b/quay.io/biocontainers/c/corneto:1.0.0a0--pyhdfd78af_0.json new file mode 100644 index 0000000..dd8fe88 --- /dev/null +++ b/quay.io/biocontainers/c/corneto:1.0.0a0--pyhdfd78af_0.json @@ -0,0 +1,74 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.12": "/usr/local/bin/2to3-3.12", + "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", + "f2py": "/usr/local/bin/f2py", + "idle3": "/usr/local/bin/idle3", + "idle3.12": "/usr/local/bin/idle3.12", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "openssl": "/usr/local/bin/openssl", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.12": "/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", + "reset": "/usr/local/bin/reset", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tset": "/usr/local/bin/tset", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore" +} \ No newline at end of file diff --git a/quay.io/biocontainers/d/deepchopper-cli:1.2.5--py310h77ce02f_0.json b/quay.io/biocontainers/d/deepchopper-cli:1.2.5--py310h77ce02f_0.json new file mode 100644 index 0000000..3c72eb3 --- /dev/null +++ b/quay.io/biocontainers/d/deepchopper-cli:1.2.5--py310h77ce02f_0.json @@ -0,0 +1,74 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.10": "/usr/local/bin/2to3-3.10", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "clear": "/usr/local/bin/clear", + "deepchopper-chop": "/usr/local/bin/deepchopper-chop", + "idle3": "/usr/local/bin/idle3", + "idle3.10": "/usr/local/bin/idle3.10", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "openssl": "/usr/local/bin/openssl", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.10": "/usr/local/bin/pydoc3.10", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.10": "/usr/local/bin/python3.10", + "python3.10-config": "/usr/local/bin/python3.10-config", + "reset": "/usr/local/bin/reset", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tset": "/usr/local/bin/tset", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore" +} \ No newline at end of file diff --git a/quay.io/biocontainers/d/doubletdetection:4.2--pyhdfd78af_0.json b/quay.io/biocontainers/d/doubletdetection:4.2--pyhdfd78af_0.json new file mode 100644 index 0000000..43d0d7b --- /dev/null +++ b/quay.io/biocontainers/d/doubletdetection:4.2--pyhdfd78af_0.json @@ -0,0 +1,205 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.12": "/usr/local/bin/2to3-3.12", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "brotli": "/usr/local/bin/brotli", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "curl-config": "/usr/local/bin/curl-config", + "djpeg": "/usr/local/bin/djpeg", + "f2py": "/usr/local/bin/f2py", + "fax2ps": "/usr/local/bin/fax2ps", + "fax2tiff": "/usr/local/bin/fax2tiff", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "gif2h5": "/usr/local/bin/gif2h5", + "glpsol": "/usr/local/bin/glpsol", + "gss-client": "/usr/local/bin/gss-client", + "h52gif": "/usr/local/bin/h52gif", + "h5c++": "/usr/local/bin/h5c++", + "h5cc": "/usr/local/bin/h5cc", + "h5clear": "/usr/local/bin/h5clear", + "h5copy": "/usr/local/bin/h5copy", + "h5debug": "/usr/local/bin/h5debug", + "h5delete": "/usr/local/bin/h5delete", + "h5diff": "/usr/local/bin/h5diff", + "h5dump": "/usr/local/bin/h5dump", + "h5fc": "/usr/local/bin/h5fc", + "h5format_convert": "/usr/local/bin/h5format_convert", + "h5fuse.sh": "/usr/local/bin/h5fuse.sh", + "h5import": "/usr/local/bin/h5import", + "h5jam": "/usr/local/bin/h5jam", + "h5ls": "/usr/local/bin/h5ls", + "h5mkgrp": "/usr/local/bin/h5mkgrp", + "h5perf_serial": "/usr/local/bin/h5perf_serial", + "h5redeploy": "/usr/local/bin/h5redeploy", + "h5repack": "/usr/local/bin/h5repack", + "h5repart": "/usr/local/bin/h5repart", + "h5stat": "/usr/local/bin/h5stat", + "h5tools_test_utils": "/usr/local/bin/h5tools_test_utils", + "h5unjam": "/usr/local/bin/h5unjam", + "h5watch": "/usr/local/bin/h5watch", + "hwloc-annotate": "/usr/local/bin/hwloc-annotate", + "hwloc-bind": "/usr/local/bin/hwloc-bind", + "hwloc-calc": "/usr/local/bin/hwloc-calc", + "hwloc-compress-dir": "/usr/local/bin/hwloc-compress-dir", + "hwloc-diff": "/usr/local/bin/hwloc-diff", + "hwloc-distrib": "/usr/local/bin/hwloc-distrib", + "hwloc-gather-cpuid": "/usr/local/bin/hwloc-gather-cpuid", + "hwloc-gather-topology": "/usr/local/bin/hwloc-gather-topology", + "hwloc-info": "/usr/local/bin/hwloc-info", + "hwloc-ls": "/usr/local/bin/hwloc-ls", + "hwloc-patch": "/usr/local/bin/hwloc-patch", + "hwloc-ps": "/usr/local/bin/hwloc-ps", + "idle3": "/usr/local/bin/idle3", + "idle3.12": "/usr/local/bin/idle3.12", + "igraph": "/usr/local/bin/igraph", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "ipython": "/usr/local/bin/ipython", + "ipython3": "/usr/local/bin/ipython3", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "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", + "natsort": "/usr/local/bin/natsort", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "numba": "/usr/local/bin/numba", + "numpy-config": "/usr/local/bin/numpy-config", + "openssl": "/usr/local/bin/openssl", + "opj_compress": "/usr/local/bin/opj_compress", + "opj_decompress": "/usr/local/bin/opj_decompress", + "opj_dump": "/usr/local/bin/opj_dump", + "pal2rgb": "/usr/local/bin/pal2rgb", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "ppm2tiff": "/usr/local/bin/ppm2tiff", + "psicc": "/usr/local/bin/psicc", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.12": "/usr/local/bin/pydoc3.12", + "pyftmerge": "/usr/local/bin/pyftmerge", + "pyftsubset": "/usr/local/bin/pyftsubset", + "pygmentize": "/usr/local/bin/pygmentize", + "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", + "qconvex": "/usr/local/bin/qconvex", + "qdelaunay": "/usr/local/bin/qdelaunay", + "qhalf": "/usr/local/bin/qhalf", + "qhull": "/usr/local/bin/qhull", + "qvoronoi": "/usr/local/bin/qvoronoi", + "raw2tiff": "/usr/local/bin/raw2tiff", + "rbox": "/usr/local/bin/rbox", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "reset": "/usr/local/bin/reset", + "scanpy": "/usr/local/bin/scanpy", + "sclient": "/usr/local/bin/sclient", + "sim_client": "/usr/local/bin/sim_client", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "tiff2bw": "/usr/local/bin/tiff2bw", + "tiff2pdf": "/usr/local/bin/tiff2pdf", + "tiff2ps": "/usr/local/bin/tiff2ps", + "tiff2rgba": "/usr/local/bin/tiff2rgba", + "tiffcmp": "/usr/local/bin/tiffcmp", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffcrop": "/usr/local/bin/tiffcrop", + "tiffdither": "/usr/local/bin/tiffdither", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffmedian": "/usr/local/bin/tiffmedian", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tqdm": "/usr/local/bin/tqdm", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xml2-config": "/usr/local/bin/xml2-config", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/j/jarvis3:3.7--h031d066_1.json b/quay.io/biocontainers/j/jarvis3:3.7--h031d066_1.json new file mode 100644 index 0000000..7f5b570 --- /dev/null +++ b/quay.io/biocontainers/j/jarvis3:3.7--h031d066_1.json @@ -0,0 +1,8 @@ +{ + "JARVIS3": "/usr/local/bin/JARVIS3", + "JARVIS3.sh": "/usr/local/bin/JARVIS3.sh", + "JARVIS3.sh.bak": "/usr/local/bin/JARVIS3.sh.bak", + "XScoreC": "/usr/local/bin/XScoreC", + "XScoreD": "/usr/local/bin/XScoreD", + "bzip2": "/usr/local/bin/bzip2" +} \ No newline at end of file diff --git a/quay.io/biocontainers/l/libgff:2.0.0--hdcf5f25_1.json b/quay.io/biocontainers/l/libgff:2.0.0--hdcf5f25_1.json new file mode 100644 index 0000000..9e26dfe --- /dev/null +++ b/quay.io/biocontainers/l/libgff:2.0.0--hdcf5f25_1.json @@ -0,0 +1 @@ +{} \ No newline at end of file diff --git a/quay.io/biocontainers/p/phenograph:1.5.7--pyhdfd78af_0.json b/quay.io/biocontainers/p/phenograph:1.5.7--pyhdfd78af_0.json new file mode 100644 index 0000000..e36f34a --- /dev/null +++ b/quay.io/biocontainers/p/phenograph:1.5.7--pyhdfd78af_0.json @@ -0,0 +1,80 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.12": "/usr/local/bin/2to3-3.12", + "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", + "f2py": "/usr/local/bin/f2py", + "glpsol": "/usr/local/bin/glpsol", + "idle3": "/usr/local/bin/idle3", + "idle3.12": "/usr/local/bin/idle3.12", + "igraph": "/usr/local/bin/igraph", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "numpy-config": "/usr/local/bin/numpy-config", + "openssl": "/usr/local/bin/openssl", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.12": "/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", + "reset": "/usr/local/bin/reset", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tset": "/usr/local/bin/tset", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xml2-config": "/usr/local/bin/xml2-config", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore" +} \ No newline at end of file diff --git a/quay.io/biocontainers/p/pyscenic:0.12.1--pyhdfd78af_0.json b/quay.io/biocontainers/p/pyscenic:0.12.1--pyhdfd78af_0.json new file mode 100644 index 0000000..6b38afd --- /dev/null +++ b/quay.io/biocontainers/p/pyscenic:0.12.1--pyhdfd78af_0.json @@ -0,0 +1,245 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.11": "/usr/local/bin/2to3-3.11", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "arboreto_with_multiprocessing.py": "/usr/local/bin/arboreto_with_multiprocessing.py", + "bokeh": "/usr/local/bin/bokeh", + "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", + "checksum-profile": "/usr/local/bin/checksum-profile", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "csv-import": "/usr/local/bin/csv-import", + "csv2loom": "/usr/local/bin/csv2loom", + "curl-config": "/usr/local/bin/curl-config", + "dask": "/usr/local/bin/dask", + "dask-scheduler": "/usr/local/bin/dask-scheduler", + "dask-ssh": "/usr/local/bin/dask-ssh", + "dask-worker": "/usr/local/bin/dask-worker", + "db2feather": "/usr/local/bin/db2feather", + "derb": "/usr/local/bin/derb", + "djpeg": "/usr/local/bin/djpeg", + "elasticurl": "/usr/local/bin/elasticurl", + "elasticurl_cpp": "/usr/local/bin/elasticurl_cpp", + "elastipubsub": "/usr/local/bin/elastipubsub", + "elastipubsub5": "/usr/local/bin/elastipubsub5", + "elastishadow": "/usr/local/bin/elastishadow", + "f2py": "/usr/local/bin/f2py", + "f2py3": "/usr/local/bin/f2py3", + "f2py3.11": "/usr/local/bin/f2py3.11", + "fax2ps": "/usr/local/bin/fax2ps", + "fax2tiff": "/usr/local/bin/fax2tiff", + "freetype-config": "/usr/local/bin/freetype-config", + "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", + "get_gprof": "/usr/local/bin/get_gprof", + "get_objgraph": "/usr/local/bin/get_objgraph", + "gflags_completions.sh": "/usr/local/bin/gflags_completions.sh", + "gif2h5": "/usr/local/bin/gif2h5", + "gmt2regions": "/usr/local/bin/gmt2regions", + "grpc_cpp_plugin": "/usr/local/bin/grpc_cpp_plugin", + "grpc_csharp_plugin": "/usr/local/bin/grpc_csharp_plugin", + "grpc_node_plugin": "/usr/local/bin/grpc_node_plugin", + "grpc_objective_c_plugin": "/usr/local/bin/grpc_objective_c_plugin", + "grpc_php_plugin": "/usr/local/bin/grpc_php_plugin", + "grpc_python_plugin": "/usr/local/bin/grpc_python_plugin", + "grpc_ruby_plugin": "/usr/local/bin/grpc_ruby_plugin", + "gss-client": "/usr/local/bin/gss-client", + "h52gif": "/usr/local/bin/h52gif", + "h5c++": "/usr/local/bin/h5c++", + "h5cc": "/usr/local/bin/h5cc", + "h5clear": "/usr/local/bin/h5clear", + "h5copy": "/usr/local/bin/h5copy", + "h5debug": "/usr/local/bin/h5debug", + "h5delete": "/usr/local/bin/h5delete", + "h5diff": "/usr/local/bin/h5diff", + "h5dump": "/usr/local/bin/h5dump", + "h5fc": "/usr/local/bin/h5fc", + "h5format_convert": "/usr/local/bin/h5format_convert", + "h5fuse.sh": "/usr/local/bin/h5fuse.sh", + "h5import": "/usr/local/bin/h5import", + "h5jam": "/usr/local/bin/h5jam", + "h5ls": "/usr/local/bin/h5ls", + "h5mkgrp": "/usr/local/bin/h5mkgrp", + "h5perf_serial": "/usr/local/bin/h5perf_serial", + "h5redeploy": "/usr/local/bin/h5redeploy", + "h5repack": "/usr/local/bin/h5repack", + "h5repart": "/usr/local/bin/h5repart", + "h5stat": "/usr/local/bin/h5stat", + "h5tools_test_utils": "/usr/local/bin/h5tools_test_utils", + "h5unjam": "/usr/local/bin/h5unjam", + "h5watch": "/usr/local/bin/h5watch", + "hwloc-annotate": "/usr/local/bin/hwloc-annotate", + "hwloc-bind": "/usr/local/bin/hwloc-bind", + "hwloc-calc": "/usr/local/bin/hwloc-calc", + "hwloc-compress-dir": "/usr/local/bin/hwloc-compress-dir", + "hwloc-diff": "/usr/local/bin/hwloc-diff", + "hwloc-distrib": "/usr/local/bin/hwloc-distrib", + "hwloc-gather-cpuid": "/usr/local/bin/hwloc-gather-cpuid", + "hwloc-gather-topology": "/usr/local/bin/hwloc-gather-topology", + "hwloc-info": "/usr/local/bin/hwloc-info", + "hwloc-ls": "/usr/local/bin/hwloc-ls", + "hwloc-patch": "/usr/local/bin/hwloc-patch", + "hwloc-ps": "/usr/local/bin/hwloc-ps", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "idle3": "/usr/local/bin/idle3", + "idle3.11": "/usr/local/bin/idle3.11", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "invertdb": "/usr/local/bin/invertdb", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "loompy": "/usr/local/bin/loompy", + "lstopo": "/usr/local/bin/lstopo", + "lstopo-no-graphics": "/usr/local/bin/lstopo-no-graphics", + "lz4": "/usr/local/bin/lz4", + "lz4c": "/usr/local/bin/lz4c", + "lz4cat": "/usr/local/bin/lz4cat", + "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", + "mqtt5_app": "/usr/local/bin/mqtt5_app", + "mqtt5_canary": "/usr/local/bin/mqtt5_canary", + "mqtt5canary": "/usr/local/bin/mqtt5canary", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "normalizer": "/usr/local/bin/normalizer", + "numba": "/usr/local/bin/numba", + "openssl": "/usr/local/bin/openssl", + "opj_compress": "/usr/local/bin/opj_compress", + "opj_decompress": "/usr/local/bin/opj_decompress", + "opj_dump": "/usr/local/bin/opj_dump", + "orc-contents": "/usr/local/bin/orc-contents", + "orc-memory": "/usr/local/bin/orc-memory", + "orc-metadata": "/usr/local/bin/orc-metadata", + "orc-scan": "/usr/local/bin/orc-scan", + "orc-statistics": "/usr/local/bin/orc-statistics", + "pal2rgb": "/usr/local/bin/pal2rgb", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pkgdata": "/usr/local/bin/pkgdata", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "ppm2tiff": "/usr/local/bin/ppm2tiff", + "protoc": "/usr/local/bin/protoc", + "protoc-27.5.0": "/usr/local/bin/protoc-27.5.0", + "psicc": "/usr/local/bin/psicc", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.11": "/usr/local/bin/pydoc3.11", + "pyscenic": "/usr/local/bin/pyscenic", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.11": "/usr/local/bin/python3.11", + "python3.11-config": "/usr/local/bin/python3.11-config", + "raw2tiff": "/usr/local/bin/raw2tiff", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "reset": "/usr/local/bin/reset", + "sclient": "/usr/local/bin/sclient", + "sim_client": "/usr/local/bin/sim_client", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "tiff2bw": "/usr/local/bin/tiff2bw", + "tiff2pdf": "/usr/local/bin/tiff2pdf", + "tiff2ps": "/usr/local/bin/tiff2ps", + "tiff2rgba": "/usr/local/bin/tiff2rgba", + "tiffcmp": "/usr/local/bin/tiffcmp", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffcrop": "/usr/local/bin/tiffcrop", + "tiffdither": "/usr/local/bin/tiffdither", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffmedian": "/usr/local/bin/tiffmedian", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "timezone-dump": "/usr/local/bin/timezone-dump", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "tqdm": "/usr/local/bin/tqdm", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "undill": "/usr/local/bin/undill", + "unlz4": "/usr/local/bin/unlz4", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xml2-config": "/usr/local/bin/xml2-config", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/s/sopa:1.1.5--pyhdfd78af_0.json b/quay.io/biocontainers/s/sopa:1.1.5--pyhdfd78af_0.json new file mode 100644 index 0000000..f433114 --- /dev/null +++ b/quay.io/biocontainers/s/sopa:1.1.5--pyhdfd78af_0.json @@ -0,0 +1,360 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.11": "/usr/local/bin/2to3-3.11", + "CreateDOMDocument": "/usr/local/bin/CreateDOMDocument", + "DOMCount": "/usr/local/bin/DOMCount", + "DOMPrint": "/usr/local/bin/DOMPrint", + "EnumVal": "/usr/local/bin/EnumVal", + "JxrDecApp": "/usr/local/bin/JxrDecApp", + "JxrEncApp": "/usr/local/bin/JxrEncApp", + "MemParse": "/usr/local/bin/MemParse", + "PParse": "/usr/local/bin/PParse", + "PSVIWriter": "/usr/local/bin/PSVIWriter", + "Redirect": "/usr/local/bin/Redirect", + "SAX2Count": "/usr/local/bin/SAX2Count", + "SAX2Print": "/usr/local/bin/SAX2Print", + "SAXCount": "/usr/local/bin/SAXCount", + "SAXPrint": "/usr/local/bin/SAXPrint", + "SCMPrint": "/usr/local/bin/SCMPrint", + "SEnumVal": "/usr/local/bin/SEnumVal", + "StdInParse": "/usr/local/bin/StdInParse", + "SvtAv1EncApp": "/usr/local/bin/SvtAv1EncApp", + "XInclude": "/usr/local/bin/XInclude", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "aomdec": "/usr/local/bin/aomdec", + "aomenc": "/usr/local/bin/aomenc", + "applygeo": "/usr/local/bin/applygeo", + "bokeh": "/usr/local/bin/bokeh", + "brotli": "/usr/local/bin/brotli", + "bsdcat": "/usr/local/bin/bsdcat", + "bsdcpio": "/usr/local/bin/bsdcpio", + "bsdtar": "/usr/local/bin/bsdtar", + "bsdunzip": "/usr/local/bin/bsdunzip", + "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", + "cbrunsli": "/usr/local/bin/cbrunsli", + "cct": "/usr/local/bin/cct", + "checksum-profile": "/usr/local/bin/checksum-profile", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "convert-caffe2-to-onnx": "/usr/local/bin/convert-caffe2-to-onnx", + "convert-onnx-to-caffe2": "/usr/local/bin/convert-onnx-to-caffe2", + "cs2cs": "/usr/local/bin/cs2cs", + "csv-import": "/usr/local/bin/csv-import", + "curl-config": "/usr/local/bin/curl-config", + "dask": "/usr/local/bin/dask", + "dask-scheduler": "/usr/local/bin/dask-scheduler", + "dask-ssh": "/usr/local/bin/dask-ssh", + "dask-worker": "/usr/local/bin/dask-worker", + "datashader": "/usr/local/bin/datashader", + "dav1d": "/usr/local/bin/dav1d", + "dbrunsli": "/usr/local/bin/dbrunsli", + "derb": "/usr/local/bin/derb", + "djpeg": "/usr/local/bin/djpeg", + "elasticurl": "/usr/local/bin/elasticurl", + "elasticurl_cpp": "/usr/local/bin/elasticurl_cpp", + "elastipubsub": "/usr/local/bin/elastipubsub", + "elastipubsub5": "/usr/local/bin/elastipubsub5", + "elastishadow": "/usr/local/bin/elastishadow", + "f2py": "/usr/local/bin/f2py", + "fax2ps": "/usr/local/bin/fax2ps", + "fax2tiff": "/usr/local/bin/fax2tiff", + "flake8": "/usr/local/bin/flake8", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "gdal-config": "/usr/local/bin/gdal-config", + "gdal_contour": "/usr/local/bin/gdal_contour", + "gdal_create": "/usr/local/bin/gdal_create", + "gdal_footprint": "/usr/local/bin/gdal_footprint", + "gdal_grid": "/usr/local/bin/gdal_grid", + "gdal_rasterize": "/usr/local/bin/gdal_rasterize", + "gdal_translate": "/usr/local/bin/gdal_translate", + "gdal_viewshed": "/usr/local/bin/gdal_viewshed", + "gdaladdo": "/usr/local/bin/gdaladdo", + "gdalbuildvrt": "/usr/local/bin/gdalbuildvrt", + "gdaldem": "/usr/local/bin/gdaldem", + "gdalenhance": "/usr/local/bin/gdalenhance", + "gdalinfo": "/usr/local/bin/gdalinfo", + "gdallocationinfo": "/usr/local/bin/gdallocationinfo", + "gdalmanage": "/usr/local/bin/gdalmanage", + "gdalmdiminfo": "/usr/local/bin/gdalmdiminfo", + "gdalmdimtranslate": "/usr/local/bin/gdalmdimtranslate", + "gdalsrsinfo": "/usr/local/bin/gdalsrsinfo", + "gdaltindex": "/usr/local/bin/gdaltindex", + "gdaltransform": "/usr/local/bin/gdaltransform", + "gdalwarp": "/usr/local/bin/gdalwarp", + "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", + "geod": "/usr/local/bin/geod", + "geos-config": "/usr/local/bin/geos-config", + "geosop": "/usr/local/bin/geosop", + "geotifcp": "/usr/local/bin/geotifcp", + "gflags_completions.sh": "/usr/local/bin/gflags_completions.sh", + "gie": "/usr/local/bin/gie", + "gif2h5": "/usr/local/bin/gif2h5", + "gif2rgb": "/usr/local/bin/gif2rgb", + "gifbuild": "/usr/local/bin/gifbuild", + "gifclrmp": "/usr/local/bin/gifclrmp", + "giffix": "/usr/local/bin/giffix", + "giftext": "/usr/local/bin/giftext", + "giftool": "/usr/local/bin/giftool", + "gnmanalyse": "/usr/local/bin/gnmanalyse", + "gnmmanage": "/usr/local/bin/gnmmanage", + "grpc_cpp_plugin": "/usr/local/bin/grpc_cpp_plugin", + "grpc_csharp_plugin": "/usr/local/bin/grpc_csharp_plugin", + "grpc_node_plugin": "/usr/local/bin/grpc_node_plugin", + "grpc_objective_c_plugin": "/usr/local/bin/grpc_objective_c_plugin", + "grpc_php_plugin": "/usr/local/bin/grpc_php_plugin", + "grpc_python_plugin": "/usr/local/bin/grpc_python_plugin", + "grpc_ruby_plugin": "/usr/local/bin/grpc_ruby_plugin", + "gss-client": "/usr/local/bin/gss-client", + "h52gif": "/usr/local/bin/h52gif", + "h5c++": "/usr/local/bin/h5c++", + "h5cc": "/usr/local/bin/h5cc", + "h5clear": "/usr/local/bin/h5clear", + "h5copy": "/usr/local/bin/h5copy", + "h5debug": "/usr/local/bin/h5debug", + "h5delete": "/usr/local/bin/h5delete", + "h5diff": "/usr/local/bin/h5diff", + "h5dump": "/usr/local/bin/h5dump", + "h5fc": "/usr/local/bin/h5fc", + "h5format_convert": "/usr/local/bin/h5format_convert", + "h5fuse.sh": "/usr/local/bin/h5fuse.sh", + "h5import": "/usr/local/bin/h5import", + "h5jam": "/usr/local/bin/h5jam", + "h5ls": "/usr/local/bin/h5ls", + "h5mkgrp": "/usr/local/bin/h5mkgrp", + "h5perf_serial": "/usr/local/bin/h5perf_serial", + "h5redeploy": "/usr/local/bin/h5redeploy", + "h5repack": "/usr/local/bin/h5repack", + "h5repart": "/usr/local/bin/h5repart", + "h5stat": "/usr/local/bin/h5stat", + "h5tools_test_utils": "/usr/local/bin/h5tools_test_utils", + "h5unjam": "/usr/local/bin/h5unjam", + "h5watch": "/usr/local/bin/h5watch", + "hwloc-annotate": "/usr/local/bin/hwloc-annotate", + "hwloc-bind": "/usr/local/bin/hwloc-bind", + "hwloc-calc": "/usr/local/bin/hwloc-calc", + "hwloc-compress-dir": "/usr/local/bin/hwloc-compress-dir", + "hwloc-diff": "/usr/local/bin/hwloc-diff", + "hwloc-distrib": "/usr/local/bin/hwloc-distrib", + "hwloc-gather-cpuid": "/usr/local/bin/hwloc-gather-cpuid", + "hwloc-gather-topology": "/usr/local/bin/hwloc-gather-topology", + "hwloc-info": "/usr/local/bin/hwloc-info", + "hwloc-ls": "/usr/local/bin/hwloc-ls", + "hwloc-patch": "/usr/local/bin/hwloc-patch", + "hwloc-ps": "/usr/local/bin/hwloc-ps", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "idle3": "/usr/local/bin/idle3", + "idle3.11": "/usr/local/bin/idle3.11", + "imagecodecs": "/usr/local/bin/imagecodecs", + "imageio_download_bin": "/usr/local/bin/imageio_download_bin", + "imageio_remove_bin": "/usr/local/bin/imageio_remove_bin", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "invgeod": "/usr/local/bin/invgeod", + "invproj": "/usr/local/bin/invproj", + "isympy": "/usr/local/bin/isympy", + "jp.py": "/usr/local/bin/jp.py", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "listgeo": "/usr/local/bin/listgeo", + "lsm2bin": "/usr/local/bin/lsm2bin", + "lstopo": "/usr/local/bin/lstopo", + "lstopo-no-graphics": "/usr/local/bin/lstopo-no-graphics", + "lz4": "/usr/local/bin/lz4", + "lz4c": "/usr/local/bin/lz4c", + "lz4cat": "/usr/local/bin/lz4cat", + "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", + "makegeo": "/usr/local/bin/makegeo", + "markdown-it": "/usr/local/bin/markdown-it", + "minigzip": "/usr/local/bin/minigzip", + "minizip": "/usr/local/bin/minizip", + "mqtt5_app": "/usr/local/bin/mqtt5_app", + "mqtt5_canary": "/usr/local/bin/mqtt5_canary", + "mqtt5canary": "/usr/local/bin/mqtt5canary", + "natsort": "/usr/local/bin/natsort", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "nearblack": "/usr/local/bin/nearblack", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "normalizer": "/usr/local/bin/normalizer", + "numba": "/usr/local/bin/numba", + "ogr2ogr": "/usr/local/bin/ogr2ogr", + "ogrinfo": "/usr/local/bin/ogrinfo", + "ogrlineref": "/usr/local/bin/ogrlineref", + "ogrtindex": "/usr/local/bin/ogrtindex", + "ome_zarr": "/usr/local/bin/ome_zarr", + "openssl": "/usr/local/bin/openssl", + "opj_compress": "/usr/local/bin/opj_compress", + "opj_decompress": "/usr/local/bin/opj_decompress", + "opj_dump": "/usr/local/bin/opj_dump", + "orc-contents": "/usr/local/bin/orc-contents", + "orc-memory": "/usr/local/bin/orc-memory", + "orc-metadata": "/usr/local/bin/orc-metadata", + "orc-scan": "/usr/local/bin/orc-scan", + "orc-statistics": "/usr/local/bin/orc-statistics", + "pal2rgb": "/usr/local/bin/pal2rgb", + "pcre2-config": "/usr/local/bin/pcre2-config", + "pcre2grep": "/usr/local/bin/pcre2grep", + "pcre2test": "/usr/local/bin/pcre2test", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pkgdata": "/usr/local/bin/pkgdata", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "ppm2tiff": "/usr/local/bin/ppm2tiff", + "proj": "/usr/local/bin/proj", + "projinfo": "/usr/local/bin/projinfo", + "projsync": "/usr/local/bin/projsync", + "protoc": "/usr/local/bin/protoc", + "protoc-27.5.0": "/usr/local/bin/protoc-27.5.0", + "psicc": "/usr/local/bin/psicc", + "pycodestyle": "/usr/local/bin/pycodestyle", + "pyct": "/usr/local/bin/pyct", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.11": "/usr/local/bin/pydoc3.11", + "pyflakes": "/usr/local/bin/pyflakes", + "pyftmerge": "/usr/local/bin/pyftmerge", + "pyftsubset": "/usr/local/bin/pyftsubset", + "pygmentize": "/usr/local/bin/pygmentize", + "pyproj": "/usr/local/bin/pyproj", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.11": "/usr/local/bin/python3.11", + "python3.11-config": "/usr/local/bin/python3.11-config", + "qconvex": "/usr/local/bin/qconvex", + "qdelaunay": "/usr/local/bin/qdelaunay", + "qhalf": "/usr/local/bin/qhalf", + "qhull": "/usr/local/bin/qhull", + "qvoronoi": "/usr/local/bin/qvoronoi", + "rav1e": "/usr/local/bin/rav1e", + "raw2tiff": "/usr/local/bin/raw2tiff", + "rbox": "/usr/local/bin/rbox", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "reset": "/usr/local/bin/reset", + "scanpy": "/usr/local/bin/scanpy", + "sclient": "/usr/local/bin/sclient", + "sim_client": "/usr/local/bin/sim_client", + "skivi": "/usr/local/bin/skivi", + "sopa": "/usr/local/bin/sopa", + "sozip": "/usr/local/bin/sozip", + "sqlite3": "/usr/local/bin/sqlite3", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "tabs": "/usr/local/bin/tabs", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "tic": "/usr/local/bin/tic", + "tiff2bw": "/usr/local/bin/tiff2bw", + "tiff2fsspec": "/usr/local/bin/tiff2fsspec", + "tiff2pdf": "/usr/local/bin/tiff2pdf", + "tiff2ps": "/usr/local/bin/tiff2ps", + "tiff2rgba": "/usr/local/bin/tiff2rgba", + "tiffcmp": "/usr/local/bin/tiffcmp", + "tiffcomment": "/usr/local/bin/tiffcomment", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffcrop": "/usr/local/bin/tiffcrop", + "tiffdither": "/usr/local/bin/tiffdither", + "tiffdump": "/usr/local/bin/tiffdump", + "tifffile": "/usr/local/bin/tifffile", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffmedian": "/usr/local/bin/tiffmedian", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "timezone-dump": "/usr/local/bin/timezone-dump", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "torch_shm_manager": "/usr/local/bin/torch_shm_manager", + "torchrun": "/usr/local/bin/torchrun", + "tput": "/usr/local/bin/tput", + "tqdm": "/usr/local/bin/tqdm", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "typer": "/usr/local/bin/typer", + "unlz4": "/usr/local/bin/unlz4", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xml2-config": "/usr/local/bin/xml2-config", + "xmlcatalog": "/usr/local/bin/xmlcatalog", + "xmllint": "/usr/local/bin/xmllint", + "xrspatial": "/usr/local/bin/xrspatial", + "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", + "zfp": "/usr/local/bin/zfp", + "zopfli": "/usr/local/bin/zopfli", + "zopflipng": "/usr/local/bin/zopflipng", + "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" +} \ No newline at end of file diff --git a/quay.io/biocontainers/s/stxtyper:1.0.25--hdcf5f25_0.json b/quay.io/biocontainers/s/stxtyper:1.0.25--hdcf5f25_0.json new file mode 100644 index 0000000..b55cae3 --- /dev/null +++ b/quay.io/biocontainers/s/stxtyper:1.0.25--hdcf5f25_0.json @@ -0,0 +1,259 @@ +{ + "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", + "bsmp2info": "/usr/local/bin/bsmp2info", + "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", + "fasta_check": "/usr/local/bin/fasta_check", + "fasta_extract": "/usr/local/bin/fasta_extract", + "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", + "fsa2xml": "/usr/local/bin/fsa2xml", + "fuse-ranges": "/usr/local/bin/fuse-ranges", + "fuse-segments": "/usr/local/bin/fuse-segments", + "gbf2fsa": "/usr/local/bin/gbf2fsa", + "gbf2info": "/usr/local/bin/gbf2info", + "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", + "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-top-hits": "/usr/local/bin/just-top-hits", + "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", + "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", + "stx.prot": "/usr/local/bin/stx.prot", + "stxtyper": "/usr/local/bin/stxtyper", + "systematic-mutations": "/usr/local/bin/systematic-mutations", + "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", + "test_stxtyper.sh": "/usr/local/bin/test_stxtyper.sh", + "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", + "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" +} \ No newline at end of file