diff --git a/counts.json b/counts.json index 5334aa5..8dc1c88 100644 --- a/counts.json +++ b/counts.json @@ -2326,10 +2326,10 @@ "2csfastq_1csfastq": 1, "2ft": 2, "2ndscore": 1, - "2to3": 3822, + "2to3": 3824, "2to3-3.10": 836, "2to3-3.11": 283, - "2to3-3.12": 295, + "2to3-3.12": 297, "2to3-3.4": 6, "2to3-3.5": 103, "2to3-3.6": 344, @@ -5103,7 +5103,7 @@ "acc2locus": 2, "acc2tax": 1, "accession_retrieve": 1, - "accn-at-a-time": 285, + "accn-at-a-time": 286, "accurate_bkp.py": 1, "acdc": 28, "acdc-filter-fasta-by-name.awk": 1, @@ -5215,7 +5215,7 @@ "addtit.pl": 2, "adf_checker.pl": 1, "adhocfilelist": 1, - "adig": 4629, + "adig": 4631, "adjustPeakFile.pl": 5, "adjustRedunGroupFile.pl": 5, "adjustScanRankerScoreByGroup": 2, @@ -5332,7 +5332,7 @@ "agrvate": 1, "agtsampleinforw.dll": 2, "ahmm-s": 1, - "ahost": 4629, + "ahost": 4631, "airr-tools": 5, "akita_data.py": 1, "akita_data_read.py": 1, @@ -5376,7 +5376,7 @@ "align-cache.2.11.0": 10, "align-cache.3": 2, "align-cache.3.0.0": 2, - "align-columns": 228, + "align-columns": 229, "align-ema.smk": 1, "align-families.py": 1, "align-info": 23, @@ -5506,7 +5506,7 @@ "amdgpu-arch": 1, "ame": 13, "amgr": 1, - "amino-acid-composition": 316, + "amino-acid-composition": 317, "aminoextract": 2, "amk_ccc": 2, "amk_fft2": 2, @@ -5619,7 +5619,7 @@ "annotate.py": 39, "annotate.pyc": 1, "annotateBAM.py": 1, - "annotateBed": 280, + "annotateBed": 281, "annotateBed_2way.pl": 1, "annotateInteractions.pl": 5, "annotatePeaks.pl": 5, @@ -5946,12 +5946,12 @@ "arcasHLA": 1, "archer": 1, "architeuthis": 1, - "archive-ncbinlp": 39, - "archive-nihocc": 39, - "archive-nmcds": 39, - "archive-pmc": 39, - "archive-pubmed": 315, - "archive-taxonomy": 39, + "archive-ncbinlp": 40, + "archive-nihocc": 40, + "archive-nmcds": 40, + "archive-pmc": 40, + "archive-pubmed": 316, + "archive-taxonomy": 40, "archive_directory.py": 2, "archosv": 2, "archspec": 11, @@ -5962,7 +5962,7 @@ "argnorm": 1, "argparse2tool": 1, "argparse2tool_check_path": 1, - "args2slice": 39, + "args2slice": 40, "args_oap": 1, "aria2c": 28, "ariba": 3, @@ -6013,7 +6013,7 @@ "ase-gui": 4, "ase-info": 4, "ase-run": 4, - "aserver": 465, + "aserver": 466, "asession": 3, "asgal": 1, "asgal_BitVector.py": 1, @@ -6039,8 +6039,8 @@ "asn2ff": 1, "asn2gb": 2, "asn2idx": 1, - "asn2ref": 39, - "asn2xml": 229, + "asn2ref": 40, + "asn2xml": 230, "asndhuff": 1, "asntool": 1, "asp-cp": 87, @@ -6146,7 +6146,7 @@ "autometa-taxonomy-majority-vote": 2, "autometa-unclustered-recruitment": 2, "autometa-update-databases": 2, - "autopoint": 5323, + "autopoint": 5324, "autoreconf.bak": 10, "autoscan.bak": 10, "autoupdate.bak": 10, @@ -6332,9 +6332,9 @@ "bamCoverage": 12, "bamFlags": 3, "bamPEFragmentSize": 12, - "bamToBed": 280, + "bamToBed": 281, "bamToBw.pl": 3, - "bamToFastq": 280, + "bamToFastq": 281, "bamToGBrowse.pl": 92, "bamToPsl": 1, "bamToWig.py": 12, @@ -6663,7 +6663,7 @@ "beav_db": 1, "bed-to-bigBed": 1, "bed12-to-gtf": 3, - "bed12ToBed6": 280, + "bed12ToBed6": 281, "bed2DtoUCSCbed.pl": 5, "bed2associated_genes.py": 1, "bed2bedGraph.pl": 1, @@ -6682,10 +6682,10 @@ "bedGraphPack": 1, "bedGraphToBigWig": 19, "bedSort": 2, - "bedToBam": 280, + "bedToBam": 281, "bedToBigBed": 18, "bedToGenePred": 6, - "bedToIgv": 280, + "bedToIgv": 281, "bed_bigwig_profile.py": 60, "bed_build_windows.py": 60, "bed_complement.py": 60, @@ -6720,12 +6720,12 @@ "bedops-typical": 15, "bedoverlap": 1, "bedparse": 2, - "bedpeToBam": 280, + "bedpeToBam": 281, "bedpeToBam.py": 1, "bedpeToBed12.py": 1, "bedtk": 2, "bedtobigbed": 1, - "bedtools": 280, + "bedtools": 281, "bedutils": 1, "bedx-to-bedy": 3, "beeline": 6, @@ -6751,7 +6751,7 @@ "beta_diversity.py": 4, "beta_diversity_through_plots.py": 1, "beta_significance.py": 1, - "between-two-genes": 316, + "between-two-genes": 317, "bf.sh": 1, "bfc": 1, "bfconvert": 1, @@ -6969,7 +6969,7 @@ "blast_check_pair.pl": 1, "blast_filter.pl": 1, "blast_format_unit_test": 5, - "blast_formatter": 350, + "blast_formatter": 351, "blast_names_mapping.tsv": 1, "blast_outfmt6_replace_trans_id_w_gene_symbol.pl": 1, "blast_report": 21, @@ -6984,12 +6984,12 @@ "blastbesties": 1, "blastcl3": 1, "blastclust": 38, - "blastdb_aliastool": 350, + "blastdb_aliastool": 351, "blastdb_convert": 21, "blastdb_format_unit_test": 5, "blastdb_path": 21, - "blastdbcheck": 350, - "blastdbcmd": 350, + "blastdbcheck": 351, + "blastdbcmd": 351, "blastdbcp": 55, "blastdiag_unit_test": 5, "blastengine_unit_test": 5, @@ -6998,13 +6998,13 @@ "blastfilter_unit_test": 5, "blasthits_unit_test": 5, "blastinput_unit_test": 5, - "blastn": 350, - "blastn_vdb": 63, + "blastn": 351, + "blastn_vdb": 64, "blastoptions_unit_test": 5, - "blastp": 350, + "blastp": 351, "blastpgp": 38, "blastsetup_unit_test": 5, - "blastx": 350, + "blastx": 351, "blastzWrapper": 1, "blat": 19, "blat2gbrowse.pl": 15, @@ -7030,8 +7030,8 @@ "blossom5": 1, "blossom_randGraph.py": 1, "blosum62.fas": 2, - "blst2gm": 39, - "blst2tkns": 228, + "blst2gm": 40, + "blst2tkns": 229, "bmaToLinks.pl": 1, "bmfilter": 4, "bmge": 1, @@ -7252,7 +7252,7 @@ "broad_utils.py": 1, "brockman_pipeline": 1, "brooklyn_plot": 1, - "brotli": 476, + "brotli": 478, "browse": 18, "bs_call": 2, "bs_seeker2-align.py": 1, @@ -7267,7 +7267,7 @@ "bseqc2": 4, "bseqc2mbiasplot.R": 4, "bsmap": 5, - "bsmp2info": 19, + "bsmp2info": 20, "bsp2sam.py": 1, "bsrate": 1, "bsseeker2bismark.pl": 1, @@ -7357,7 +7357,7 @@ "bundlelinks": 2, "bundler": 19, "bunwarpj": 4, - "bunzip2": 6827, + "bunzip2": 6832, "burden_test_vase": 1, "burst_linux_DB12": 1, "burst_linux_DB15": 1, @@ -7411,16 +7411,16 @@ "bxStats.py": 1, "bxcl_seqqc": 1, "bxtools": 1, - "bzcat": 6827, - "bzcmp": 6827, - "bzdiff": 6827, - "bzegrep": 6827, - "bzfgrep": 6827, - "bzgrep": 6827, - "bzip2": 6828, - "bzip2recover": 6827, - "bzless": 6827, - "bzmore": 6827, + "bzcat": 6832, + "bzcmp": 6832, + "bzdiff": 6832, + "bzegrep": 6832, + "bzfgrep": 6832, + "bzgrep": 6832, + "bzip2": 6833, + "bzip2recover": 6832, + "bzless": 6832, + "bzmore": 6832, "c++": 5, "c++filt": 8, "c-index-test": 8, @@ -7437,7 +7437,7 @@ "cPecanLibTests": 1, "cPecanModifyHmm": 1, "cPecanRealign": 1, - "c_rehash": 7973, + "c_rehash": 7978, "ca2ace.pl": 3, "ca2ctg": 2, "ca2mates": 2, @@ -7514,7 +7514,7 @@ "cagecatProcess.py": 1, "cagee": 1, "cai": 28, - "cairo-trace": 5182, + "cairo-trace": 5183, "cairosvg": 6, "cal": 13, "calD": 1, @@ -7619,7 +7619,7 @@ "capnpc-cython": 1, "capost2gnu": 1, "capri_eval": 1, - "captoinfo": 7904, + "captoinfo": 7909, "captus_assembly": 1, "caqc.pl": 3, "caqc_help.ini": 3, @@ -8065,10 +8065,10 @@ "circulocov": 1, "cirdna": 27, "cirtap": 1, - "cit2pmid": 39, + "cit2pmid": 40, "civicpy": 1, "cjk-gs-integrate": 1, - "cjpeg": 5863, + "cjpeg": 5866, "ckeygen": 1, "cksum": 86, "claMLST": 1, @@ -8175,11 +8175,11 @@ "cleanmap.awk": 1, "cleanme.pl": 1, "cleanpp.sh": 3, - "cleanup-blastdb-volumes.py": 277, + "cleanup-blastdb-volumes.py": 278, "cleanup-coverage.py": 2, "cleanup-stale-gcp-resources.py": 1, "cleanup.py": 1, - "clear": 7904, + "clear": 7909, "clearCNV": 1, "clearcut": 1, "cleric": 1, @@ -8229,7 +8229,7 @@ "closest-features-float128": 15, "closest-features-megarow": 15, "closest-features-typical": 15, - "closestBed": 280, + "closestBed": 281, "closest_residues": 1, "cloudgene.yaml": 1, "clove": 1, @@ -8276,7 +8276,7 @@ "cluster2bed.pl": 5, "cluster2bedgraph.pl": 5, "clusterAndSplitGenes.pl": 15, - "clusterBed": 280, + "clusterBed": 281, "clusterGenes": 1, "clusterHeatmap.R": 2, "clusterSnps": 2, @@ -8451,7 +8451,7 @@ "combine": 4, "combine-assembled-files.sh": 1, "combine-subexons": 1, - "combine-uid-lists": 39, + "combine-uid-lists": 40, "combineAndAnnotateReferences.pl": 1, "combineFile": 2, "combineFragandDBGraph_fastg.py": 1, @@ -8557,10 +8557,10 @@ "compileSpliceCands": 13, "compile_STARE_Linux.sh": 1, "compile_STARE_macOS.sh": 1, - "compile_et": 5922, + "compile_et": 5925, "compiled_table.py": 1, "compleasm": 1, - "complementBed": 280, + "complementBed": 281, "complete-ant-cmd.pl": 1, "complete_locus": 1, "completion.bash": 1, @@ -8747,7 +8747,7 @@ "convert2bed-float128": 15, "convert2bed-megarow": 15, "convert2bed-typical": 15, - "convert2blastmask": 350, + "convert2blastmask": 351, "convert2snns": 2, "convertCoordinates.pl": 5, "convertFastaQualToFastQ.rb": 1, @@ -8871,7 +8871,7 @@ "core_diversity_analyses.py": 1, "core_methods.py": 1, "core_overlap_plot.py": 1, - "corelist": 1746, + "corelist": 1747, "corepack": 12, "coreprocess.pl": 3, "coresnpfilter": 1, @@ -8955,7 +8955,7 @@ "coverage.py": 1, "coverage2cytosine": 2, "coverage3": 2, - "coverageBed": 280, + "coverageBed": 281, "coverage_estimator.py": 1, "coverage_from_bam": 1, "coverage_from_fastx": 1, @@ -8979,7 +8979,7 @@ "cp2k_run": 1, "cp2k_shell.ssmp": 1, "cpack": 12, - "cpan": 1746, + "cpan": 1747, "cpancover": 6, "cpanm": 245, "cpat.py": 1, @@ -9180,7 +9180,7 @@ "csv2rdf": 34, "csv2tsv": 1, "csv2xlsx": 1, - "csv2xml": 228, + "csv2xml": 229, "csvExtractBorders": 1, "csvFrags2text": 1, "csv_to_tsv": 1, @@ -9220,7 +9220,7 @@ "cuffquant": 2, "cuppa": 1, "cuppa-chart": 1, - "cups-config": 218, + "cups-config": 219, "curare": 1, "curare_wizard": 1, "curate_chemical_data": 1, @@ -9228,8 +9228,8 @@ "curate_spatial_data": 1, "curate_universe": 1, "curesim": 2, - "curl": 5152, - "curl-config": 6024, + "curl": 5153, + "curl-config": 6026, "curlywhirly": 1, "curve_keygen": 73, "cusp": 27, @@ -9385,7 +9385,7 @@ "datasets": 3, "datasets-cli": 5, "datashader": 3, - "datatool": 350, + "datatool": 351, "datavzrd": 2, "date": 86, "datma.py": 1, @@ -9634,7 +9634,7 @@ "deltaBS.pl": 1, "delta_filter_wrapper.py": 5, "delta_unit_test": 5, - "deltablast": 350, + "deltablast": 351, "deltapd": 1, "demes": 5, "demesdraw": 1, @@ -9686,7 +9686,7 @@ "depth_calc.py": 1, "depth_estim_from_vcf.sh": 1, "depythontex": 1, - "derb": 5932, + "derb": 5933, "derep_stuff.py": 2, "deripcal": 1, "derna": 1, @@ -9775,7 +9775,7 @@ "diff_iso_usage": 1, "diff_motif": 1, "diffacto": 1, - "difference-uid-lists": 39, + "difference-uid-lists": 40, "difference_from_first_TSS_script_mordor.r": 1, "difference_from_first_TSS_script_mordor_chrom_wide.r": 1, "differentialBindingAffinity_multipleSNPs": 1, @@ -9853,7 +9853,7 @@ "dirmngr-client": 2, "dirname": 86, "dirseq": 2, - "disambiguate-nucleotides": 228, + "disambiguate-nucleotides": 229, "disco": 18, "disco.cfg": 1, "disco_2.cfg": 1, @@ -9894,7 +9894,7 @@ "django-admin": 4, "django-admin.py": 3, "django-admin.pyc": 1, - "djpeg": 5863, + "djpeg": 5866, "dkfzbiasfilter.py": 1, "dkfzbiasfilter_summarize.py": 1, "dlcoal_to_dlcpar": 1, @@ -10007,15 +10007,15 @@ "download-db.sh": 9, "download-dfam.py": 1, "download-entities.pl": 2, - "download-ncbi-data": 301, + "download-ncbi-data": 302, "download-ncbi-genomes": 1, - "download-ncbi-software": 228, + "download-ncbi-software": 229, "download-ncbi-taxa.sh": 1, "download-ncbi-taxmaps": 1, "download-ncbi-taxonomy": 1, - "download-pmc": 39, - "download-pubmed": 315, - "download-sequence": 315, + "download-pmc": 40, + "download-pubmed": 316, + "download-sequence": 316, "download-spatypes.sh": 1, "download-srr-files": 3, "download-taxonomy.sh": 1, @@ -10117,7 +10117,7 @@ "drtext": 27, "drttest": 1, "drugbank": 1, - "ds2pme": 39, + "ds2pme": 40, "dsCompareCurves": 1, "dsComputeBEDDensity": 1, "dsComputeGCCoverage": 1, @@ -10255,7 +10255,7 @@ "dupre": 1, "dupsifter": 1, "dust": 13, - "dustmasker": 350, + "dustmasker": 351, "dv_call_variants.py": 1, "dv_make_examples.py": 1, "dv_postprocess_variants.py": 1, @@ -10344,7 +10344,7 @@ "ecodbtaxstat": 1, "ecofind": 1, "ecogrep": 1, - "ecommon.sh": 228, + "ecommon.sh": 229, "econtact": 88, "ecotag": 1, "ecotaxspecificity": 1, @@ -10383,14 +10383,15 @@ "edonr256-hash": 10, "edonr512-hash": 10, "eel": 1, - "efetch": 316, + "efetch": 317, "effectivet3": 1, - "efilter": 316, + "efilter": 317, "efishent": 1, "efn": 1, "efn2": 6, "efn2-smp": 5, "efpa": 2, + "ega-cryptor": 1, "ega2": 1, "eggnog_to_sqlite3.py": 2, "egrep": 24, @@ -10401,7 +10402,7 @@ "eigenstrat_database_tools": 1, "eigenstrat_rename_snps": 1, "eigenstrat_snp_coverage": 1, - "einfo": 316, + "einfo": 317, "einsi": 113, "einverted": 27, "eject": 13, @@ -10431,7 +10432,7 @@ "elfedit": 8, "elgato_report.py": 1, "eliminateBadSuperReadsUsingList": 1, - "elink": 316, + "elink": 317, "elm2meme": 13, "elprep": 1, "elsize": 7, @@ -10468,8 +10469,8 @@ "enano": 1, "enasearch": 1, "enc": 1, - "enc2xs": 1746, - "encguess": 1746, + "enc2xs": 1747, + "encguess": 1747, "encode2var": 1, "encode_dir": 1, "encode_exclude_loci": 1, @@ -10518,7 +10519,7 @@ "environment.yml": 1, "envpath": 3, "envset.cmd": 1, - "envsubst": 5323, + "envsubst": 5324, "eoulsan.sh": 1, "epa-ng": 4, "epestfind": 27, @@ -10534,7 +10535,7 @@ "epimuller-define": 1, "epimuller-draw": 1, "epimuller-parse": 1, - "epost": 316, + "epost": 317, "eprimer3": 27, "eprimer32": 27, "eproxy": 88, @@ -10570,11 +10571,11 @@ "errorEstimate": 6, "error_corrected2frg": 1, "ervdetective": 1, - "esample": 301, + "esample": 302, "esbuild": 1, "esd2esi": 12, "esdcompat": 12, - "esearch": 316, + "esearch": 317, "esh": 1, "esimsa": 1, "eskrim": 1, @@ -10636,7 +10637,7 @@ "estscan": 1, "estwise": 3, "estwisedb": 3, - "esummary": 316, + "esummary": 317, "esvee": 1, "etandem": 27, "ete": 2, @@ -10714,7 +10715,7 @@ "excise_precursors.pl": 1, "excise_precursors_iterative_final.pl": 1, "excl_seqs": 2, - "exclude-uid-lists": 301, + "exclude-uid-lists": 302, "exclude_N": 1, "exclude_loci": 1, "exclude_loci_backup": 1, @@ -10740,8 +10741,8 @@ "expam": 1, "expam_limit": 1, "expand": 86, - "expand-current": 301, - "expandCols": 280, + "expand-current": 302, + "expandCols": 281, "expand_fastq": 1, "expand_links.pl": 7, "expand_refseq_isoforms.pl": 1, @@ -10925,7 +10926,7 @@ "ezez4makefile_v4.pl": 1, "ezez4qsub_vx1.pl": 1, "ezez_vx1.pl": 1, - "f2py": 2177, + "f2py": 2180, "f2py2": 136, "f2py2.7": 136, "f2py3": 1601, @@ -11090,7 +11091,7 @@ "fasta2tab.pl": 5, "fasta2upper": 1, "fasta36": 7, - "fastaFromBed": 280, + "fastaFromBed": 281, "fastaToCA": 3, "fastaToRead": 1, "fasta_base_content.py": 2, @@ -11390,19 +11391,19 @@ "fasxl": 2, "fathom": 2, "favites_lite.py": 1, - "fax2ps": 5334, - "fax2tiff": 5334, + "fax2ps": 5337, + "fax2tiff": 5337, "fba": 1, "fc": 1, - "fc-cache": 5386, - "fc-cat": 5386, - "fc-conflist": 4903, - "fc-list": 5386, - "fc-match": 5386, - "fc-pattern": 5386, - "fc-query": 5386, - "fc-scan": 5386, - "fc-validate": 5386, + "fc-cache": 5387, + "fc-cat": 5387, + "fc-conflist": 4904, + "fc-list": 5387, + "fc-match": 5387, + "fc-pattern": 5387, + "fc-query": 5387, + "fc-scan": 5387, + "fc-validate": 5387, "fc_actg_coordinate": 1, "fc_calc_cutoff": 1, "fc_consensus": 1, @@ -11483,12 +11484,12 @@ "fermi2.pl": 2, "fetch": 4, "fetch-extras": 73, - "fetch-local": 39, - "fetch-nmcds": 39, - "fetch-pmc": 39, - "fetch-pubmed": 315, + "fetch-local": 40, + "fetch-nmcds": 40, + "fetch-pmc": 40, + "fetch-pubmed": 316, "fetch-tax.pl": 1, - "fetch-taxonomy": 39, + "fetch-taxonomy": 40, "fetchChromSizes": 5, "fetchEnaLibraryFastqs.sh": 1, "fetchFastq.sh": 1, @@ -11568,18 +11569,18 @@ "filter-alignments.py": 1, "filter-bam": 2, "filter-bam-by-ids": 3, - "filter-columns": 216, - "filter-genbank": 39, + "filter-columns": 217, + "filter-genbank": 40, "filter-gff": 1, "filter-nonunique-peptide-matches": 2, "filter-positions.pl": 1, "filter-ppx.pl": 15, - "filter-record": 39, + "filter-record": 40, "filter-sort": 1, "filter-stage-1.prl": 5, "filter-stage-2.prl": 5, "filter-stats.pl": 1, - "filter-stop-words": 316, + "filter-stop-words": 317, "filter-stoptags.py": 7, "filter-sync-by-gtf.pl": 1, "filter-table": 12, @@ -11759,7 +11760,7 @@ "find-all-symbols": 2, "find-compounds.pl": 2, "find-duplicate-reads": 2, - "find-in-gene": 228, + "find-in-gene": 229, "find-knots.py": 7, "find-mango-assembly.sh": 1, "find-mango-home": 1, @@ -11913,7 +11914,7 @@ "flaimapper": 1, "flair": 1, "flake8": 5, - "flankBed": 280, + "flankBed": 281, "flanker": 1, "flapjack": 1, "flash": 16, @@ -11983,7 +11984,7 @@ "font-awesome-to-png": 2, "font2c": 3, "fontinst": 1, - "fonttools": 450, + "fonttools": 452, "fop": 1, "forceOneClusterPerPairMem.py": 1, "forest.py": 1, @@ -12075,7 +12076,7 @@ "freec": 1, "freec2bed.pl": 1, "freec2circos.pl": 1, - "freetype-config": 5926, + "freetype-config": 5929, "freeze_graph": 25, "freq2group.pl": 5, "frequency.py": 1, @@ -12110,7 +12111,7 @@ "from_unionbed_to_ratio_per_window_CC0": 1, "fs": 1, "fsa": 1, - "fsa2xml": 19, + "fsa2xml": 20, "fsc": 1, "fsc.bat": 1, "fseq": 1, @@ -12225,8 +12226,8 @@ "funr": 1, "funzip": 25, "fuse": 1, - "fuse-ranges": 228, - "fuse-segments": 216, + "fuse-ranges": 229, + "fuse-segments": 217, "fuse.sh": 31, "fusion-bloom": 1, "fusion-bloom.makefile": 1, @@ -12511,10 +12512,10 @@ "gb2fasta": 1, "gbSmallDNA2gff.pl": 15, "gbase": 2, - "gbf2fsa": 39, - "gbf2info": 19, - "gbf2ref": 39, - "gbf2xml": 315, + "gbf2fsa": 40, + "gbf2info": 20, + "gbf2ref": 40, + "gbf2xml": 316, "gbf2xml.bak": 1, "gbfalncut": 2, "gbfcut": 2, @@ -12689,20 +12690,20 @@ "genbank_to": 1, "genblastG": 1, "genbox": 1, - "genbrk": 5932, - "gencfu": 5932, + "genbrk": 5933, + "gencfu": 5933, "genclust": 1, - "gencnval": 5932, + "gencnval": 5933, "gencode_extract_relevant_gtf_exons.pl": 1, "gencode_singleton_unit_test": 5, "genconf": 1, "gencore": 1, "gencove": 1, "gendb": 13, - "gendict": 5932, + "gendict": 5933, "gendist": 10, "gene2protein.db3": 2, - "gene2range": 216, + "gene2range": 217, "gene2xml": 1, "geneAssociationZscore.py": 1, "geneBody_coverage.py": 3, @@ -12827,7 +12828,7 @@ "genome-complexity-fast": 2, "genome-to-blast-db": 1, "genome2cg": 1, - "genomeCoverageBed": 280, + "genomeCoverageBed": 281, "genomeCoverageBed.pl": 92, "genomeOntology": 5, "genome_LenFilter_stats.pl": 3, @@ -12867,7 +12868,7 @@ "genotyphi.py": 1, "genpcz": 2, "genpept2gsi.pl": 2, - "genrb": 5932, + "genrb": 5933, "genreflex": 3, "genremdinputs.py": 7, "genrestr": 4, @@ -12953,7 +12954,7 @@ "getOntology.R": 1, "getOntology.py": 1, "getOrthologList": 4, - "getOverlap": 280, + "getOverlap": 281, "getPartOfPromoter.pl": 5, "getPatch": 2, "getPeakTags": 5, @@ -13072,7 +13073,7 @@ "get_sequence_type": 1, "get_sequences_for_meme.py": 1, "get_simple_cycs.py": 1, - "get_species_taxids.sh": 315, + "get_species_taxids.sh": 316, "get_species_taxids.sh.bak": 300, "get_standard_headers": 1, "get_stats_summary.pl": 1, @@ -13146,9 +13147,9 @@ "getscu": 1, "getsize": 13, "getsnvfreq_by_interval": 1, - "gettext": 5323, - "gettext.sh": 5323, - "gettextize": 5323, + "gettext": 5324, + "gettext.sh": 5324, + "gettextize": 5324, "getu0.X86_64.LINUX": 1, "getu0.X86_64.SUNOS": 1, "getuniqgenomealign": 1, @@ -13264,14 +13265,14 @@ "gie": 44, "gif2h5": 575, "gif2hdf": 129, - "gif2rgb": 778, + "gif2rgb": 779, "gif2tiff": 189, "gif2webp": 357, - "gifbuild": 778, - "gifclrmp": 778, + "gifbuild": 779, + "gifclrmp": 779, "gifecho": 39, "giffilter": 25, - "giffix": 778, + "giffix": 779, "gifinto": 39, "gifmaker.py": 20, "gifrop": 1, @@ -13282,9 +13283,9 @@ "gifrop_pannotate.R": 1, "gifrop_plots.R": 1, "gifsponge": 25, - "giftext": 778, + "giftext": 779, "giftogd2": 243, - "giftool": 778, + "giftool": 779, "gigrnd.py": 1, "gil2bin": 1, "gimbleprep": 1, @@ -13340,8 +13341,8 @@ "glpsol": 252, "glsearch36": 7, "gm": 2, - "gm2ranges": 39, - "gm2segs": 39, + "gm2ranges": 40, + "gm2segs": 40, "gmap": 14, "gmap.nosimd": 9, "gmap.sse42": 12, @@ -13634,7 +13635,7 @@ "groopm": 1, "groot": 2, "groovy_script": 4, - "groupBy": 280, + "groupBy": 281, "groupSequences.pl": 5, "group_ORF_sequences.py": 1, "group_bp_reads.pl": 1, @@ -13678,7 +13679,7 @@ "gsnapl.sse42": 12, "gsnd": 106, "gsort": 5, - "gss-client": 5922, + "gss-client": 5925, "gss-server": 2, "gst-completion-helper": 1, "gst-device-monitor-1.0": 242, @@ -13903,8 +13904,8 @@ "h264dec": 12, "h264enc": 12, "h2load": 3929, - "h2ph": 1746, - "h2xs": 1746, + "h2ph": 1747, + "h2xs": 1747, "h4_ncdump": 129, "h4_ncgen": 129, "h4cc": 129, @@ -14083,11 +14084,11 @@ "haystack_pipeline": 1, "haystack_run_test": 1, "haystack_tf_activity_plane": 1, - "hb-info": 320, - "hb-ot-shape-closure": 5121, - "hb-shape": 5121, - "hb-subset": 4685, - "hb-view": 5078, + "hb-info": 321, + "hb-ot-shape-closure": 5122, + "hb-shape": 5122, + "hb-subset": 4686, + "hb-view": 5079, "hbvblast.sh": 1, "hca-matrix-downloader": 1, "hca-mtx-to-10x": 1, @@ -14143,7 +14144,7 @@ "hg2hg_net": 1, "hgGcPercent": 3, "hgvs-shell": 1, - "hgvs2spdi": 228, + "hgvs2spdi": 229, "hhalign": 4, "hhalign_omp": 4, "hhblits": 4, @@ -14548,9 +14549,9 @@ "ichar": 1, "icon-font-to-png": 2, "iconv": 5462, - "icu-config": 5932, - "icuexportdata": 2144, - "icuinfo": 5932, + "icu-config": 5933, + "icuexportdata": 2145, + "icuinfo": 5933, "id": 86, "id_conserved_regions.pl": 1, "idba": 10, @@ -14584,11 +14585,11 @@ "idfetch": 1, "idiag-socket-details": 14, "idle": 334, - "idle3": 3504, + "idle3": 3509, "idle3.10": 836, "idle3.11": 283, - "idle3.12": 295, - "idle3.13": 15, + "idle3.12": 297, + "idle3.13": 18, "idle3.4": 6, "idle3.5": 103, "idle3.6": 344, @@ -14598,7 +14599,7 @@ "idlj": 117, "idmatrix.sh": 31, "idn": 31, - "idn2": 296, + "idn2": 297, "idpAssemble": 2, "idpQonvert": 2, "idpQuery": 2, @@ -14809,12 +14810,12 @@ "infoalign": 27, "infoassembly": 27, "infobase": 27, - "infocmp": 7904, + "infocmp": 7909, "inforesidue": 27, "informant.py": 1, "infoseq": 27, - "infotocap": 7904, - "ini2xml": 39, + "infotocap": 7909, + "ini2xml": 40, "init_Trinotate_sqlite_db.pl": 1, "init_db.sh": 1, "initdb": 48, @@ -14875,7 +14876,7 @@ "installpackages.R": 1, "installvst": 16, "instance_events": 29, - "instmodsh": 1746, + "instmodsh": 1747, "int_seqs_to_char_strings.py": 60, "intake": 1, "intake-server": 1, @@ -14910,8 +14911,8 @@ "interprophet.rb": 1, "interproscan.sh": 1, "intersect": 5, - "intersect-uid-lists": 314, - "intersectBed": 280, + "intersect-uid-lists": 315, + "intersectBed": 281, "intersectFiles.py": 2, "intersectGenomicSets.py": 1, "intersect_assembly_errors": 1, @@ -14978,8 +14979,8 @@ "ipopt": 1, "ipopt_sens": 1, "ipostproc": 1, - "ippeveprinter": 218, - "ipptool": 218, + "ippeveprinter": 219, + "ipptool": 219, "ipr_update_gff": 1, "iprocdic": 1, "iprscan2gff3": 1, @@ -15147,9 +15148,9 @@ "jalview": 1, "jamo-normalize": 1, "jannovar": 1, - "jaotc": 311, - "jar": 555, - "jarsigner": 555, + "jaotc": 312, + "jar": 556, + "jarsigner": 556, "jasmine": 3, "jasmine.jar": 1, "jasmine_igv.jar": 1, @@ -15160,22 +15161,22 @@ "jaspscan": 27, "jass": 1, "jass_preprocessing": 1, - "java": 555, + "java": 556, "java-rmi.cgi": 112, - "javac": 555, - "javadoc": 555, + "javac": 556, + "javadoc": 556, "javah": 112, - "javap": 555, + "javap": 556, "javareconf": 1, "jbig2dec": 1, "jbrowse": 1, "jcast": 1, "jclusterfunk": 2, - "jcmd": 555, - "jconsole": 555, - "jdb": 555, - "jdeprscan": 446, - "jdeps": 554, + "jcmd": 556, + "jconsole": 556, + "jdb": 556, + "jdeprscan": 447, + "jdeps": 555, "je": 2, "jellyfish": 48, "jemalloc-config": 14, @@ -15183,22 +15184,22 @@ "jembossctl": 27, "jeprof": 14, "jf_aligner": 1, - "jfr": 390, + "jfr": 391, "jgiDwnld": 2, "jgi_gc": 1, "jgi_summarize_bam_contig_depths": 6, "jgoslin": 1, "jhat": 112, - "jhsdb": 446, - "jimage": 446, - "jinfo": 555, + "jhsdb": 447, + "jimage": 447, + "jinfo": 556, "jiv": 6, "jiwer": 1, - "jjs": 421, - "jlink": 446, + "jjs": 422, + "jlink": 447, "jlpm": 4, - "jmap": 555, - "jmod": 446, + "jmap": 556, + "jmod": 447, "jmztab-m": 1, "job-shop": 1, "jobTreeKill": 2, @@ -15208,7 +15209,7 @@ "jobTreeStatus": 2, "jobTreeTest_Dependencies.py": 1, "join": 86, - "join-into-groups-of": 316, + "join-into-groups-of": 317, "join-long-chromosomes": 3, "join.pl": 1, "join.pl.bak": 1, @@ -15232,33 +15233,33 @@ "jp.py": 107, "jpackage": 135, "jpeg2hdf": 129, - "jpegtran": 5863, - "jpgicc": 1065, + "jpegtran": 5866, + "jpgicc": 1068, "jpredapi": 1, - "jps": 555, + "jps": 556, "jq": 311, "jronn": 1, - "jrunscript": 555, + "jrunscript": 556, "js-beautify": 1, "jsadebugd": 112, "jscan": 1, "jsearch": 1, - "jshell": 446, + "jshell": 447, "json2gff": 1, - "json2xml": 228, + "json2xml": 229, "json_collect_data_source.py": 1, - "json_pp": 1746, - "json_xs": 374, + "json_pp": 1747, + "json_xs": 375, "jsondiff": 9, - "jsonl2xml": 39, + "jsonl2xml": 40, "jsonpatch": 9, "jsonpath.py": 1, "jsonpath_ng": 1, "jsonpointer": 14, "jsonschema": 230, - "jstack": 555, - "jstat": 555, - "jstatd": 555, + "jstack": 556, + "jstat": 556, + "jstatd": 556, "juicer": 1, "juicer_shortform2pairs.pl": 22, "julia": 6, @@ -15306,17 +15307,17 @@ "jupyter-troubleshoot": 158, "jupyter-trust": 151, "just-first-key": 20, - "just-top-hits": 19, + "just-top-hits": 20, "just_blast_test.pl": 1, "jwebserver": 51, - "k5srvutil": 5922, + "k5srvutil": 5925, "k8": 170, "k8-Linux": 1, "k_means": 1, "k_means_coefficient": 1, "k_neighbors": 1, "k_neighbors_coefficient": 1, - "kadmin": 5922, + "kadmin": 5925, "kadmin.local": 2, "kadmind": 2, "kaiju": 4, @@ -15411,7 +15412,7 @@ "kdbmeta.3.0.3": 1, "kdbmeta.3.1.0": 1, "kdbmeta.3.1.1": 1, - "kdestroy": 5922, + "kdestroy": 5925, "kea-config": 38, "keep-header": 1, "keep-ribo-periodic": 1, @@ -15423,10 +15424,10 @@ "keggpathway_map.py": 1, "kestrel": 1, "keyFreq": 1, - "keyctl": 2551, + "keyctl": 2554, "keygen": 1, "keyring": 10, - "keytool": 555, + "keytool": 556, "kget": 18, "kget.2": 18, "kget.2.10.0": 1, @@ -15454,7 +15455,7 @@ "kinSimRiboswitch": 1, "king": 1, "kingfisher": 1, - "kinit": 5922, + "kinit": 5925, "kinship-read": 1, "kinshipDecompose": 1, "kinwalker": 56, @@ -15467,7 +15468,7 @@ "kitsch": 10, "kitsune": 1, "kleborate": 1, - "klist": 5922, + "klist": 5925, "kma": 19, "kma_index": 19, "kma_shm": 19, @@ -15557,7 +15558,7 @@ "kp1mer_to_kmer.py": 1, "kp2np.py": 1, "kpal": 2, - "kpasswd": 5922, + "kpasswd": 5925, "kpileup.py": 1, "kprop": 2, "kpropd": 2, @@ -15604,7 +15605,7 @@ "krakenuniq-report": 1, "krakenuniq-translate": 1, "krakmeopen": 1, - "krb5-config": 5922, + "krb5-config": 5925, "krb5-send-pr": 2, "krb5kdc": 2, "kreport2krona.py": 3, @@ -15620,9 +15621,9 @@ "kseq_split": 1, "ksnp": 1, "kssd": 1, - "ksu": 5922, + "ksu": 5925, "ksw": 1, - "kswitch": 5922, + "kswitch": 5925, "ktClassifyBLAST": 17, "ktClassifyHits": 13, "ktGetContigMagnitudes": 17, @@ -15653,12 +15654,12 @@ "ktserver": 2, "kttimedmgr": 2, "kttimedtest": 2, - "ktutil": 5922, + "ktutil": 5925, "ktutilmgr": 2, "ktutilserv": 2, "ktutiltest": 2, "kubectl": 1, - "kvno": 5922, + "kvno": 5925, "kwip": 2, "kwip-stats": 2, "l4p-tmpl": 32, @@ -15794,7 +15795,7 @@ "lefse_plot_features.py": 1, "lefse_plot_res.py": 1, "lefse_run.py": 1, - "legacy_blast.pl": 350, + "legacy_blast.pl": 351, "legsta": 1, "lemon-0.x-to-1.x.sh": 4, "lemur": 1, @@ -15829,8 +15830,8 @@ "libclair3.cpython-36m-x86_64-linux-gnu.so": 1, "libclair3.o": 1, "libclair3.so": 1, - "libdeflate-gunzip": 4240, - "libdeflate-gzip": 4240, + "libdeflate-gunzip": 4243, + "libdeflate-gzip": 4243, "libdrawgram.so": 5, "libdrawtree.so": 5, "libfile.pl": 1, @@ -15839,9 +15840,9 @@ "libiomp5md.dll": 1, "liblist.pl": 1, "liblist.pl.bak": 1, - "libnetcfg": 1746, - "libpng-config": 5982, - "libpng16-config": 5982, + "libnetcfg": 1747, + "libpng-config": 5985, + "libpng16-config": 5985, "libpypy-c.so": 1, "libpypy-c.so.debug": 1, "libpypy3-c.so.debug": 3, @@ -15901,10 +15902,10 @@ "link_ssv.py": 1, "linkage2allegro": 1, "linkhsp_unit_test": 5, - "linkicc": 1065, + "linkicc": 1068, "linknets": 2, "links2sql.pl": 7, - "linksBed": 280, + "linksBed": 281, "linsi": 113, "linux32": 13, "linux64": 13, @@ -16224,17 +16225,17 @@ "lz4_decompress": 2, "lz4c": 3550, "lz4cat": 3550, - "lzcat": 7729, - "lzcmp": 7729, - "lzdiff": 7729, - "lzegrep": 7729, - "lzfgrep": 7729, - "lzgrep": 7729, - "lzless": 7729, - "lzma": 7729, - "lzmadec": 7729, - "lzmainfo": 7729, - "lzmore": 7729, + "lzcat": 7734, + "lzcmp": 7734, + "lzdiff": 7734, + "lzegrep": 7734, + "lzfgrep": 7734, + "lzgrep": 7734, + "lzless": 7734, + "lzma": 7734, + "lzmadec": 7734, + "lzmainfo": 7734, + "lzmore": 7734, "lzop_build_offset_table.py": 60, "m-party": 1, "m-tx": 1, @@ -16547,12 +16548,12 @@ "makeagp2.awk": 1, "makeagp_full.awk": 1, "makeagp_full2.awk": 1, - "makeblastdb": 352, + "makeblastdb": 353, "makecert": 16, "makechimeras.sh": 31, "makeclusterdb": 5, "makecontaminatedgenomes.sh": 31, - "makeconv": 5932, + "makeconv": 5933, "makedtx": 1, "makefasta.awk": 1, "makegeo": 39, @@ -16561,13 +16562,13 @@ "makehmmerdb": 189, "makeidx.pl": 4, "makemat": 38, - "makembindex": 350, + "makembindex": 351, "makenucseq": 27, "makepBAM_genome.sh": 1, "makepBAM_transcriptome.sh": 1, "makeplot.pl": 3, "makepolymers.sh": 31, - "makeprofiledb": 350, + "makeprofiledb": 351, "makeprotseq": 27, "maker": 1, "maker2chado": 1, @@ -16621,7 +16622,7 @@ "map2flank53": 1, "map2gtf": 3, "map2slim": 1, - "mapBed": 280, + "mapBed": 281, "mapCounter": 1, "mapDIA": 1, "mapDamage": 2, @@ -16715,7 +16716,7 @@ "mask-ali.pl": 1, "mask-consensus.py": 2, "maskAlignedReads.py": 1, - "maskFastaFromBed": 280, + "maskFastaFromBed": 281, "maskFile.pl": 11, "maskNregions.pl": 15, "mask_and_chain.smk": 1, @@ -17096,7 +17097,7 @@ "merge.py": 1, "merge2Dbed.pl": 5, "mergeBamWithSameSM.pl": 1, - "mergeBed": 280, + "mergeBed": 281, "mergeBreakpoints.py": 1, "mergeCharges.pl": 2, "mergeCounts": 3, @@ -17802,24 +17803,24 @@ "mseqtools": 1, "msformatter": 1, "msfragger": 2, - "msgattrib": 5323, - "msgcat": 5323, - "msgcmp": 5323, - "msgcomm": 5323, - "msgconv": 5323, - "msgen": 5323, - "msgexec": 5323, + "msgattrib": 5324, + "msgcat": 5324, + "msgcmp": 5324, + "msgcomm": 5324, + "msgconv": 5324, + "msgen": 5324, + "msgexec": 5324, "msgf2pin": 1, "msgf_plus": 3, - "msgfilter": 5323, - "msgfmt": 5323, + "msgfilter": 5324, + "msgfmt": 5324, "msgfplus_search.rb": 1, - "msggrep": 5323, - "msginit": 5323, - "msgmerge": 5323, + "msggrep": 5324, + "msginit": 5324, + "msgmerge": 5324, "msgserv": 1, - "msgunfmt": 5323, - "msguniq": 5323, + "msgunfmt": 5324, + "msguniq": 5324, "msi": 1, "msi_cluster2reads": 1, "msi_clustr2map.pl": 1, @@ -17900,10 +17901,10 @@ "multi.heatmap.py": 1, "multi.histogram.py": 1, "multi.scatter.py": 1, - "multiBamCov": 280, + "multiBamCov": 281, "multiBamSummary": 12, "multiBigwigSummary": 12, - "multiIntersectBed": 280, + "multiIntersectBed": 281, "multiSub": 1, "multi_length_hist.py": 1, "multi_parallel_pick_otus.py": 1, @@ -18045,6 +18046,7 @@ "mzml2isa": 2, "mzn-gecode": 2, "mzrt_match.py": 2, + "mzspeclib": 1, "n50": 1, "nLength.pl": 2, "nab": 6, @@ -18129,9 +18131,9 @@ "ncrf_to_bed": 2, "ncrf_to_bed.py": 2, "ncurses5-config": 565, - "ncurses6-config": 7197, + "ncurses6-config": 7202, "ncursesw5-config": 703, - "ncursesw6-config": 7198, + "ncursesw6-config": 7203, "ndfes": 1, "ndfes-AvgFESs.py": 1, "ndfes-CheckEquil.py": 1, @@ -18167,8 +18169,8 @@ "neokit": 2, "neoloop-caller": 1, "neotad-caller": 1, - "neptune": 2, - "neptune-conda": 1, + "neptune": 3, + "neptune-conda": 2, "nerpa.py": 1, "nerpa_init.py": 1, "net2communities.py": 1, @@ -18236,7 +18238,7 @@ "nf-test": 1, "nfe-umbrella-slice": 7, "ngd": 12, - "ngettext": 5323, + "ngettext": 5324, "ngg_barabasi_albert": 2, "ngg_barbell": 2, "ngg_complete": 2, @@ -18246,9 +18248,9 @@ "ngg_newman_watts_strogatz": 2, "ngg_path": 2, "ngg_ring_lattice": 2, - "nghttp": 4576, - "nghttpd": 4576, - "nghttpx": 4576, + "nghttp": 4578, + "nghttpd": 4578, + "nghttpx": 4578, "ngless": 2, "ngless-wrapped": 1, "nglview": 2, @@ -18283,7 +18285,7 @@ "ngsngs": 1, "ngsplotdb.py": 5, "ngsutils": 1, - "nhance.sh": 39, + "nhance.sh": 40, "nhmmer": 189, "nhmmscan": 189, "nib-conform": 3, @@ -18434,7 +18436,7 @@ "nproc": 86, "npth-config": 2, "npx": 16, - "nquire": 316, + "nquire": 317, "nquire.bak": 1, "nrForwardSplicedReads.pl": 1, "nr_ORFs_gff3.pl": 5, @@ -18477,7 +18479,7 @@ "ntsynt_run_pipeline.smk": 1, "ntsynt_synteny.py": 1, "ntthal": 1, - "nucBed": 280, + "nucBed": 281, "nuc_trans.py": 1, "nucamino": 1, "nucdiff": 1, @@ -18497,11 +18499,11 @@ "nullarbor.pl": 1, "nulltype_module.py": 1, "numCI": 4, - "numba": 167, + "numba": 168, "number-lines": 1, "numfmt": 86, "numlines": 1, - "numpy-config": 74, + "numpy-config": 76, "nunit-console": 10, "nunit-console2": 10, "nunit-console4": 10, @@ -18787,12 +18789,12 @@ "openslide-quickhash1sum": 2, "openslide-show-properties": 2, "openslide-write-png": 2, - "openssl": 7973, + "openssl": 7978, "opentargets_validator": 1, "operation.py": 1, - "opj_compress": 705, - "opj_decompress": 705, - "opj_dump": 705, + "opj_compress": 707, + "opj_decompress": 707, + "opj_dump": 707, "opl2ofm": 1, "opsin": 1, "opt": 6, @@ -18994,7 +18996,7 @@ "pacbio-loadxml.3": 2, "pacbio-loadxml.3.0.0": 2, "pacbio_post_process": 4, - "pack200": 422, + "pack200": 423, "package-stash-conflicts": 135, "package_output.py": 1, "packagemanager": 1, @@ -19018,8 +19020,8 @@ "painter.py": 20, "pair2tb": 1, "pairDiscordants.py": 1, - "pairToBed": 280, - "pairToPair": 280, + "pairToBed": 281, + "pairToPair": 281, "pair_sequences": 1, "pairalign": 2, "pairaln": 1, @@ -19034,7 +19036,7 @@ "pairtools": 3, "pairwise_comparison": 1, "pal2nal.pl": 9, - "pal2rgb": 5334, + "pal2rgb": 5337, "pal_finder": 1, "paladin": 2, "palindrome": 27, @@ -19340,11 +19342,11 @@ "pcoaPlot.py": 2, "pcor": 1, "pcre-config": 4952, - "pcre2-config": 3772, + "pcre2-config": 3773, "pcre2_jit_test": 3685, - "pcre2grep": 3772, + "pcre2grep": 3773, "pcre2posix_test": 113, - "pcre2test": 3772, + "pcre2test": 3773, "pcregrep": 4952, "pcretest": 4952, "pct2rgb": 1, @@ -19551,7 +19553,7 @@ "perf": 1, "perfect-square": 2, "perform_controls.pl": 1, - "perl": 1746, + "perl": 1747, "perl-doc": 2, "perl-reversion": 9, "perl5.22.0": 55, @@ -19559,12 +19561,12 @@ "perl5.26.2": 369, "perl5.30.3": 5, "perl5.32.0": 64, - "perl5.32.1": 1253, - "perlbug": 1746, - "perldoc": 1746, - "perlivp": 1746, + "perl5.32.1": 1254, + "perlbug": 1747, + "perldoc": 1747, + "perlivp": 1747, "perltex": 1, - "perlthanks": 1746, + "perlthanks": 1747, "permuteGPAT++": 32, "permuteSmooth": 32, "permute_structure.pl": 1, @@ -19722,7 +19724,7 @@ "phonopy-vasp-born": 1, "phonopy-vasp-efe": 1, "photo": 2, - "phrase-search": 314, + "phrase-search": 315, "phsolverserver": 3, "phy2nex": 1, "phykit": 1, @@ -19921,7 +19923,7 @@ "pickle_cat.py": 1, "pickorientation.awk": 1, "pickout": 1, - "piconv": 1746, + "piconv": 1747, "picopore": 1, "picopore-realtime": 1, "picopore-rename": 1, @@ -19960,10 +19962,10 @@ "pints_caller": 1, "pints_normalizer": 1, "pints_visualizer": 1, - "pip": 3838, + "pip": 3843, "pip2": 1, "pip2.7": 1, - "pip3": 2761, + "pip3": 2766, "pipdeptree": 1, "pipelign": 1, "pipeline.py": 3, @@ -20116,13 +20118,13 @@ "pkfix-helper": 1, "pkg-config": 78, "pkg-config.bin": 78, - "pkgdata": 5932, + "pkgdata": 5933, "pkginfo": 10, "pkill": 1, "pktogf": 1, "pktype": 1, "pl2bat.pl": 6, - "pl2pm": 1746, + "pl2pm": 1747, "plaScope.sh": 1, "plac_runner.py": 70, "place_orient1.smk": 1, @@ -20293,11 +20295,11 @@ "pm4ngs-rnaseq-demo": 1, "pm4ngs-server": 1, "pm_which": 2, - "pma2apa": 39, - "pma2pme": 39, + "pma2apa": 40, + "pma2pme": 40, "pmap": 1, - "pmc2bioc": 39, - "pmc2info": 39, + "pmc2bioc": 40, + "pmc2info": 40, "pmd": 1, "pmdtools": 1, "pmemd_mdrun": 1, @@ -20323,22 +20325,22 @@ "pmxmutate": 1, "pn2pdf": 1, "pneumo-typer": 1, - "png-fix-itxt": 5982, + "png-fix-itxt": 5985, "pngcp": 89, - "pngfix": 5982, + "pngfix": 5985, "pngtogd": 243, "pngtogd2": 243, "pnps-gen": 1, "poa": 24, "pocheck": 1, "poclcc": 3, - "pod2html": 1746, - "pod2man": 1746, - "pod2text": 1746, - "pod2usage": 1746, + "pod2html": 1747, + "pod2man": 1747, + "pod2text": 1747, + "pod2usage": 1747, "pod5": 1, "pod_cover": 12, - "podchecker": 1746, + "podchecker": 1747, "podselect": 438, "poetry": 6, "pointwise_datasets_concatenator.py": 1, @@ -20446,7 +20448,7 @@ "ppi2html": 2, "pplacer": 22, "ppltotf": 1, - "ppm2tiff": 5334, + "ppm2tiff": 5337, "pprodigal": 2, "pprof": 2, "pprof-symbolize": 1, @@ -20583,7 +20585,7 @@ "prinseq-graphs-noPCA.pl": 3, "prinseq-graphs.pl": 3, "prinseq-lite.pl": 3, - "print-columns": 228, + "print-columns": 229, "print.pl": 1, "printIcounts": 1, "printScaff": 2, @@ -20682,7 +20684,7 @@ "project.sh.orig": 1, "projectAndStrip": 4, "projectFeatures": 3, - "project_tree_builder": 350, + "project_tree_builder": 351, "projinfo": 43, "projsync": 40, "prokka": 24, @@ -20830,7 +20832,7 @@ "protxml_to_table.rb": 1, "prov-compare": 9, "prov-convert": 9, - "prove": 1746, + "prove": 1747, "provean": 1, "provean.sh": 1, "provis": 1, @@ -20876,10 +20878,10 @@ "psiCalculator.py": 1, "psiPerGene.py": 1, "psibl2seq_unit_test": 5, - "psiblast": 350, + "psiblast": 351, "psiblast_iteration_unit_test": 5, "psiblast_unit_test": 5, - "psicc": 1065, + "psicc": 1068, "psiclass": 1, "psiphi": 27, "psirc": 1, @@ -20937,9 +20939,9 @@ "pt2to3": 76, "ptGAUL.sh": 1, "ptangle": 1, - "ptar": 1746, - "ptardiff": 1746, - "ptargrep": 1746, + "ptar": 1747, + "ptardiff": 1747, + "ptargrep": 1747, "ptdump": 76, "ptest": 1, "ptex": 1, @@ -21119,12 +21121,12 @@ "pydemult": 1, "pydicom": 1, "pydna_repeatfinder": 1, - "pydoc": 3837, - "pydoc3": 3504, + "pydoc": 3842, + "pydoc3": 3509, "pydoc3.10": 836, "pydoc3.11": 283, - "pydoc3.12": 295, - "pydoc3.13": 15, + "pydoc3.12": 297, + "pydoc3.13": 18, "pydoc3.4": 6, "pydoc3.5": 103, "pydoc3.6": 344, @@ -21145,8 +21147,8 @@ "pyflyte-execute": 1, "pyflyte-fast-execute": 1, "pyflyte-map-execute": 1, - "pyftmerge": 450, - "pyftsubset": 450, + "pyftmerge": 452, + "pyftsubset": 452, "pygal_gen.py": 2, "pygcap": 1, "pygenetic_code": 1, @@ -21257,7 +21259,7 @@ "pytest": 151, "pytest-benchmark": 1, "pythia8-config": 1, - "python": 3838, + "python": 3843, "python-argcomplete-check-easy-install-script": 348, "python-argcomplete-tcsh": 191, "python-build": 2, @@ -21268,17 +21270,17 @@ "python2.5-config": 1, "python2.7": 333, "python2.7-config": 316, - "python3": 3505, - "python3-config": 3504, - "python3.1": 1429, + "python3": 3510, + "python3-config": 3509, + "python3.1": 1434, "python3.10": 836, "python3.10-config": 836, "python3.11": 283, "python3.11-config": 283, - "python3.12": 295, - "python3.12-config": 295, - "python3.13": 15, - "python3.13-config": 15, + "python3.12": 297, + "python3.12-config": 297, + "python3.13": 18, + "python3.13-config": 18, "python3.4": 6, "python3.4-config": 6, "python3.4m": 6, @@ -21335,7 +21337,7 @@ "qcli_make_script": 3, "qcollectiongenerator": 258, "qcollectiongenerator-qt4": 3, - "qconvex": 54, + "qconvex": 56, "qcp": 2, "qcreporter.py": 1, "qcs": 2, @@ -21350,7 +21352,7 @@ "qdbusviewer6": 3, "qdbusxml2cpp": 256, "qdbusxml2cpp-qt4": 3, - "qdelaunay": 54, + "qdelaunay": 56, "qdistancefieldgenerator": 142, "qdistancefieldgenerator6": 3, "qdoc": 230, @@ -21361,13 +21363,13 @@ "qfy.py": 1, "qgltf": 190, "qgrs": 1, - "qhalf": 54, + "qhalf": 56, "qhelpconverter": 116, "qhelpconverter-qt4": 3, "qhelpgenerator": 258, "qhelpgenerator-qt4": 3, "qhery": 1, - "qhull": 54, + "qhull": 56, "qiime2lefse.py": 1, "qiimeToMaaslin.py": 1, "qiskit-xyz2pdb": 1, @@ -21505,7 +21507,7 @@ "quorum_create_database": 4, "quorum_error_correct_reads": 4, "quota_Anchor": 1, - "quote-grouped-elements": 39, + "quote-grouped-elements": 40, "qv_to_bqv.py": 60, "qvality": 1, "qvalue": 13, @@ -21514,7 +21516,7 @@ "qvinaw": 1, "qvinaw_split": 1, "qvkgen": 142, - "qvoronoi": 54, + "qvoronoi": 56, "qwebengine_convert_dict": 141, "r-seurat-scripts-post-install-tests.bats": 2, "r-seurat-scripts-post-install-tests.sh": 2, @@ -21571,7 +21573,7 @@ "randRemoveBackground.pl": 5, "rand_sel_reads_from_bam": 1, "randfold": 3, - "randomBed": 280, + "randomBed": 281, "randomFQ": 1, "randomGeneSample": 4, "randomJunctionFilter": 1, @@ -21626,7 +21628,7 @@ "ratt": 2, "rav1e": 13, "raven": 4, - "raw2tiff": 5334, + "raw2tiff": 5337, "raw_n50": 10, "raw_n50.o": 10, "raw_vcf_parse.py": 1, @@ -21654,7 +21656,7 @@ "rbhtfinder": 1, "rblist": 2, "rbmoegrid": 2, - "rbox": 54, + "rbox": 56, "rbpbench": 1, "rbrms": 1, "rbs": 9, @@ -21676,8 +21678,8 @@ "rcexplain.3.1.0": 1, "rcexplain.3.1.1": 1, "rcf": 1, - "rchive": 315, - "rchive.Linux": 315, + "rchive": 316, + "rchive.Linux": 316, "rchive.go": 14, "rcl": 3, "rcl-dot-resmap.pl": 3, @@ -21695,7 +21697,7 @@ "rdfgraphisomorphism": 34, "rdfpipe": 34, "rdfs2dot": 34, - "rdjpgcom": 5863, + "rdjpgcom": 5866, "rdkit2fps": 1, "rdma_client": 25, "rdma_server": 25, @@ -21795,7 +21797,7 @@ "recgraph": 1, "reciprocal_blast_local": 1, "reciprocal_blast_local.py": 1, - "recode-sr-latin": 5323, + "recode-sr-latin": 5324, "recode_dir": 1, "recode_dir_legacy": 1, "recoder": 27, @@ -21844,7 +21846,7 @@ "ref-variation.3.0.3": 1, "ref-variation.3.1.0": 1, "ref-variation.3.1.1": 1, - "ref2pmid": 39, + "ref2pmid": 40, "refFinder": 1, "ref_map.pl": 1, "ref_seqs_from_bam": 1, @@ -21884,7 +21886,7 @@ "refresh-versioned": 1, "refseq-download": 1, "refseq-extract": 1, - "refseq-nm-cds": 39, + "refseq-nm-cds": 40, "refseq_masher": 1, "refseqget": 27, "refseqsplit.py": 2, @@ -22098,7 +22100,7 @@ "renumberRMFiles.pl": 4, "renumber_structure": 1, "reorder": 1, - "reorder-columns": 316, + "reorder-columns": 317, "reorder-fasta": 3, "reorder.smk": 1, "reorient_sequences_by_id.py": 2, @@ -22166,7 +22168,7 @@ "reseek": 1, "reseq": 1, "reseq-prepare-names.py": 1, - "reset": 7904, + "reset": 7909, "resetFragLibrary": 2, "reset_array.pl": 1, "reset_experiment.pl": 1, @@ -22312,9 +22314,9 @@ "rmats2sashimiplot": 1, "rmblastn": 17, "rmdir": 86, - "rmic": 422, - "rmid": 422, - "rmiregistry": 555, + "rmic": 423, + "rmid": 423, + "rmiregistry": 556, "rmkdepend": 1, "rmlst-api": 1, "rmsk2bed": 15, @@ -22437,9 +22439,9 @@ "rpkmforgenes.py": 1, "rppr": 17, "rps_unit_test": 5, - "rpsblast": 359, - "rpsbproc": 277, - "rpstblastn": 350, + "rpsblast": 360, + "rpsbproc": 278, + "rpstblastn": 351, "rpt_map": 1, "rqcfilter.sh": 31, "rqcfilter2.sh": 30, @@ -22541,7 +22543,7 @@ "run-htseq-workflow": 1, "run-mummer1": 45, "run-mummer3": 45, - "run-ncbi-converter": 315, + "run-ncbi-converter": 316, "run-ncbi-converter.bak": 1, "run-ntedit": 1, "run-polap-genes.R": 1, @@ -22757,7 +22759,7 @@ "run_vote.py": 1, "run_voteSpecies.py": 1, "run_vsclust_app.R": 1, - "run_with_lock": 340, + "run_with_lock": 341, "run_workflows.py": 1, "run_x_platform_fuzz_corpus": 38, "runabyss.py": 1, @@ -23161,7 +23163,7 @@ "scitokens-test-access": 1, "scitokens-verify": 1, "sclass.X86_64.LINUX": 1, - "sclient": 5922, + "sclient": 5925, "sclust_summary.sh": 1, "scluster": 3, "scmap-cli-post-install-tests.bats": 1, @@ -23180,7 +23182,7 @@ "scn-post-install-tests.sh": 1, "scn-predict.R": 1, "scn-train-model.R": 1, - "scn2xml": 39, + "scn2xml": 40, "scoary": 3, "scoary_GUI": 3, "scompare": 6, @@ -23303,7 +23305,7 @@ "segalign": 2, "segalign_repeat_masker": 2, "segemehl.x": 1, - "segmasker": 350, + "segmasker": 351, "segment-cnv": 1, "segment.py": 1, "segmentFst": 32, @@ -23467,7 +23469,7 @@ "seqyclean": 1, "serialize_hmm_models": 1, "serialize_kofam_models": 1, - "serialver": 555, + "serialver": 556, "seroba": 1, "serotypefinder": 1, "servertell": 27, @@ -23600,13 +23602,13 @@ "sharq.3": 2, "sharq.3.0.0": 2, "shasta": 1, - "shasum": 1746, + "shasum": 1747, "shed-tools": 2, "shell_utils.py": 1, "shiboken2": 2, "shiboken6": 2, "shiboken_tool.py": 4, - "shiftBed": 267, + "shiftBed": 268, "shigatyper": 1, "shigeifinder": 1, "shims.py": 1, @@ -23663,7 +23665,7 @@ "shuffle.sh": 31, "shuffle2.sh": 30, "shuffleBank": 2, - "shuffleBed": 280, + "shuffleBed": 281, "shuffleCodons.rb": 2, "shuffleCodonsAddMotifs.rb": 2, "shuffleSequences_fasta.pl": 1, @@ -23698,7 +23700,7 @@ "sim-cover2": 2, "sim-shotgun": 2, "sim4db": 3, - "sim_client": 5922, + "sim_client": 5925, "sim_reads": 10, "sim_reads.o": 10, "sim_reads_tran": 10, @@ -23818,7 +23820,7 @@ "sketchy": 1, "skewer": 1, "skg_convert.py": 2, - "skip-if-file-exists": 285, + "skip-if-file-exists": 286, "skip_psl_self.awk": 2, "skip_psl_self_ss.awk": 2, "skip_selfmatches.py": 1, @@ -23850,7 +23852,7 @@ "slivar": 1, "slncky": 2, "slncky.v1.0": 2, - "slopBed": 280, + "slopBed": 281, "slow5curl": 1, "slow5tools": 1, "slsh": 2, @@ -23971,8 +23973,8 @@ "snp-pileup": 2, "snp-pileup-quickbam": 1, "snp-sites": 13, - "snp2hgvs": 228, - "snp2tbl": 228, + "snp2hgvs": 229, + "snp2tbl": 229, "snpEff": 24, "snpEffAnnotate.py": 3, "snp_diversity.py": 1, @@ -24047,11 +24049,11 @@ "sort-last-maf": 1, "sort-snos": 2, "sort-snos.pl": 2, - "sort-table": 228, - "sort-uniq-count": 316, - "sort-uniq-count-rank": 316, + "sort-table": 229, + "sort-uniq-count": 317, + "sort-uniq-count-rank": 317, "sort2": 2, - "sortBed": 280, + "sortBed": 281, "sortByRefAndCor.pl": 1, "sortGeneMark.py": 2, "sortHits": 4, @@ -24128,7 +24130,7 @@ "sparsetable_unittest": 1, "spatypes.txt": 1, "spdi2prod": 12, - "spdi2tbl": 228, + "spdi2tbl": 229, "specialk": 1, "species_abundance_cal.py": 1, "spectra-cluster-cli": 1, @@ -24152,7 +24154,7 @@ "sphinx-quickstart": 42, "spine.pl": 1, "spinner.py": 1, - "splain": 1746, + "splain": 1747, "splash": 2, "splice_site_summary.pl": 1, "spliceai": 1, @@ -24161,7 +24163,7 @@ "splinter.pl": 1, "splinter_scaffolds.pl": 1, "split": 86, - "split-at-intron": 228, + "split-at-intron": 229, "split-bed12-blocks": 3, "split-coverages.py": 1, "split-fasta": 1, @@ -24279,6 +24281,7 @@ "spring_minz.py": 1, "spring_model.py": 1, "spring_model_all.py": 1, + "sprinter": 1, "spspaln.pl": 4, "spyder": 1, "spython": 1, @@ -24292,7 +24295,7 @@ "sqlformat": 9, "sqlite.pl": 1, "sqlite3": 2727, - "sqlite3_analyzer": 7291, + "sqlite3_analyzer": 7296, "sqlitebrowser": 1, "sqlmetal": 16, "sqlsharp": 16, @@ -24639,15 +24642,15 @@ "stranger": 1, "strawk": 1, "stream": 77, - "stream-local": 39, - "stream-pubmed": 314, + "stream-local": 40, + "stream-pubmed": 315, "stream_atac": 1, "stream_run_test": 1, "streamer_1d": 22, "streamlit": 6, "streamlit.cmd": 6, "streamsam.sh": 31, - "streamzip": 1317, + "streamzip": 1318, "streme": 6, "streme_xml_to_html": 6, "stress-ng": 1, @@ -24728,7 +24731,7 @@ "subsetdb": 2, "subsketch.sh": 30, "subtract-bed": 3, - "subtractBed": 280, + "subtractBed": 281, "subtractBedGraphs.pl": 5, "subtractBedGraphsDirectory.pl": 5, "sucos": 1, @@ -24901,7 +24904,7 @@ "syri": 1, "syrupy.py": 1, "sysc": 1, - "systematic-mutations": 19, + "systematic-mutations": 20, "t1k-build.pl": 1, "t1k-merge.py": 1, "t1k-smartseq.pl": 1, @@ -24931,7 +24934,7 @@ "tableschema": 1, "tablet": 1, "tabnum2id": 1, - "tabs": 7904, + "tabs": 7909, "tabulate": 144, "tabulate.py": 1, "tabulator": 1, @@ -24954,7 +24957,7 @@ "tag2bed.pl": 5, "tag2pos.pl": 5, "tag2sort": 1, - "tagBam": 280, + "tagBam": 281, "tagDir2HiCsummary.pl": 5, "tagDir2bed.pl": 5, "tagDir2hicFile.pl": 5, @@ -25093,11 +25096,11 @@ "tba": 1, "tbl2asn": 30, "tbl2asn-test": 13, - "tbl2prod": 216, - "tbl2xml": 228, - "tblastn": 350, - "tblastn_vdb": 63, - "tblastx": 350, + "tbl2prod": 217, + "tbl2xml": 229, + "tblastn": 351, + "tblastn_vdb": 64, + "tblastx": 351, "tblite": 1, "tbox-scan": 1, "tbpore": 1, @@ -25105,9 +25108,9 @@ "tbvcfreport": 1, "tcdemux": 1, "tcfinder": 1, - "tclsh": 7528, + "tclsh": 7533, "tclsh8.5": 473, - "tclsh8.6": 7291, + "tclsh8.6": 7296, "tcode": 27, "tcsh": 3, "td_bignet": 2, @@ -25148,12 +25151,12 @@ "test-download": 2, "test-download.3": 2, "test-download.3.0.0": 2, - "test-edirect": 285, - "test-eutils": 314, + "test-edirect": 286, + "test-eutils": 315, "test-gzip": 1, "test-merStream": 5, - "test-pmc-index": 39, - "test-pubmed-index": 314, + "test-pmc-index": 40, + "test-pubmed-index": 315, "test-read-write-cursor": 2, "test-read-write-cursor.3": 2, "test-read-write-cursor.3.0.0": 2, @@ -25207,7 +25210,7 @@ "test_install.bak": 1, "test_miso": 1, "test_musicc.py": 2, - "test_pcre": 111, + "test_pcre": 112, "test_proton.bam": 1, "test_proton.bam.bai": 1, "test_regexp": 1, @@ -25322,7 +25325,7 @@ "tiara-test": 2, "tiberius": 1, "tiberius.py": 1, - "tic": 7904, + "tic": 7909, "tiddit": 1, "tides": 1, "tidk": 1, @@ -25330,23 +25333,23 @@ "tidygff3": 1, "tidyp": 66, "tie": 1, - "tiff2bw": 5334, + "tiff2bw": 5337, "tiff2fsspec": 24, - "tiff2pdf": 5334, - "tiff2ps": 5334, - "tiff2rgba": 5334, - "tiffcmp": 5334, + "tiff2pdf": 5337, + "tiff2ps": 5337, + "tiff2rgba": 5337, + "tiffcmp": 5337, "tiffcomment": 26, - "tiffcp": 5609, - "tiffcrop": 5334, - "tiffdither": 5334, - "tiffdump": 5609, + "tiffcp": 5612, + "tiffcrop": 5337, + "tiffdither": 5337, + "tiffdump": 5612, "tifffile": 30, - "tiffinfo": 5609, - "tiffmedian": 5334, - "tiffset": 5609, - "tiffsplit": 5609, - "tificc": 1065, + "tiffinfo": 5612, + "tiffmedian": 5337, + "tiffset": 5612, + "tiffsplit": 5612, + "tificc": 1068, "tigStore": 3, "tiger-hash": 12, "tigge_check": 1, @@ -25400,7 +25403,7 @@ "titan-gc-prepare.py": 1, "titan.py": 1, "titration": 2, - "tjbench": 482, + "tjbench": 485, "tkconch": 1, "tkpp": 1, "tksm": 1, @@ -25431,14 +25434,14 @@ "to_upper_case.pl.bak": 1, "toco": 80, "toco_from_protos": 80, - "toe": 7904, + "toe": 7909, "tohnsw": 1, "toil": 3, "toil-cwl-runner": 3, "toil-wdl-runner": 2, "tolkein": 1, "tombo": 2, - "toml2xml": 39, + "toml2xml": 40, "tomlq": 299, "tomsimilarity": 1, "tomtom": 13, @@ -25484,7 +25487,7 @@ "tpp_hostname": 2, "tpp_models.pl": 2, "tpptray.bat": 2, - "tput": 7904, + "tput": 7909, "tqdm": 400, "tr": 86, "tr-trimmer": 1, @@ -25559,7 +25562,7 @@ "transform_gfa.py": 1, "transformers-cli": 4, "transformseq": 13, - "transicc": 1065, + "transicc": 1068, "transit": 1, "transition_counter": 1, "transl": 1, @@ -25575,8 +25578,8 @@ "translate_reduced_reads.pl": 1, "translatorx": 1, "translatorx_vLocal.pl": 1, - "transmute": 314, - "transmute.Linux": 228, + "transmute": 315, + "transmute.Linux": 229, "transposcope": 1, "transpose.pl": 1, "transpose.pl.bak": 1, @@ -25715,7 +25718,7 @@ "tryptic.py": 1, "ts": 3, "tsebra.py": 3, - "tset": 7904, + "tset": 7909, "tskit": 7, "tsort": 86, "tsp": 2, @@ -25752,7 +25755,7 @@ "ttree": 66, "tts": 5, "tttrlib": 1, - "ttx": 450, + "ttx": 452, "tty": 86, "tune": 1, "turbocor": 1, @@ -25862,13 +25865,13 @@ "unimod2storable.pl": 1, "unimod_to_loc.rb": 1, "union": 27, - "unionBedGraphs": 280, + "unionBedGraphs": 281, "uniprobe2meme": 13, "uniprot_mapper.rb": 1, "uniprot_sprot_to_sqlite3.py": 2, "uniprot_support.py": 1, "uniq": 87, - "uniq-table": 216, + "uniq-table": 217, "uniqLine.pl": 1, "uniqPolishes": 3, "uniqscan": 1, @@ -25897,12 +25900,12 @@ "unix2mac": 2, "unlink": 86, "unlz4": 3550, - "unlzma": 7729, + "unlzma": 7734, "unmapped2anchors.py": 1, "unmerge": 1, "unmerge-paired-reads.sh": 2, "unnaf": 1, - "unpack200": 422, + "unpack200": 423, "unparse": 1, "unpickle.py": 1, "unpigz": 130, @@ -25915,7 +25918,7 @@ "unstarch-typical": 15, "untangle": 2, "unweight_fasta.py": 1, - "unxz": 7954, + "unxz": 7959, "unzip": 32, "unzip.sh": 30, "unziphdf5": 1, @@ -25923,7 +25926,7 @@ "unzipont": 1, "unzipont_dir": 1, "unzipsfx": 25, - "unzstd": 5355, + "unzstd": 5359, "update-blastdb.py": 2, "update-serotypefinder-db": 1, "update-sort-bed-migrate-candidates": 15, @@ -25943,7 +25946,7 @@ "updateDeltaClr": 2, "updateLibSizes": 2, "update_alias.py": 1, - "update_blastdb.pl": 350, + "update_blastdb.pl": 351, "update_blastdb.pl.bak": 309, "update_database": 1, "update_info.py": 3, @@ -25997,7 +26000,7 @@ "utmpdump": 13, "utrgff2gbrowse.pl": 15, "utrrnaseq": 13, - "uuclient": 5922, + "uuclient": 5925, "uuid": 38, "uuid-config": 38, "uuidgen": 13, @@ -26704,7 +26707,7 @@ "wgMLST": 1, "wgatools": 1, "wgdi": 1, - "wget": 451, + "wget": 452, "wgetdir": 1, "wgmlst": 1, "wgs2ncbi": 1, @@ -26713,7 +26716,7 @@ "wham": 1, "whamg": 1, "whatshap": 14, - "wheel": 3820, + "wheel": 3822, "wheezy.template": 2, "whereis": 13, "which": 1, @@ -26751,17 +26754,18 @@ "winconfig.bat": 3, "window-acgt": 2, "window.py": 1, - "windowBed": 280, - "windowMaker": 280, - "windowmasker": 350, - "windowmasker_2.2.22_adapter.py": 350, + "windowBed": 281, + "windowMaker": 281, + "windowmasker": 351, + "windowmasker_2.2.22_adapter.py": 351, "winextract": 1, "winnowmap": 3, + "wipertools": 1, "wiq.py": 1, "wisestork": 1, - "wish": 7528, + "wish": 7533, "wish8.5": 473, - "wish8.6": 7291, + "wish8.6": 7296, "wkhtmltoimage": 2, "wkhtmltopdf": 2, "wlmscpfs": 1, @@ -26771,7 +26775,7 @@ "woltka": 1, "womtool": 4, "wopl2ofm": 1, - "word-at-a-time": 316, + "word-at-a-time": 317, "word-square": 2, "word_enrich.pl": 1, "wordcloud_cli": 1, @@ -26812,7 +26816,7 @@ "write_tfrecord_species.py": 1, "writedb_entry": 1, "writedb_unit_test": 5, - "wrjpgcom": 5863, + "wrjpgcom": 5866, "ws": 2, "wsdl": 16, "wsdl2": 16, @@ -26878,7 +26882,7 @@ "x86_64-conda-linux-gnu-gfortran": 3365, "x86_64-conda-linux-gnu-gfortran.bin": 575, "x86_64-conda-linux-gnu-gprof": 3403, - "x86_64-conda-linux-gnu-ld": 5680, + "x86_64-conda-linux-gnu-ld": 5685, "x86_64-conda-linux-gnu-ld.bfd": 3403, "x86_64-conda-linux-gnu-ld.gold": 3403, "x86_64-conda-linux-gnu-nm": 3403, @@ -26915,7 +26919,7 @@ "x86_64-conda_cos6-linux-gnu-gfortran": 4134, "x86_64-conda_cos6-linux-gnu-gfortran.bin": 1344, "x86_64-conda_cos6-linux-gnu-gprof": 4170, - "x86_64-conda_cos6-linux-gnu-ld": 6514, + "x86_64-conda_cos6-linux-gnu-ld": 6519, "x86_64-conda_cos6-linux-gnu-ld.bfd": 4170, "x86_64-conda_cos6-linux-gnu-ld.gold": 4170, "x86_64-conda_cos6-linux-gnu-nm": 4170, @@ -26954,7 +26958,7 @@ "xgboost": 30, "xgboost.dll": 1, "xgboost.lib": 1, - "xgettext": 5323, + "xgettext": 5324, "xgui": 2, "xhmm": 1, "xinteract": 2, @@ -26968,23 +26972,23 @@ "xmfa2maf": 4, "xmfa2maf.pl": 1, "xml": 1, - "xml2-config": 5459, + "xml2-config": 5460, "xml2-config.bak": 34, "xml2dcm": 1, "xml2dsr": 1, - "xml2fsa": 228, - "xml2json": 228, - "xml2tbl": 301, + "xml2fsa": 229, + "xml2json": 229, + "xml2tbl": 302, "xml_grep": 64, "xml_merge": 64, "xml_pp": 64, "xml_spellcheck": 64, "xml_split": 64, "xml_to_bas.pl": 3, - "xmlcatalog": 5459, + "xmlcatalog": 5460, "xmlget": 23, "xmlindent": 1, - "xmllint": 5459, + "xmllint": 5460, "xmlpatterns": 256, "xmlpatterns-qt4": 3, "xmlpatternsvalidator": 256, @@ -27021,12 +27025,12 @@ "xrootd-config": 1, "xrspatial": 3, "xsd": 18, - "xslt-config": 272, - "xsltproc": 272, + "xslt-config": 273, + "xsltproc": 273, "xsltproc_lite": 7, "xstreme": 2, "xstreme_html_to_tsv": 2, - "xsubpp": 1746, + "xsubpp": 1747, "xsv": 1, "xtandem": 3, "xtb": 1, @@ -27034,8 +27038,8 @@ "xtea_hg19": 1, "xtea_long": 1, "xtermcolor": 2, - "xtract": 316, - "xtract.Linux": 228, + "xtract": 317, + "xtract.Linux": 229, "xtract.go": 15, "xtract.pl": 1, "xtractcol": 1, @@ -27049,16 +27053,16 @@ "xy-plot": 88, "xyalign": 1, "xyz_sfetch": 1, - "xz": 7954, - "xzcat": 7729, - "xzcmp": 7729, - "xzdec": 7729, - "xzdiff": 7729, - "xzegrep": 7729, - "xzfgrep": 7729, - "xzgrep": 7729, - "xzless": 7729, - "xzmore": 7729, + "xz": 7959, + "xzcat": 7734, + "xzcmp": 7734, + "xzdec": 7734, + "xzdiff": 7734, + "xzegrep": 7734, + "xzfgrep": 7734, + "xzgrep": 7734, + "xzless": 7734, + "xzmore": 7734, "y2racc": 7, "yacc": 4, "yacht": 1, @@ -27069,7 +27073,7 @@ "yak": 2, "yaml2gff.1.4.pl": 15, "yaml2obj": 4, - "yaml2xml": 39, + "yaml2xml": 40, "yamllint": 1, "yamlpp5-events": 4, "yamlpp5-highlight": 4, @@ -27121,7 +27125,7 @@ "zipHomerResults.pl": 5, "zipcloak": 3, "zipcmp": 97, - "zipdetails": 1746, + "zipdetails": 1747, "zipgrep": 25, "zipinfo": 25, "zipmerge": 97, @@ -27146,10 +27150,10 @@ "zrun": 3, "zsh": 3, "zsh-5.8": 3, - "zstd": 5355, - "zstdcat": 5355, - "zstdgrep": 5153, - "zstdless": 5153, - "zstdmt": 5355, + "zstd": 5359, + "zstdcat": 5359, + "zstdgrep": 5157, + "zstdless": 5157, + "zstdmt": 5359, "ztr_dump": 2 } \ No newline at end of file diff --git a/quay.io/biocontainers/e/ega-cryptor:2.0.0--hdfd78af_0.json b/quay.io/biocontainers/e/ega-cryptor:2.0.0--hdfd78af_0.json new file mode 100644 index 0000000..b9f3729 --- /dev/null +++ b/quay.io/biocontainers/e/ega-cryptor:2.0.0--hdfd78af_0.json @@ -0,0 +1,202 @@ +{ + "aserver": "/usr/local/bin/aserver", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "cairo-trace": "/usr/local/bin/cairo-trace", + "captoinfo": "/usr/local/bin/captoinfo", + "cjpeg": "/usr/local/bin/cjpeg", + "clear": "/usr/local/bin/clear", + "compile_et": "/usr/local/bin/compile_et", + "cups-config": "/usr/local/bin/cups-config", + "derb": "/usr/local/bin/derb", + "djpeg": "/usr/local/bin/djpeg", + "ega-cryptor": "/usr/local/bin/ega-cryptor", + "fax2ps": "/usr/local/bin/fax2ps", + "fax2tiff": "/usr/local/bin/fax2tiff", + "fc-cache": "/usr/local/bin/fc-cache", + "fc-cat": "/usr/local/bin/fc-cat", + "fc-conflist": "/usr/local/bin/fc-conflist", + "fc-list": "/usr/local/bin/fc-list", + "fc-match": "/usr/local/bin/fc-match", + "fc-pattern": "/usr/local/bin/fc-pattern", + "fc-query": "/usr/local/bin/fc-query", + "fc-scan": "/usr/local/bin/fc-scan", + "fc-validate": "/usr/local/bin/fc-validate", + "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", + "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", + "gss-client": "/usr/local/bin/gss-client", + "hb-info": "/usr/local/bin/hb-info", + "hb-ot-shape-closure": "/usr/local/bin/hb-ot-shape-closure", + "hb-shape": "/usr/local/bin/hb-shape", + "hb-subset": "/usr/local/bin/hb-subset", + "hb-view": "/usr/local/bin/hb-view", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "idle3": "/usr/local/bin/idle3", + "idle3.13": "/usr/local/bin/idle3.13", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "ippeveprinter": "/usr/local/bin/ippeveprinter", + "ipptool": "/usr/local/bin/ipptool", + "jaotc": "/usr/local/bin/jaotc", + "jar": "/usr/local/bin/jar", + "jarsigner": "/usr/local/bin/jarsigner", + "java": "/usr/local/bin/java", + "javac": "/usr/local/bin/javac", + "javadoc": "/usr/local/bin/javadoc", + "javap": "/usr/local/bin/javap", + "jcmd": "/usr/local/bin/jcmd", + "jconsole": "/usr/local/bin/jconsole", + "jdb": "/usr/local/bin/jdb", + "jdeprscan": "/usr/local/bin/jdeprscan", + "jdeps": "/usr/local/bin/jdeps", + "jfr": "/usr/local/bin/jfr", + "jhsdb": "/usr/local/bin/jhsdb", + "jimage": "/usr/local/bin/jimage", + "jinfo": "/usr/local/bin/jinfo", + "jjs": "/usr/local/bin/jjs", + "jlink": "/usr/local/bin/jlink", + "jmap": "/usr/local/bin/jmap", + "jmod": "/usr/local/bin/jmod", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "jps": "/usr/local/bin/jps", + "jrunscript": "/usr/local/bin/jrunscript", + "jshell": "/usr/local/bin/jshell", + "jstack": "/usr/local/bin/jstack", + "jstat": "/usr/local/bin/jstat", + "jstatd": "/usr/local/bin/jstatd", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "keytool": "/usr/local/bin/keytool", + "kinit": "/usr/local/bin/kinit", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "makeconv": "/usr/local/bin/makeconv", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "openssl": "/usr/local/bin/openssl", + "pack200": "/usr/local/bin/pack200", + "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", + "psicc": "/usr/local/bin/psicc", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.13": "/usr/local/bin/pydoc3.13", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.13": "/usr/local/bin/python3.13", + "python3.13-config": "/usr/local/bin/python3.13-config", + "raw2tiff": "/usr/local/bin/raw2tiff", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "reset": "/usr/local/bin/reset", + "rmic": "/usr/local/bin/rmic", + "rmid": "/usr/local/bin/rmid", + "rmiregistry": "/usr/local/bin/rmiregistry", + "sclient": "/usr/local/bin/sclient", + "serialver": "/usr/local/bin/serialver", + "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", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "unlzma": "/usr/local/bin/unlzma", + "unpack200": "/usr/local/bin/unpack200", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "uuclient": "/usr/local/bin/uuclient", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/m/mzspeclib:1.0.1--pyhdfd78af_0.json b/quay.io/biocontainers/m/mzspeclib:1.0.1--pyhdfd78af_0.json new file mode 100644 index 0000000..1fb1667 --- /dev/null +++ b/quay.io/biocontainers/m/mzspeclib:1.0.1--pyhdfd78af_0.json @@ -0,0 +1,134 @@ +{ + "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", + "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", + "idle3": "/usr/local/bin/idle3", + "idle3.13": "/usr/local/bin/idle3.13", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "jpegtran": "/usr/local/bin/jpegtran", + "jpgicc": "/usr/local/bin/jpgicc", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linkicc": "/usr/local/bin/linkicc", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "mzspeclib": "/usr/local/bin/mzspeclib", + "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", + "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", + "pydoc3.13": "/usr/local/bin/pydoc3.13", + "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", + "python3.13": "/usr/local/bin/python3.13", + "python3.13-config": "/usr/local/bin/python3.13-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", + "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", + "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", + "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", + "xslt-config": "/usr/local/bin/xslt-config", + "xsltproc": "/usr/local/bin/xsltproc", + "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/n/neptune-signature:2.0.0--pyhdfd78af_0.json b/quay.io/biocontainers/n/neptune-signature:2.0.0--pyhdfd78af_0.json new file mode 100644 index 0000000..9fb0cda --- /dev/null +++ b/quay.io/biocontainers/n/neptune-signature:2.0.0--pyhdfd78af_0.json @@ -0,0 +1,304 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.12": "/usr/local/bin/2to3-3.12", + "accn-at-a-time": "/usr/local/bin/accn-at-a-time", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "align-columns": "/usr/local/bin/align-columns", + "amino-acid-composition": "/usr/local/bin/amino-acid-composition", + "archive-ncbinlp": "/usr/local/bin/archive-ncbinlp", + "archive-nihocc": "/usr/local/bin/archive-nihocc", + "archive-nmcds": "/usr/local/bin/archive-nmcds", + "archive-pmc": "/usr/local/bin/archive-pmc", + "archive-pubmed": "/usr/local/bin/archive-pubmed", + "archive-taxonomy": "/usr/local/bin/archive-taxonomy", + "args2slice": "/usr/local/bin/args2slice", + "asn2ref": "/usr/local/bin/asn2ref", + "asn2xml": "/usr/local/bin/asn2xml", + "autopoint": "/usr/local/bin/autopoint", + "between-two-genes": "/usr/local/bin/between-two-genes", + "blast_formatter": "/usr/local/bin/blast_formatter", + "blastdb_aliastool": "/usr/local/bin/blastdb_aliastool", + "blastdbcheck": "/usr/local/bin/blastdbcheck", + "blastdbcmd": "/usr/local/bin/blastdbcmd", + "blastn": "/usr/local/bin/blastn", + "blastn_vdb": "/usr/local/bin/blastn_vdb", + "blastp": "/usr/local/bin/blastp", + "blastx": "/usr/local/bin/blastx", + "blst2gm": "/usr/local/bin/blst2gm", + "blst2tkns": "/usr/local/bin/blst2tkns", + "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", + "f2py": "/usr/local/bin/f2py", + "fetch-local": "/usr/local/bin/fetch-local", + "fetch-nmcds": "/usr/local/bin/fetch-nmcds", + "fetch-pmc": "/usr/local/bin/fetch-pmc", + "fetch-pubmed": "/usr/local/bin/fetch-pubmed", + "fetch-taxonomy": "/usr/local/bin/fetch-taxonomy", + "filter-columns": "/usr/local/bin/filter-columns", + "filter-genbank": "/usr/local/bin/filter-genbank", + "filter-record": "/usr/local/bin/filter-record", + "filter-stop-words": "/usr/local/bin/filter-stop-words", + "find-in-gene": "/usr/local/bin/find-in-gene", + "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", + "idle3": "/usr/local/bin/idle3", + "idle3.12": "/usr/local/bin/idle3.12", + "idn2": "/usr/local/bin/idn2", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "ini2xml": "/usr/local/bin/ini2xml", + "instmodsh": "/usr/local/bin/instmodsh", + "intersect-uid-lists": "/usr/local/bin/intersect-uid-lists", + "join-into-groups-of": "/usr/local/bin/join-into-groups-of", + "json2xml": "/usr/local/bin/json2xml", + "json_pp": "/usr/local/bin/json_pp", + "json_xs": "/usr/local/bin/json_xs", + "jsonl2xml": "/usr/local/bin/jsonl2xml", + "just-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", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "makeblastdb": "/usr/local/bin/makeblastdb", + "makembindex": "/usr/local/bin/makembindex", + "makeprofiledb": "/usr/local/bin/makeprofiledb", + "msgattrib": "/usr/local/bin/msgattrib", + "msgcat": "/usr/local/bin/msgcat", + "msgcmp": "/usr/local/bin/msgcmp", + "msgcomm": "/usr/local/bin/msgcomm", + "msgconv": "/usr/local/bin/msgconv", + "msgen": "/usr/local/bin/msgen", + "msgexec": "/usr/local/bin/msgexec", + "msgfilter": "/usr/local/bin/msgfilter", + "msgfmt": "/usr/local/bin/msgfmt", + "msggrep": "/usr/local/bin/msggrep", + "msginit": "/usr/local/bin/msginit", + "msgmerge": "/usr/local/bin/msgmerge", + "msgunfmt": "/usr/local/bin/msgunfmt", + "msguniq": "/usr/local/bin/msguniq", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "neptune": "/usr/local/bin/neptune", + "neptune-conda": "/usr/local/bin/neptune-conda", + "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", + "numpy-config": "/usr/local/bin/numpy-config", + "openssl": "/usr/local/bin/openssl", + "perl": "/usr/local/bin/perl", + "perl5.32.1": "/usr/local/bin/perl5.32.1", + "perlbug": "/usr/local/bin/perlbug", + "perldoc": "/usr/local/bin/perldoc", + "perlivp": "/usr/local/bin/perlivp", + "perlthanks": "/usr/local/bin/perlthanks", + "phrase-search": "/usr/local/bin/phrase-search", + "piconv": "/usr/local/bin/piconv", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pl2pm": "/usr/local/bin/pl2pm", + "pma2apa": "/usr/local/bin/pma2apa", + "pma2pme": "/usr/local/bin/pma2pme", + "pmc2bioc": "/usr/local/bin/pmc2bioc", + "pmc2info": "/usr/local/bin/pmc2info", + "pod2html": "/usr/local/bin/pod2html", + "pod2man": "/usr/local/bin/pod2man", + "pod2text": "/usr/local/bin/pod2text", + "pod2usage": "/usr/local/bin/pod2usage", + "podchecker": "/usr/local/bin/podchecker", + "print-columns": "/usr/local/bin/print-columns", + "project_tree_builder": "/usr/local/bin/project_tree_builder", + "prove": "/usr/local/bin/prove", + "psiblast": "/usr/local/bin/psiblast", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.12": "/usr/local/bin/pydoc3.12", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.12": "/usr/local/bin/python3.12", + "python3.12-config": "/usr/local/bin/python3.12-config", + "quote-grouped-elements": "/usr/local/bin/quote-grouped-elements", + "rchive": "/usr/local/bin/rchive", + "rchive.Linux": "/usr/local/bin/rchive.Linux", + "recode-sr-latin": "/usr/local/bin/recode-sr-latin", + "ref2pmid": "/usr/local/bin/ref2pmid", + "refseq-nm-cds": "/usr/local/bin/refseq-nm-cds", + "reorder-columns": "/usr/local/bin/reorder-columns", + "reset": "/usr/local/bin/reset", + "rpsblast": "/usr/local/bin/rpsblast", + "rpsbproc": "/usr/local/bin/rpsbproc", + "rpstblastn": "/usr/local/bin/rpstblastn", + "run-ncbi-converter": "/usr/local/bin/run-ncbi-converter", + "run_with_lock": "/usr/local/bin/run_with_lock", + "sclient": "/usr/local/bin/sclient", + "scn2xml": "/usr/local/bin/scn2xml", + "segmasker": "/usr/local/bin/segmasker", + "shasum": "/usr/local/bin/shasum", + "sim_client": "/usr/local/bin/sim_client", + "skip-if-file-exists": "/usr/local/bin/skip-if-file-exists", + "snp2hgvs": "/usr/local/bin/snp2hgvs", + "snp2tbl": "/usr/local/bin/snp2tbl", + "sort-table": "/usr/local/bin/sort-table", + "sort-uniq-count": "/usr/local/bin/sort-uniq-count", + "sort-uniq-count-rank": "/usr/local/bin/sort-uniq-count-rank", + "spdi2tbl": "/usr/local/bin/spdi2tbl", + "splain": "/usr/local/bin/splain", + "split-at-intron": "/usr/local/bin/split-at-intron", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "stream-local": "/usr/local/bin/stream-local", + "stream-pubmed": "/usr/local/bin/stream-pubmed", + "streamzip": "/usr/local/bin/streamzip", + "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", + "tclsh": "/usr/local/bin/tclsh", + "tclsh8.6": "/usr/local/bin/tclsh8.6", + "test-edirect": "/usr/local/bin/test-edirect", + "test-eutils": "/usr/local/bin/test-eutils", + "test-pmc-index": "/usr/local/bin/test-pmc-index", + "test-pubmed-index": "/usr/local/bin/test-pubmed-index", + "test_pcre": "/usr/local/bin/test_pcre", + "tic": "/usr/local/bin/tic", + "toe": "/usr/local/bin/toe", + "toml2xml": "/usr/local/bin/toml2xml", + "tput": "/usr/local/bin/tput", + "transmute": "/usr/local/bin/transmute", + "transmute.Linux": "/usr/local/bin/transmute.Linux", + "tset": "/usr/local/bin/tset", + "uniq-table": "/usr/local/bin/uniq-table", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "update_blastdb.pl": "/usr/local/bin/update_blastdb.pl", + "uuclient": "/usr/local/bin/uuclient", + "wget": "/usr/local/bin/wget", + "wheel": "/usr/local/bin/wheel", + "windowmasker": "/usr/local/bin/windowmasker", + "windowmasker_2.2.22_adapter.py": "/usr/local/bin/windowmasker_2.2.22_adapter.py", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "word-at-a-time": "/usr/local/bin/word-at-a-time", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xgettext": "/usr/local/bin/xgettext", + "xml2fsa": "/usr/local/bin/xml2fsa", + "xml2json": "/usr/local/bin/xml2json", + "xml2tbl": "/usr/local/bin/xml2tbl", + "xsubpp": "/usr/local/bin/xsubpp", + "xtract": "/usr/local/bin/xtract", + "xtract.Linux": "/usr/local/bin/xtract.Linux", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "yaml2xml": "/usr/local/bin/yaml2xml", + "zipdetails": "/usr/local/bin/zipdetails", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/s/sprinter:1.0.0--pyhdfd78af_0.json b/quay.io/biocontainers/s/sprinter:1.0.0--pyhdfd78af_0.json new file mode 100644 index 0000000..cb40aa3 --- /dev/null +++ b/quay.io/biocontainers/s/sprinter:1.0.0--pyhdfd78af_0.json @@ -0,0 +1,193 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.12": "/usr/local/bin/2to3-3.12", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "annotateBed": "/usr/local/bin/annotateBed", + "bamToBed": "/usr/local/bin/bamToBed", + "bamToFastq": "/usr/local/bin/bamToFastq", + "bed12ToBed6": "/usr/local/bin/bed12ToBed6", + "bedToBam": "/usr/local/bin/bedToBam", + "bedToIgv": "/usr/local/bin/bedToIgv", + "bedpeToBam": "/usr/local/bin/bedpeToBam", + "bedtools": "/usr/local/bin/bedtools", + "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", + "closestBed": "/usr/local/bin/closestBed", + "clusterBed": "/usr/local/bin/clusterBed", + "compile_et": "/usr/local/bin/compile_et", + "complementBed": "/usr/local/bin/complementBed", + "coverageBed": "/usr/local/bin/coverageBed", + "curl-config": "/usr/local/bin/curl-config", + "djpeg": "/usr/local/bin/djpeg", + "expandCols": "/usr/local/bin/expandCols", + "f2py": "/usr/local/bin/f2py", + "fastaFromBed": "/usr/local/bin/fastaFromBed", + "fax2ps": "/usr/local/bin/fax2ps", + "fax2tiff": "/usr/local/bin/fax2tiff", + "flankBed": "/usr/local/bin/flankBed", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "genomeCoverageBed": "/usr/local/bin/genomeCoverageBed", + "getOverlap": "/usr/local/bin/getOverlap", + "groupBy": "/usr/local/bin/groupBy", + "gss-client": "/usr/local/bin/gss-client", + "idle3": "/usr/local/bin/idle3", + "idle3.12": "/usr/local/bin/idle3.12", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "intersectBed": "/usr/local/bin/intersectBed", + "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", + "linksBed": "/usr/local/bin/linksBed", + "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", + "mapBed": "/usr/local/bin/mapBed", + "maskFastaFromBed": "/usr/local/bin/maskFastaFromBed", + "mergeBed": "/usr/local/bin/mergeBed", + "multiBamCov": "/usr/local/bin/multiBamCov", + "multiIntersectBed": "/usr/local/bin/multiIntersectBed", + "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", + "nucBed": "/usr/local/bin/nucBed", + "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", + "pairToBed": "/usr/local/bin/pairToBed", + "pairToPair": "/usr/local/bin/pairToPair", + "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", + "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", + "randomBed": "/usr/local/bin/randomBed", + "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", + "shiftBed": "/usr/local/bin/shiftBed", + "shuffleBed": "/usr/local/bin/shuffleBed", + "sim_client": "/usr/local/bin/sim_client", + "slopBed": "/usr/local/bin/slopBed", + "sortBed": "/usr/local/bin/sortBed", + "sprinter": "/usr/local/bin/sprinter", + "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer", + "subtractBed": "/usr/local/bin/subtractBed", + "tabs": "/usr/local/bin/tabs", + "tagBam": "/usr/local/bin/tagBam", + "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", + "unionBedGraphs": "/usr/local/bin/unionBedGraphs", + "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", + "windowBed": "/usr/local/bin/windowBed", + "windowMaker": "/usr/local/bin/windowMaker", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt" +} \ No newline at end of file diff --git a/quay.io/biocontainers/w/wipertools:1.1.1--pyhdfd78af_0.json b/quay.io/biocontainers/w/wipertools:1.1.1--pyhdfd78af_0.json new file mode 100644 index 0000000..9ee3f5c --- /dev/null +++ b/quay.io/biocontainers/w/wipertools:1.1.1--pyhdfd78af_0.json @@ -0,0 +1,71 @@ +{ + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "clear": "/usr/local/bin/clear", + "idle3": "/usr/local/bin/idle3", + "idle3.13": "/usr/local/bin/idle3.13", + "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", + "pydoc3.13": "/usr/local/bin/pydoc3.13", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.13": "/usr/local/bin/python3.13", + "python3.13-config": "/usr/local/bin/python3.13-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", + "wipertools": "/usr/local/bin/wipertools", + "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