diff --git a/counts.json b/counts.json index 232b233..b19ea91 100644 --- a/counts.json +++ b/counts.json @@ -2326,9 +2326,9 @@ "2csfastq_1csfastq": 1, "2ft": 2, "2ndscore": 1, - "2to3": 3616, - "2to3-3.10": 794, - "2to3-3.11": 262, + "2to3": 3618, + "2to3-3.10": 795, + "2to3-3.11": 263, "2to3-3.12": 171, "2to3-3.4": 6, "2to3-3.5": 103, @@ -2419,8 +2419,8 @@ "AminoExtract": 2, "AmpliGone": 1, "AmpliconSuite-pipeline.py": 1, - "AnalyseDists": 45, - "AnalyseSeqs": 45, + "AnalyseDists": 46, + "AnalyseSeqs": 46, "AnnotSV": 1, "AnnotateInexactHomology": 1, "AnnotateInexactHomologyBedpe": 1, @@ -3276,7 +3276,7 @@ "KatComp": 1, "KatGC": 1, "KinamineY-shaker": 1, - "Kinfold": 54, + "Kinfold": 55, "Kmasker": 1, "KmerCount.py": 1, "KmerFilter": 5, @@ -3899,7 +3899,7 @@ "QueueingSystem.dll": 1, "QuickDeconvolution": 1, "QuickSNP.py": 1, - "R": 4645, + "R": 4646, "R-scape": 2, "R-scape-sim": 2, "R-scape-sim-nobps": 2, @@ -3929,19 +3929,19 @@ "RKP.py": 1, "RLPipes": 1, "RM2Bed.py": 12, - "RNA2Dfold": 52, + "RNA2Dfold": 53, "RNADigestor": 2, - "RNALalifold": 52, - "RNALfold": 54, + "RNALalifold": 53, + "RNALfold": 55, "RNAMassCalculator": 1, - "RNAPKplex": 52, + "RNAPKplex": 53, "RNAPhylo": 1, "RNARedPrint": 1, "RNARedPrintSampler.py": 1, "RNARedPrintStructure.py": 1, "RNA_fragment_size.py": 3, - "RNAaliduplex": 54, - "RNAalifold": 54, + "RNAaliduplex": 55, + "RNAalifold": 55, "RNAalisplit.pl": 1, "RNAblueprint": 2, "RNAcalibrate": 1, @@ -3949,32 +3949,32 @@ "RNAcentralHTTPRequest-bin": 1, "RNAclust.pl": 1, "RNAcode": 2, - "RNAcofold": 54, - "RNAdistance": 54, - "RNAdos": 37, - "RNAduplex": 54, + "RNAcofold": 55, + "RNAdistance": 55, + "RNAdos": 38, + "RNAduplex": 55, "RNAeffective": 1, - "RNAeval": 54, - "RNAfold": 53, - "RNAforester": 54, - "RNAheat": 54, + "RNAeval": 55, + "RNAfold": 54, + "RNAforester": 55, + "RNAheat": 55, "RNAhybrid": 1, - "RNAinverse": 54, + "RNAinverse": 55, "RNAlien": 1, "RNAlien-bin": 1, "RNAlienScan": 1, "RNAlienScan-bin": 1, "RNAlienStatistics": 1, "RNAlienStatistics-bin": 1, - "RNAlocmin": 45, - "RNAmultifold": 22, - "RNApaln": 54, - "RNAparconv": 52, - "RNApdist": 54, - "RNAplex": 52, - "RNAplfold": 54, - "RNAplot": 54, - "RNApvmin": 47, + "RNAlocmin": 46, + "RNAmultifold": 23, + "RNApaln": 55, + "RNAparconv": 53, + "RNApdist": 55, + "RNAplex": 53, + "RNAplfold": 55, + "RNAplot": 55, + "RNApvmin": 48, "RNAshapes": 4, "RNAshapes_eval_macrostate": 1, "RNAshapes_eval_microstate": 1, @@ -4045,11 +4045,11 @@ "RNAshapes_subopt_nodangle_window": 1, "RNAshapes_subopt_overdangle": 1, "RNAshapes_subopt_overdangle_window": 1, - "RNAsnoop": 52, + "RNAsnoop": 53, "RNAsnp": 1, "RNAsoup": 1, - "RNAsubopt": 54, - "RNAup": 54, + "RNAsubopt": 55, + "RNAup": 55, "RNAz": 3, "RNAz.pm": 4, "RNPxlSearch": 2, @@ -4129,7 +4129,7 @@ "Rprof": 1, "Rsample": 4, "Rsample-smp": 4, - "Rscript": 4646, + "Rscript": 4647, "RunTHetA.py": 1, "SAGE": 1, "SAMMPileUpReader.py": 1, @@ -4275,7 +4275,8 @@ "ShortestPathTN93": 1, "ShowLDSVG": 1, "Sibelia": 3, - "SigProfilerPlotting": 1, + "SigProfilerMatrixGenerator": 1, + "SigProfilerPlotting": 2, "SigiCRF": 1, "SigiHMM": 1, "SignalGenerator.sh": 1, @@ -4392,7 +4393,7 @@ "THESIAS": 1, "TICCalculator": 2, "TIR-Learner": 1, - "TMalign": 14, + "TMalign": 15, "TMscore": 6, "TNS": 2, "TOBIAS": 2, @@ -4894,7 +4895,7 @@ "abyss-tofastq": 17, "ac-diamond": 1, "accession_retrieve": 1, - "accn-at-a-time": 252, + "accn-at-a-time": 254, "accurate_bkp.py": 1, "acdc": 25, "acdc-filter-fasta-by-name.awk": 1, @@ -4996,7 +4997,7 @@ "addtit.pl": 2, "adf_checker.pl": 1, "adhocfilelist": 1, - "adig": 4478, + "adig": 4481, "adjustPeakFile.pl": 5, "adjustRedunGroupFile.pl": 5, "adjustScanRankerScoreByGroup": 2, @@ -5112,7 +5113,7 @@ "agrvate": 1, "agtsampleinforw.dll": 2, "ahmm-s": 1, - "ahost": 4478, + "ahost": 4481, "airr-tools": 5, "akita_data.py": 1, "akita_data_read.py": 1, @@ -5155,7 +5156,7 @@ "align-cache.2.11.0": 9, "align-cache.3": 2, "align-cache.3.0.0": 2, - "align-columns": 195, + "align-columns": 197, "align-ema.smk": 1, "align-families.py": 1, "align-info": 21, @@ -5278,7 +5279,7 @@ "amdgpu-arch": 1, "ame": 13, "amgr": 1, - "amino-acid-composition": 283, + "amino-acid-composition": 285, "aminoextract": 2, "amk_ccc": 2, "amk_fft2": 2, @@ -5383,7 +5384,7 @@ "annosine2": 1, "annot-tsv": 21, "annot_blast_btop2.pl": 7, - "annotate": 245, + "annotate": 246, "annotate-partitions.py": 7, "annotate.py": 39, "annotate.pyc": 1, @@ -5708,12 +5709,12 @@ "arcasHLA": 1, "archer": 1, "architeuthis": 1, - "archive-ncbinlp": 7, - "archive-nihocc": 7, - "archive-nmcds": 7, - "archive-pmc": 7, - "archive-pubmed": 282, - "archive-taxonomy": 7, + "archive-ncbinlp": 9, + "archive-nihocc": 9, + "archive-nmcds": 9, + "archive-pmc": 9, + "archive-pubmed": 284, + "archive-taxonomy": 9, "archive_directory.py": 2, "archosv": 2, "archspec": 6, @@ -5724,7 +5725,7 @@ "argnorm": 1, "argparse2tool": 1, "argparse2tool_check_path": 1, - "args2slice": 7, + "args2slice": 9, "args_oap": 1, "aria2c": 17, "ariba": 3, @@ -5801,8 +5802,8 @@ "asn2ff": 1, "asn2gb": 2, "asn2idx": 1, - "asn2ref": 7, - "asn2xml": 196, + "asn2ref": 9, + "asn2xml": 198, "asndhuff": 1, "asntool": 1, "asp-cp": 87, @@ -5904,7 +5905,7 @@ "autometa-taxonomy-majority-vote": 2, "autometa-unclustered-recruitment": 2, "autometa-update-databases": 2, - "autopoint": 5264, + "autopoint": 5267, "autoreconf.bak": 10, "autoscan.bak": 10, "autoupdate.bak": 10, @@ -5918,7 +5919,7 @@ "avgEpsGrid": 2, "aviary": 1, "avro": 13, - "awk": 85, + "awk": 86, "aws": 6, "aws-create-elastic-blast-janitor-role.sh": 1, "aws-delete-elastic-blast-janitor-role.sh": 1, @@ -5954,7 +5955,7 @@ "axt_to_lav.py": 58, "axt_to_maf.py": 58, "b2": 2, - "b2ct": 47, + "b2ct": 48, "b2sum": 81, "b2w": 1, "bFst": 31, @@ -6091,7 +6092,7 @@ "bamToBed": 269, "bamToBw.pl": 3, "bamToFastq": 269, - "bamToGBrowse.pl": 84, + "bamToGBrowse.pl": 85, "bamToPsl": 1, "bamToWig.py": 11, "bam_accuracy.py": 1, @@ -6254,8 +6255,8 @@ "baseCalling_Matrix_merger": 1, "base_evolve": 2, "basecall_network.py": 1, - "baseml": 64, - "basemlg": 64, + "baseml": 65, + "basemlg": 65, "basename": 82, "basenc": 79, "basenji_annot_chr.py": 1, @@ -6394,8 +6395,8 @@ "bdbag-utils": 1, "bdbloader_unit_test": 5, "bdf2gdfont.PLS": 5, - "bdf2gdfont.pl": 88, - "bdftogd": 231, + "bdf2gdfont.pl": 89, + "bdftogd": 232, "beacon": 1, "beacon2-import": 1, "beacon2-search": 1, @@ -6497,7 +6498,7 @@ "beta_diversity.py": 4, "beta_diversity_through_plots.py": 1, "beta_significance.py": 1, - "between-two-genes": 283, + "between-two-genes": 285, "bf.sh": 1, "bfc": 1, "bfconvert": 1, @@ -6676,7 +6677,7 @@ "bl-pileup-stats": 1, "bl-randomize": 1, "bl-threshold": 1, - "bl2seq": 29, + "bl2seq": 30, "bl2seq_unit_test": 5, "black": 11, "black-hole": 2, @@ -6705,7 +6706,7 @@ "blast_check_pair.pl": 1, "blast_filter.pl": 1, "blast_format_unit_test": 5, - "blast_formatter": 315, + "blast_formatter": 317, "blast_names_mapping.tsv": 1, "blast_outfmt6_replace_trans_id_w_gene_symbol.pl": 1, "blast_report": 20, @@ -6716,16 +6717,16 @@ "blast_to_link.sh": 1, "blast_unit_test": 5, "blast_wrapper.py": 1, - "blastall": 29, + "blastall": 30, "blastbesties": 1, "blastcl3": 1, - "blastclust": 29, - "blastdb_aliastool": 315, + "blastclust": 30, + "blastdb_aliastool": 317, "blastdb_convert": 20, "blastdb_format_unit_test": 5, "blastdb_path": 20, - "blastdbcheck": 315, - "blastdbcmd": 315, + "blastdbcheck": 317, + "blastdbcmd": 317, "blastdbcp": 52, "blastdiag_unit_test": 5, "blastengine_unit_test": 5, @@ -6733,13 +6734,13 @@ "blastfilter_unit_test": 5, "blasthits_unit_test": 5, "blastinput_unit_test": 5, - "blastn": 315, - "blastn_vdb": 30, + "blastn": 317, + "blastn_vdb": 32, "blastoptions_unit_test": 5, - "blastp": 315, - "blastpgp": 29, + "blastp": 317, + "blastpgp": 30, "blastsetup_unit_test": 5, - "blastx": 315, + "blastx": 317, "blastzWrapper": 1, "blat": 19, "blat2gbrowse.pl": 14, @@ -6762,8 +6763,8 @@ "blossom5": 1, "blossom_randGraph.py": 1, "blosum62.fas": 2, - "blst2gm": 7, - "blst2tkns": 195, + "blst2gm": 9, + "blst2tkns": 197, "bmaToLinks.pl": 1, "bmfilter": 4, "bmge": 1, @@ -6825,12 +6826,12 @@ "boxplot_ng": 1, "bp": 2, "bp-analyze": 1, - "bp_aacomp": 47, + "bp_aacomp": 48, "bp_aacomp.pl": 73, "bp_biofetch_genbank_proxy.pl": 73, - "bp_bioflat_index": 47, + "bp_bioflat_index": 48, "bp_bioflat_index.pl": 73, - "bp_biogetseq": 47, + "bp_biogetseq": 48, "bp_biogetseq.pl": 73, "bp_blast2tree.pl": 73, "bp_bulk_load_gff.pl": 73, @@ -6838,107 +6839,107 @@ "bp_classify_hits_kingdom.pl": 73, "bp_composite_LD.pl": 73, "bp_das_server.pl": 73, - "bp_dbsplit": 47, + "bp_dbsplit": 48, "bp_dbsplit.pl": 73, "bp_download_query_genbank.pl": 73, "bp_einfo": 3, "bp_export_proteins.py": 1, "bp_export_tags.py": 1, - "bp_extract_feature_seq": 47, + "bp_extract_feature_seq": 48, "bp_extract_feature_seq.pl": 73, "bp_fast_load_gff.pl": 73, "bp_fasta_prepare.py": 1, - "bp_fastam9_to_table": 47, + "bp_fastam9_to_table": 48, "bp_fastam9_to_table.pl": 73, - "bp_fetch": 47, + "bp_fetch": 48, "bp_fetch.pl": 73, - "bp_filter_search": 47, + "bp_filter_search": 48, "bp_filter_search.pl": 73, - "bp_find-blast-matches": 47, + "bp_find-blast-matches": 48, "bp_find-blast-matches.pl": 51, "bp_flanks.pl": 73, - "bp_gccalc": 47, + "bp_gccalc": 48, "bp_gccalc.pl": 73, "bp_genbank2gff.pl": 73, - "bp_genbank2gff3": 47, + "bp_genbank2gff3": 48, "bp_genbank2gff3.pl": 73, "bp_genbank_ref_extractor": 3, "bp_generate_histogram.pl": 73, "bp_heterogeneity_test.pl": 73, "bp_hivq.pl": 73, - "bp_hmmer_to_table.pl": 93, - "bp_index": 47, + "bp_hmmer_to_table.pl": 94, + "bp_index": 48, "bp_index.pl": 73, "bp_load_gff.pl": 73, - "bp_local_taxonomydb_query": 47, + "bp_local_taxonomydb_query": 48, "bp_local_taxonomydb_query.pl": 73, - "bp_make_mrna_protein": 47, + "bp_make_mrna_protein": 48, "bp_make_mrna_protein.pl": 73, "bp_mapped_tags.py": 1, - "bp_mask_by_search": 47, + "bp_mask_by_search": 48, "bp_mask_by_search.pl": 73, "bp_meta_gff.pl": 73, - "bp_mrtrans": 47, + "bp_mrtrans": 48, "bp_mrtrans.pl": 73, - "bp_mutate": 47, + "bp_mutate": 48, "bp_mutate.pl": 73, "bp_netinstall.pl": 73, - "bp_nexus2nh": 47, + "bp_nexus2nh": 48, "bp_nexus2nh.pl": 73, - "bp_nrdb": 47, + "bp_nrdb": 48, "bp_nrdb.pl": 73, - "bp_oligo_count": 47, + "bp_oligo_count": 48, "bp_oligo_count.pl": 73, - "bp_pairwise_kaks": 61, + "bp_pairwise_kaks": 62, "bp_pairwise_kaks.pl": 22, - "bp_parse_hmmsearch.pl": 93, + "bp_parse_hmmsearch.pl": 94, "bp_parse_tags.py": 1, - "bp_process_gadfly": 47, + "bp_process_gadfly": 48, "bp_process_gadfly.pl": 73, - "bp_process_sgd": 47, + "bp_process_sgd": 48, "bp_process_sgd.pl": 73, "bp_process_wormbase.pl": 73, "bp_query_entrez_taxa.pl": 73, "bp_remote_blast.pl": 76, - "bp_revtrans-motif": 47, + "bp_revtrans-motif": 48, "bp_revtrans-motif.pl": 73, "bp_search2BSML.pl": 22, - "bp_search2alnblocks": 47, + "bp_search2alnblocks": 48, "bp_search2alnblocks.pl": 73, - "bp_search2gff": 47, + "bp_search2gff": 48, "bp_search2gff.pl": 73, - "bp_search2table": 47, + "bp_search2table": 48, "bp_search2table.pl": 73, - "bp_search2tribe": 47, + "bp_search2tribe": 48, "bp_search2tribe.pl": 73, - "bp_seq_length": 47, + "bp_seq_length": 48, "bp_seq_length.pl": 73, - "bp_seqconvert": 47, + "bp_seqconvert": 48, "bp_seqconvert.pl": 73, - "bp_seqcut": 47, + "bp_seqcut": 48, "bp_seqcut.pl": 73, "bp_seqfeature_delete.pl": 73, "bp_seqfeature_gff3.pl": 73, "bp_seqfeature_load.pl": 73, - "bp_seqpart": 47, + "bp_seqpart": 48, "bp_seqpart.pl": 73, - "bp_seqret": 47, + "bp_seqret": 48, "bp_seqret.pl": 73, - "bp_seqretsplit": 47, + "bp_seqretsplit": 48, "bp_seqretsplit.pl": 73, - "bp_split_seq": 47, + "bp_split_seq": 48, "bp_split_seq.pl": 73, - "bp_sreformat": 47, + "bp_sreformat": 48, "bp_sreformat.pl": 73, - "bp_taxid4species": 47, + "bp_taxid4species": 48, "bp_taxid4species.pl": 73, - "bp_taxonomy2tree": 47, + "bp_taxonomy2tree": 48, "bp_taxonomy2tree.pl": 73, - "bp_translate_seq": 47, + "bp_translate_seq": 48, "bp_translate_seq.pl": 73, - "bp_tree2pag": 47, + "bp_tree2pag": 48, "bp_tree2pag.pl": 73, - "bp_unflatten_seq": 47, + "bp_unflatten_seq": 48, "bp_unflatten_seq.pl": 73, "bpcomp": 1, "bpipe": 4, @@ -6981,7 +6982,7 @@ "broad_utils.py": 1, "brockman_pipeline": 1, "brooklyn_plot": 1, - "brotli": 402, + "brotli": 403, "browse": 18, "bs_call": 2, "bs_seeker2-align.py": 1, @@ -7078,7 +7079,7 @@ "bundlelinks": 1, "bundler": 18, "bunwarpj": 4, - "bunzip2": 6564, + "bunzip2": 6568, "burden_test_vase": 1, "burst_linux_DB12": 1, "burst_linux_DB15": 1, @@ -7129,16 +7130,16 @@ "bxStats.py": 1, "bxcl_seqqc": 1, "bxtools": 1, - "bzcat": 6564, - "bzcmp": 6564, - "bzdiff": 6564, - "bzegrep": 6564, - "bzfgrep": 6564, - "bzgrep": 6564, - "bzip2": 6564, - "bzip2recover": 6564, - "bzless": 6564, - "bzmore": 6564, + "bzcat": 6568, + "bzcmp": 6568, + "bzdiff": 6568, + "bzegrep": 6568, + "bzfgrep": 6568, + "bzgrep": 6568, + "bzip2": 6568, + "bzip2recover": 6568, + "bzless": 6568, + "bzmore": 6568, "c++": 5, "c++filt": 8, "c-index-test": 8, @@ -7155,7 +7156,7 @@ "cPecanLibTests": 1, "cPecanModifyHmm": 1, "cPecanRealign": 1, - "c_rehash": 7713, + "c_rehash": 7717, "ca2ace.pl": 3, "ca2ctg": 2, "ca2mates": 2, @@ -7229,7 +7230,7 @@ "cage-classify.py": 1, "cagee": 1, "cai": 25, - "cairo-trace": 5101, + "cairo-trace": 5102, "cairosvg": 6, "cal": 13, "calD": 1, @@ -7329,7 +7330,7 @@ "capnpc-c++": 52, "capnpc-capnp": 52, "capnpc-cython": 1, - "captoinfo": 7645, + "captoinfo": 7649, "captus_assembly": 1, "caqc.pl": 3, "caqc_help.ini": 3, @@ -7680,7 +7681,7 @@ "chexalign": 1, "chexmix": 1, "chgrp": 82, - "chi2": 64, + "chi2": 65, "chimChe": 3, "chimera": 3, "chimerascan-exclude-transcriptome-events": 2, @@ -7718,7 +7719,7 @@ "chown": 82, "chroder": 1, "chromRegionLength.r": 1, - "chrom_sizes.pl": 84, + "chrom_sizes.pl": 85, "chromap": 1, "chromatiblock": 1, "chromograph": 1, @@ -7762,10 +7763,10 @@ "circulocov": 1, "cirdna": 24, "cirtap": 1, - "cit2pmid": 7, + "cit2pmid": 9, "civicpy": 1, "cjk-gs-integrate": 1, - "cjpeg": 5727, + "cjpeg": 5730, "ckeygen": 1, "cksum": 82, "claMLST": 1, @@ -7867,11 +7868,11 @@ "cleanmap.awk": 1, "cleanme.pl": 1, "cleanpp.sh": 3, - "cleanup-blastdb-volumes.py": 244, + "cleanup-blastdb-volumes.py": 246, "cleanup-coverage.py": 2, "cleanup-stale-gcp-resources.py": 1, "cleanup.py": 1, - "clear": 7645, + "clear": 7649, "clearCNV": 1, "clearcut": 1, "cleric": 1, @@ -7950,9 +7951,9 @@ "clust": 1, "clustal2link": 1, "clustal_to_alma.py": 1, - "clustalo": 26, - "clustalw": 71, - "clustalw2": 72, + "clustalo": 27, + "clustalw": 72, + "clustalw2": 73, "clustalw2fasta": 13, "clustalw2phylip": 13, "cluster": 203, @@ -8058,7 +8059,7 @@ "codcmp": 24, "codcopy": 24, "codecov": 2, - "codeml": 64, + "codeml": 65, "coderet": 24, "codes_bufr_filter": 1, "codes_count": 1, @@ -8121,7 +8122,7 @@ "combine": 4, "combine-assembled-files.sh": 1, "combine-subexons": 1, - "combine-uid-lists": 7, + "combine-uid-lists": 9, "combineAndAnnotateReferences.pl": 1, "combineFile": 2, "combineFragandDBGraph_fastg.py": 1, @@ -8223,7 +8224,7 @@ "compileSpliceCands": 12, "compile_STARE_Linux.sh": 1, "compile_STARE_macOS.sh": 1, - "compile_et": 5760, + "compile_et": 5763, "compiled_table.py": 1, "compleasm": 1, "complementBed": 269, @@ -8314,7 +8315,7 @@ "config.py": 1, "config.sh": 1, "configManta.py": 1, - "config_data": 57, + "config_data": 59, "config_parser.py": 1, "configure": 1, "configureESTmapper.pl": 3, @@ -8406,7 +8407,7 @@ "convert2bed-float128": 14, "convert2bed-megarow": 14, "convert2bed-typical": 14, - "convert2blastmask": 315, + "convert2blastmask": 317, "convert2snns": 2, "convertCoordinates.pl": 5, "convertFastaQualToFastQ.rb": 1, @@ -8516,13 +8517,13 @@ "copycat.3.0.0": 2, "copyfile.sh": 1, "copylink": 1, - "copymat": 29, + "copymat": 30, "coral": 1, "core-only.pl": 1, "core_diversity_analyses.py": 1, "core_methods.py": 1, "core_overlap_plot.py": 1, - "corelist": 1672, + "corelist": 1674, "corepack": 11, "coreprocess.pl": 3, "coresnpfilter": 1, @@ -8626,7 +8627,7 @@ "cp2k_run": 1, "cp2k_shell.ssmp": 1, "cpack": 11, - "cpan": 1672, + "cpan": 1674, "cpancover": 6, "cpanm": 242, "cpat.py": 1, @@ -8818,7 +8819,7 @@ "csv2rdf": 32, "csv2tsv": 1, "csv2xlsx": 1, - "csv2xml": 195, + "csv2xml": 197, "csvExtractBorders": 1, "csvFrags2text": 1, "csv_to_tsv": 1, @@ -8826,7 +8827,7 @@ "ct-energy": 3, "ct-ng.config": 1, "ct2bp": 1, - "ct2db": 47, + "ct2db": 48, "ct2dot": 4, "ct2rnaml": 3, "ct_boxplot_ng": 1, @@ -8864,8 +8865,8 @@ "curate_database.py": 1, "curate_universe": 1, "curesim": 2, - "curl": 5082, - "curl-config": 5876, + "curl": 5085, + "curl-config": 5879, "curlywhirly": 1, "curve_keygen": 68, "cusp": 24, @@ -8912,7 +8913,7 @@ "cw_get_uniprot_data": 1, "cw_query_database": 1, "cweave": 1, - "cwebp": 347, + "cwebp": 348, "cwl-cite-extract": 1, "cwl-docker-extract": 1, "cwl-explode": 1, @@ -9013,7 +9014,7 @@ "dataset_manager.py": 1, "datasets": 2, "datasets-cli": 2, - "datatool": 315, + "datatool": 317, "datavzrd": 2, "date": 82, "datma.py": 1, @@ -9033,23 +9034,23 @@ "dazcon": 4, "dbSNP_idx": 2, "dbTestScript": 1, - "db_archive": 118, - "db_checkpoint": 118, - "db_convert": 96, - "db_deadlock": 118, - "db_dump": 118, + "db_archive": 119, + "db_checkpoint": 119, + "db_convert": 97, + "db_deadlock": 119, + "db_dump": 119, "db_exclude.locs.tsv": 1, "db_graph.jl": 2, - "db_hotbackup": 118, - "db_load": 118, - "db_log_verify": 118, - "db_printlog": 118, - "db_recover": 118, - "db_replicate": 118, - "db_stat": 118, - "db_tuner": 118, - "db_upgrade": 118, - "db_verify": 118, + "db_hotbackup": 119, + "db_load": 119, + "db_log_verify": 119, + "db_printlog": 119, + "db_recover": 119, + "db_replicate": 119, + "db_stat": 119, + "db_tuner": 119, + "db_upgrade": 119, + "db_verify": 119, "dba": 3, "dbcanLight": 1, "dbcanLight-hmmparser": 1, @@ -9250,7 +9251,7 @@ "deltaBS.pl": 1, "delta_filter_wrapper.py": 5, "delta_unit_test": 5, - "deltablast": 315, + "deltablast": 317, "deltapd": 1, "demes": 4, "demesdraw": 1, @@ -9301,8 +9302,9 @@ "depth_calc.py": 1, "depth_estim_from_vcf.sh": 1, "depythontex": 1, - "derb": 5791, + "derb": 5793, "derep_stuff.py": 1, + "deripcal": 1, "derna": 1, "descPoly": 1, "descartes-folium": 2, @@ -9384,7 +9386,7 @@ "diff_iso_usage": 1, "diff_motif": 1, "diffacto": 1, - "difference-uid-lists": 7, + "difference-uid-lists": 9, "difference_from_first_TSS_script_mordor.r": 1, "difference_from_first_TSS_script_mordor_chrom_wide.r": 1, "differentialBindingAffinity_multipleSNPs": 1, @@ -9423,7 +9425,7 @@ "dirmngr-client": 2, "dirname": 82, "dirseq": 2, - "disambiguate-nucleotides": 195, + "disambiguate-nucleotides": 197, "disco": 17, "disco.cfg": 1, "disco_2.cfg": 1, @@ -9463,7 +9465,7 @@ "django-admin": 4, "django-admin.py": 3, "django-admin.pyc": 1, - "djpeg": 5727, + "djpeg": 5730, "dkfzbiasfilter.py": 1, "dkfzbiasfilter_summarize.py": 1, "dlcoal_to_dlcpar": 1, @@ -9574,21 +9576,23 @@ "download-db.sh": 9, "download-dfam.py": 1, "download-entities.pl": 2, - "download-ncbi-data": 268, + "download-ncbi-data": 270, "download-ncbi-genomes": 1, - "download-ncbi-software": 195, + "download-ncbi-software": 197, "download-ncbi-taxa.sh": 1, "download-ncbi-taxmaps": 1, "download-ncbi-taxonomy": 1, - "download-pmc": 7, - "download-pubmed": 282, - "download-sequence": 282, + "download-pmc": 9, + "download-pubmed": 284, + "download-sequence": 284, "download-spatypes.sh": 1, "download-srr-files": 3, "download-taxonomy.sh": 1, "download-uniprot-taxa.sh": 1, "download-vadr-models.sh": 1, "download-virulence-db.sh": 1, + "downloadKalamari.pl": 1, + "downloadKalamari.sh": 1, "downloadRefSeq.pl": 1, "download_and_set_models.py": 1, "download_assemblies_from_genbank.py": 2, @@ -9680,7 +9684,7 @@ "drtext": 24, "drttest": 1, "drugbank": 1, - "ds2pme": 7, + "ds2pme": 9, "dsCompareCurves": 1, "dsComputeBEDDensity": 1, "dsComputeGCCoverage": 1, @@ -9817,7 +9821,7 @@ "dupre": 1, "dupsifter": 1, "dust": 13, - "dustmasker": 315, + "dustmasker": 317, "dv_call_variants.py": 1, "dv_make_examples.py": 1, "dv_postprocess_variants.py": 1, @@ -9832,7 +9836,7 @@ "dvitomp": 1, "dvitype": 1, "dvorfs": 1, - "dwebp": 347, + "dwebp": 348, "dwgsim": 4, "dwgsim_eval": 4, "dwgsim_eval_plot.py": 1, @@ -9906,7 +9910,7 @@ "ecodbtaxstat": 1, "ecofind": 1, "ecogrep": 1, - "ecommon.sh": 195, + "ecommon.sh": 197, "econtact": 88, "ecotag": 1, "ecotaxspecificity": 1, @@ -9942,9 +9946,9 @@ "edonr256-hash": 9, "edonr512-hash": 9, "eel": 1, - "efetch": 283, + "efetch": 285, "effectivet3": 1, - "efilter": 283, + "efilter": 285, "efishent": 1, "efn": 1, "efn2": 5, @@ -9960,8 +9964,8 @@ "eigenstrat_database_tools": 1, "eigenstrat_rename_snps": 1, "eigenstrat_snp_coverage": 1, - "einfo": 283, - "einsi": 96, + "einfo": 285, + "einsi": 97, "einverted": 24, "eject": 13, "eklipseHeader.png": 1, @@ -9989,7 +9993,7 @@ "elfedit": 8, "elgato_report.py": 1, "eliminateBadSuperReadsUsingList": 1, - "elink": 283, + "elink": 285, "elm2meme": 13, "elprep": 1, "elsize": 6, @@ -10024,8 +10028,8 @@ "enano": 1, "enasearch": 1, "enc": 1, - "enc2xs": 1672, - "encguess": 1672, + "enc2xs": 1674, + "encguess": 1674, "encode2var": 1, "encode_dir": 1, "encode_exclude_loci": 1, @@ -10057,7 +10061,7 @@ "enumall": 1, "enumerate_paths.py": 1, "env": 82, - "env-execute": 6807, + "env-execute": 6812, "env.yml": 1, "env_parallel": 99, "env_parallel.ash": 99, @@ -10074,7 +10078,7 @@ "environment.yml": 1, "envpath": 3, "envset.cmd": 1, - "envsubst": 5264, + "envsubst": 5267, "eoulsan.sh": 1, "epa-ng": 4, "epestfind": 24, @@ -10090,7 +10094,7 @@ "epimuller-define": 1, "epimuller-draw": 1, "epimuller-parse": 1, - "epost": 283, + "epost": 285, "eprimer3": 24, "eprimer32": 24, "eproxy": 88, @@ -10125,11 +10129,11 @@ "errno": 3, "errorEstimate": 6, "error_corrected2frg": 1, - "esample": 268, + "esample": 270, "esbuild": 1, "esd2esi": 10, "esdcompat": 12, - "esearch": 283, + "esearch": 285, "esh": 1, "esimsa": 1, "esl-afetch": 163, @@ -10188,7 +10192,7 @@ "estscan": 1, "estwise": 3, "estwisedb": 3, - "esummary": 283, + "esummary": 285, "etandem": 24, "ete": 2, "ete3": 56, @@ -10227,7 +10231,7 @@ "eviplot.py": 1, "evol": 3, "evoluzer": 1, - "evolver": 64, + "evolver": 65, "exact-tandems": 57, "exactSNP": 6, "examine": 1, @@ -10243,7 +10247,7 @@ "excise_precursors.pl": 1, "excise_precursors_iterative_final.pl": 1, "excl_seqs": 2, - "exclude-uid-lists": 268, + "exclude-uid-lists": 270, "exclude_N": 1, "exclude_loci": 1, "exclude_loci_backup": 1, @@ -10269,7 +10273,7 @@ "expam": 1, "expam_limit": 1, "expand": 82, - "expand-current": 268, + "expand-current": 270, "expandCols": 269, "expand_fastq": 1, "expand_links.pl": 7, @@ -10438,7 +10442,7 @@ "ezez4makefile_v4.pl": 1, "ezez4qsub_vx1.pl": 1, "ezez_vx1.pl": 1, - "f2py": 2015, + "f2py": 2016, "f2py2": 135, "f2py2.7": 135, "f2py3": 1591, @@ -10642,7 +10646,7 @@ "fastachecksum": 10, "fastaclean": 11, "fastaclip": 10, - "fastacmd": 29, + "fastacmd": 30, "fastacomposition": 10, "fastadiff": 10, "fastadigest.py": 2, @@ -10891,15 +10895,15 @@ "fax2tiff": 5293, "fba": 1, "fc": 1, - "fc-cache": 5299, - "fc-cat": 5299, - "fc-conflist": 4816, - "fc-list": 5299, - "fc-match": 5299, - "fc-pattern": 5299, - "fc-query": 5299, - "fc-scan": 5299, - "fc-validate": 5299, + "fc-cache": 5301, + "fc-cat": 5301, + "fc-conflist": 4818, + "fc-list": 5301, + "fc-match": 5301, + "fc-pattern": 5301, + "fc-query": 5301, + "fc-scan": 5301, + "fc-validate": 5301, "fc_actg_coordinate": 1, "fc_calc_cutoff": 1, "fc_consensus": 1, @@ -10980,12 +10984,12 @@ "fermi2.pl": 2, "fetch": 4, "fetch-extras": 73, - "fetch-local": 7, - "fetch-nmcds": 7, - "fetch-pmc": 7, - "fetch-pubmed": 282, + "fetch-local": 9, + "fetch-nmcds": 9, + "fetch-pmc": 9, + "fetch-pubmed": 284, "fetch-tax.pl": 1, - "fetch-taxonomy": 7, + "fetch-taxonomy": 9, "fetchChromSizes": 5, "fetchEnaLibraryFastqs.sh": 1, "fetchFastq.sh": 1, @@ -11018,8 +11022,8 @@ "ffprobe": 9, "ffq": 1, "ffreqboot": 2, - "fftns": 96, - "fftnsi": 96, + "fftns": 97, + "fftnsi": 97, "fftw-wisdom": 167, "fftw-wisdom-to-conf": 167, "fftwf-wisdom": 167, @@ -11064,18 +11068,18 @@ "filter-alignments.py": 1, "filter-bam": 2, "filter-bam-by-ids": 3, - "filter-columns": 183, - "filter-genbank": 7, + "filter-columns": 185, + "filter-genbank": 9, "filter-gff": 1, "filter-nonunique-peptide-matches": 2, "filter-positions.pl": 1, "filter-ppx.pl": 14, - "filter-record": 7, + "filter-record": 9, "filter-sort": 1, "filter-stage-1.prl": 4, "filter-stage-2.prl": 4, "filter-stats.pl": 1, - "filter-stop-words": 283, + "filter-stop-words": 285, "filter-stoptags.py": 7, "filter-table": 12, "filter-variations": 2, @@ -11251,7 +11255,7 @@ "find-all-symbols": 2, "find-compounds.pl": 1, "find-duplicate-reads": 2, - "find-in-gene": 195, + "find-in-gene": 197, "find-knots.py": 7, "find-mango-assembly.sh": 1, "find-mango-home": 1, @@ -11460,7 +11464,7 @@ "font-awesome-to-png": 2, "font2c": 3, "fontinst": 1, - "fonttools": 376, + "fonttools": 377, "fop": 1, "forceOneClusterPerPairMem.py": 1, "forest.py": 1, @@ -11477,9 +11481,9 @@ "format_sintax.py": 1, "format_xml.pl": 1, "format_xml.pl.bak": 1, - "formatdb": 29, + "formatdb": 30, "formatlist": 1, - "formatrpsdb": 29, + "formatrpsdb": 30, "formcon": 2, "forwardGenomics.R": 1, "forwardGenomics_fullAnalysis.R": 1, @@ -11547,7 +11551,7 @@ "freec": 1, "freec2bed.pl": 1, "freec2circos.pl": 1, - "freetype-config": 5789, + "freetype-config": 5792, "freeze_graph": 25, "freq2group.pl": 5, "frequency.py": 1, @@ -11561,7 +11565,7 @@ "frg2fastq": 2, "frg2ta": 2, "frgs2clones": 3, - "fribidi": 3995, + "fribidi": 3996, "frictionless": 1, "frm_admin": 1, "frm_purged": 1, @@ -11691,8 +11695,8 @@ "funr": 1, "funzip": 25, "fuse": 1, - "fuse-ranges": 195, - "fuse-segments": 183, + "fuse-ranges": 197, + "fuse-segments": 185, "fuse.sh": 30, "fusion-bloom": 1, "fusion-bloom.makefile": 1, @@ -11958,22 +11962,22 @@ "gatk3": 5, "gatk3-register": 3, "gatk_to_gvcf": 1, - "gawk": 85, + "gawk": 86, "gawk-4.1.3": 1, "gawk-4.2.1": 2, "gawk-5.0.0": 1, "gawk-5.0.1": 6, "gawk-5.1.0": 64, "gawk-5.2.2": 1, - "gawk-5.3.0": 10, - "gawkbug": 11, + "gawk-5.3.0": 11, + "gawkbug": 12, "gb2fas": 1, "gb2fasta": 1, "gbSmallDNA2gff.pl": 14, "gbase": 2, - "gbf2fsa": 7, - "gbf2ref": 7, - "gbf2xml": 282, + "gbf2fsa": 9, + "gbf2ref": 9, + "gbf2xml": 284, "gbf2xml.bak": 1, "gbfalncut": 2, "gbfcut": 2, @@ -12020,9 +12024,9 @@ "gctb": 1, "gctx2gct": 2, "gcv": 2, - "gd2copypal": 231, - "gd2togif": 231, - "gd2topng": 231, + "gd2copypal": 232, + "gd2togif": 232, + "gd2topng": 232, "gdal-config": 36, "gdal2tiles.py": 4, "gdal2xyz.py": 4, @@ -12076,7 +12080,7 @@ "gdbus": 1650, "gdbus-codegen": 1648, "gdc-client": 1, - "gdcmpgif": 231, + "gdcmpgif": 232, "gddiag": 19, "gdi": 1, "gdiff": 1, @@ -12088,12 +12092,12 @@ "gdlib-config": 44, "gdmicro": 1, "gdown": 3, - "gdparttopng": 231, + "gdparttopng": 232, "gdrive": 1, "gdsctools_anova": 1, "gdsctools_regression": 1, "gdtools": 1, - "gdtopng": 231, + "gdtopng": 232, "gecco": 1, "geckodriver": 2, "geecee": 24, @@ -12127,20 +12131,20 @@ "genbank_to": 1, "genblastG": 1, "genbox": 1, - "genbrk": 5791, - "gencfu": 5791, + "genbrk": 5793, + "gencfu": 5793, "genclust": 1, - "gencnval": 5791, + "gencnval": 5793, "gencode_extract_relevant_gtf_exons.pl": 1, "gencode_singleton_unit_test": 5, "genconf": 1, "gencore": 1, "gencove": 1, "gendb": 13, - "gendict": 5791, + "gendict": 5793, "gendist": 10, "gene2protein.db3": 2, - "gene2range": 183, + "gene2range": 185, "gene2xml": 1, "geneAssociationZscore.py": 1, "geneBody_coverage.py": 3, @@ -12218,6 +12222,7 @@ "generate_report.py.bak": 1, "generate_report.pyc.bak": 1, "generate_run_scripts.py": 1, + "generate_sepia_reference.py": 1, "generate_ska_alignment.py": 1, "generate_training_data": 1, "generate_transcripts_gff.py": 1, @@ -12252,7 +12257,7 @@ "genome-to-blast-db": 1, "genome2cg": 1, "genomeCoverageBed": 269, - "genomeCoverageBed.pl": 84, + "genomeCoverageBed.pl": 85, "genomeOntology": 5, "genome_LenFilter_stats.pl": 3, "genome_anno.py": 2, @@ -12288,7 +12293,7 @@ "genotyphi.py": 1, "genpcz": 2, "genpept2gsi.pl": 2, - "genrb": 5791, + "genrb": 5793, "genreflex": 3, "genremdinputs.py": 6, "genrestr": 4, @@ -12346,6 +12351,7 @@ "getDifferentialPeaksReplicates.pl": 5, "getDistalPeaks.pl": 5, "getEndSequencesOfContigs.perl": 1, + "getExactTaxonomy.pl": 1, "getFCSheader.R": 1, "getFCSheaders.py": 1, "getFRCvalues": 2, @@ -12486,8 +12492,8 @@ "get_sequence_type": 1, "get_sequences_for_meme.py": 1, "get_simple_cycs.py": 1, - "get_species_taxids.sh": 282, - "get_species_taxids.sh.bak": 277, + "get_species_taxids.sh": 284, + "get_species_taxids.sh.bak": 279, "get_standard_headers": 1, "get_stats_summary.pl": 1, "get_subontology_from.pl": 1, @@ -12557,9 +12563,9 @@ "getscu": 1, "getsize": 13, "getsnvfreq_by_interval": 1, - "gettext": 5264, - "gettext.sh": 5264, - "gettextize": 5264, + "gettext": 5267, + "gettext.sh": 5267, + "gettextize": 5267, "getuniqgenomealign": 1, "getuniqgenomealign_interval": 1, "getuniqgenomealign_sample_names": 1, @@ -12661,14 +12667,14 @@ "gie": 39, "gif2h5": 528, "gif2hdf": 122, - "gif2rgb": 734, + "gif2rgb": 735, "gif2tiff": 189, - "gif2webp": 347, - "gifbuild": 734, - "gifclrmp": 734, + "gif2webp": 348, + "gifbuild": 735, + "gifclrmp": 735, "gifecho": 39, "giffilter": 25, - "giffix": 734, + "giffix": 735, "gifinto": 39, "gifmaker.py": 20, "gifrop": 1, @@ -12679,15 +12685,15 @@ "gifrop_pannotate.R": 1, "gifrop_plots.R": 1, "gifsponge": 25, - "giftext": 734, - "giftogd2": 231, - "giftool": 734, + "giftext": 735, + "giftogd2": 232, + "giftool": 735, "gigrnd.py": 1, "gil2bin": 1, "gimbleprep": 1, "gimme": 4, "gimme_taxa.py": 7, - "ginsi": 96, + "ginsi": 97, "gio": 1538, "gio-launch-desktop": 668, "gio-querymodules": 1650, @@ -12735,8 +12741,8 @@ "glpsol": 224, "glsearch36": 7, "gm": 2, - "gm2ranges": 7, - "gm2segs": 7, + "gm2ranges": 9, + "gm2segs": 9, "gmap": 13, "gmap.nosimd": 8, "gmap.sse42": 11, @@ -13065,7 +13071,7 @@ "gsnapl.sse42": 11, "gsnd": 104, "gsort": 5, - "gss-client": 5760, + "gss-client": 5763, "gss-server": 2, "gst-completion-helper": 1, "gst-device-monitor-1.0": 227, @@ -13286,8 +13292,8 @@ "h264dec": 9, "h264enc": 9, "h2load": 3929, - "h2ph": 1672, - "h2xs": 1672, + "h2ph": 1674, + "h2xs": 1674, "h4_ncdump": 122, "h4_ncgen": 122, "h4cc": 122, @@ -13460,11 +13466,11 @@ "haystack_pipeline": 1, "haystack_run_test": 1, "haystack_tf_activity_plane": 1, - "hb-info": 251, - "hb-ot-shape-closure": 5045, - "hb-shape": 5045, - "hb-subset": 4609, - "hb-view": 5002, + "hb-info": 252, + "hb-ot-shape-closure": 5046, + "hb-shape": 5046, + "hb-subset": 4610, + "hb-view": 5003, "hbvblast.sh": 1, "hca-matrix-downloader": 1, "hca-mtx-to-10x": 1, @@ -13517,7 +13523,7 @@ "hexdump": 13, "hgGcPercent": 3, "hgvs-shell": 1, - "hgvs2spdi": 195, + "hgvs2spdi": 197, "hhalign": 4, "hhalign_omp": 4, "hhblits": 4, @@ -13910,9 +13916,9 @@ "ichar": 1, "icon-font-to-png": 2, "iconv": 5461, - "icu-config": 5791, - "icuexportdata": 2007, - "icuinfo": 5791, + "icu-config": 5793, + "icuexportdata": 2009, + "icuinfo": 5793, "id": 82, "idba": 10, "idba.o": 10, @@ -13942,9 +13948,9 @@ "idfetch": 1, "idiag-socket-details": 8, "idle": 332, - "idle3": 3285, - "idle3.10": 794, - "idle3.11": 262, + "idle3": 3287, + "idle3.10": 795, + "idle3.11": 263, "idle3.12": 171, "idle3.4": 6, "idle3.5": 103, @@ -13955,7 +13961,7 @@ "idlj": 117, "idmatrix.sh": 30, "idn": 30, - "idn2": 253, + "idn2": 255, "idpAssemble": 2, "idpQonvert": 2, "idpQuery": 2, @@ -14072,7 +14078,7 @@ "img2dcm": 1, "img2png": 5, "img2py": 5, - "img2webp": 338, + "img2webp": 339, "img2xpm": 5, "imgcmp": 5, "imginfo": 5, @@ -14084,7 +14090,8 @@ "imode_gcc": 2, "imodview": 2, "imove": 2, - "impala": 29, + "impala": 30, + "impg": 1, "import": 75, "import-html-template": 13, "import-itol.pl": 1, @@ -14147,7 +14154,7 @@ "infer_bp_v4.pl": 1, "infer_experiment.py": 3, "infer_sv.pl": 1, - "infinitesites": 64, + "infinitesites": 65, "inflate_denoiser_output.py": 1, "influx_i": 1, "influx_i.py": 1, @@ -14158,12 +14165,12 @@ "infoalign": 24, "infoassembly": 24, "infobase": 24, - "infocmp": 7645, + "infocmp": 7649, "inforesidue": 24, "informant.py": 1, "infoseq": 24, - "infotocap": 7645, - "ini2xml": 7, + "infotocap": 7649, + "ini2xml": 9, "init_Trinotate_sqlite_db.pl": 1, "init_db.sh": 1, "initdb": 45, @@ -14221,7 +14228,7 @@ "installpackages.R": 1, "installvst": 15, "instance_events": 29, - "instmodsh": 1672, + "instmodsh": 1674, "int_seqs_to_char_strings.py": 58, "intake": 1, "intake-server": 1, @@ -14256,7 +14263,7 @@ "interprophet.rb": 1, "interproscan.sh": 1, "intersect": 5, - "intersect-uid-lists": 281, + "intersect-uid-lists": 283, "intersectBed": 269, "intersectFiles.py": 2, "intersectGenomicSets.py": 1, @@ -14504,7 +14511,7 @@ "jdeprscan": 424, "jdeps": 532, "je": 2, - "jellyfish": 43, + "jellyfish": 44, "jemalloc-config": 14, "jemalloc.sh": 15, "jembossctl": 24, @@ -14533,7 +14540,7 @@ "jobTreeStatus": 2, "jobTreeTest_Dependencies.py": 1, "join": 82, - "join-into-groups-of": 283, + "join-into-groups-of": 285, "join-long-chromosomes": 3, "join.pl": 1, "join.pl.bak": 1, @@ -14557,8 +14564,8 @@ "jp.py": 100, "jpackage": 114, "jpeg2hdf": 122, - "jpegtran": 5727, - "jpgicc": 969, + "jpegtran": 5730, + "jpgicc": 970, "jpredapi": 1, "jps": 533, "jq": 300, @@ -14570,12 +14577,12 @@ "jsearch": 1, "jshell": 424, "json2gff": 1, - "json2xml": 195, + "json2xml": 197, "json_collect_data_source.py": 1, - "json_pp": 1672, - "json_xs": 341, + "json_pp": 1674, + "json_xs": 343, "jsondiff": 8, - "jsonl2xml": 7, + "jsonl2xml": 9, "jsonpatch": 8, "jsonpointer": 10, "jsonschema": 206, @@ -14627,17 +14634,17 @@ "jupyter-serverextension": 37, "jupyter-troubleshoot": 143, "jupyter-trust": 136, - "just-first-key": 7, + "just-first-key": 9, "just_blast_test.pl": 1, "jwebserver": 32, - "k5srvutil": 5760, + "k5srvutil": 5763, "k8": 159, "k8-Linux": 1, "k_means": 1, "k_means_coefficient": 1, "k_neighbors": 1, "k_neighbors_coefficient": 1, - "kadmin": 5760, + "kadmin": 5763, "kadmin.local": 2, "kadmind": 2, "kaiju": 4, @@ -14731,7 +14738,7 @@ "kdbmeta.3.0.0": 2, "kdbmeta.3.0.3": 1, "kdbmeta.3.1.0": 1, - "kdestroy": 5760, + "kdestroy": 5763, "kea-config": 35, "keep-header": 1, "keep-ribo-periodic": 1, @@ -14741,7 +14748,7 @@ "keggcharter.py": 1, "keggpathway_map.py": 1, "keyFreq": 1, - "keyctl": 2390, + "keyctl": 2393, "keygen": 1, "keyring": 10, "keytool": 533, @@ -14772,10 +14779,10 @@ "kinSimRiboswitch": 1, "king": 1, "kingfisher": 1, - "kinit": 5760, + "kinit": 5763, "kinship-read": 1, "kinshipDecompose": 1, - "kinwalker": 47, + "kinwalker": 48, "kipoi": 2, "kissnp2": 1, "kissplice": 1, @@ -14785,7 +14792,7 @@ "kitsch": 10, "kitsune": 1, "kleborate": 1, - "klist": 5760, + "klist": 5763, "kma": 18, "kma_index": 18, "kma_shm": 18, @@ -14870,7 +14877,7 @@ "kp1mer_to_kmer.py": 1, "kp2np.py": 1, "kpal": 2, - "kpasswd": 5760, + "kpasswd": 5763, "kpileup.py": 1, "kprop": 2, "kpropd": 2, @@ -14883,23 +14890,23 @@ "kpsewhere": 1, "kpsewhich": 1, "kpsexpand": 1, - "kraken": 10, + "kraken": 11, "kraken-biom": 1, "kraken-bracken-summary.py": 1, - "kraken-build": 10, + "kraken-build": 11, "kraken-build.bak": 1, - "kraken-filter": 10, + "kraken-filter": 11, "kraken-filter.bak": 1, - "kraken-mpa-report": 10, + "kraken-mpa-report": 11, "kraken-mpa-report.bak": 1, - "kraken-report": 10, + "kraken-report": 11, "kraken-report.bak": 1, - "kraken-translate": 10, + "kraken-translate": 11, "kraken-translate.bak": 1, "kraken.bak": 1, - "kraken2": 16, - "kraken2-build": 16, - "kraken2-inspect": 16, + "kraken2": 17, + "kraken2-build": 17, + "kraken2-inspect": 17, "krakenhll": 1, "krakenhll-build": 1, "krakenhll-download": 1, @@ -14917,7 +14924,7 @@ "krakenuniq-report": 1, "krakenuniq-translate": 1, "krakmeopen": 1, - "krb5-config": 5760, + "krb5-config": 5763, "krb5-send-pr": 2, "krb5kdc": 2, "kreport2krona.py": 3, @@ -14933,9 +14940,9 @@ "kseq_split": 1, "ksnp": 1, "kssd": 1, - "ksu": 5760, + "ksu": 5763, "ksw": 1, - "kswitch": 5760, + "kswitch": 5763, "ktClassifyBLAST": 16, "ktClassifyHits": 12, "ktGetContigMagnitudes": 16, @@ -14966,12 +14973,12 @@ "ktserver": 2, "kttimedmgr": 2, "kttimedtest": 2, - "ktutil": 5760, + "ktutil": 5763, "ktutilmgr": 2, "ktutilserv": 2, "ktutiltest": 2, "kubectl": 1, - "kvno": 5760, + "kvno": 5763, "kwip": 2, "kwip-stats": 2, "l4p-tmpl": 32, @@ -15089,7 +15096,7 @@ "lefse_plot_features.py": 1, "lefse_plot_res.py": 1, "lefse_run.py": 1, - "legacy_blast.pl": 315, + "legacy_blast.pl": 317, "legsta": 1, "lemon-0.x-to-1.x.sh": 4, "lemur": 1, @@ -15123,8 +15130,8 @@ "libclair3.cpython-36m-x86_64-linux-gnu.so": 1, "libclair3.o": 1, "libclair3.so": 1, - "libdeflate-gunzip": 4089, - "libdeflate-gzip": 4089, + "libdeflate-gunzip": 4092, + "libdeflate-gzip": 4092, "libdrawgram.so": 5, "libdrawtree.so": 5, "libfile.pl": 1, @@ -15133,9 +15140,9 @@ "libiomp5md.dll": 1, "liblist.pl": 1, "liblist.pl.bak": 1, - "libnetcfg": 1672, - "libpng-config": 5841, - "libpng16-config": 5841, + "libnetcfg": 1674, + "libpng-config": 5844, + "libpng16-config": 5844, "libpypy-c.so": 1, "libpypy-c.so.debug": 1, "libpypy3-c.so.debug": 3, @@ -15191,11 +15198,11 @@ "link_ssv.py": 1, "linkage2allegro": 1, "linkhsp_unit_test": 5, - "linkicc": 969, + "linkicc": 970, "linknets": 2, "links2sql.pl": 7, "linksBed": 269, - "linsi": 96, + "linsi": 97, "linux32": 13, "linux64": 13, "linx": 1, @@ -15489,26 +15496,26 @@ "lut_pdiffCI.dat": 4, "lut_pdiffInRegion.dat": 4, "lwarpmk": 1, - "lwp-download": 192, - "lwp-dump": 192, - "lwp-mirror": 192, - "lwp-request": 192, + "lwp-download": 193, + "lwp-dump": 193, + "lwp-mirror": 193, + "lwp-request": 193, "lyner": 1, - "lz4": 3498, + "lz4": 3499, "lz4_decompress": 2, - "lz4c": 3497, - "lz4cat": 3497, - "lzcat": 7472, - "lzcmp": 7472, - "lzdiff": 7472, - "lzegrep": 7472, - "lzfgrep": 7472, - "lzgrep": 7472, - "lzless": 7472, - "lzma": 7472, - "lzmadec": 7472, - "lzmainfo": 7472, - "lzmore": 7472, + "lz4c": 3498, + "lz4cat": 3498, + "lzcat": 7475, + "lzcmp": 7475, + "lzdiff": 7475, + "lzegrep": 7475, + "lzfgrep": 7475, + "lzgrep": 7475, + "lzless": 7475, + "lzma": 7475, + "lzmadec": 7475, + "lzmainfo": 7475, + "lzmore": 7475, "lzop_build_offset_table.py": 58, "m-party": 1, "m-tx": 1, @@ -15626,20 +15633,20 @@ "maf_translate_chars.py": 58, "maf_truncate.py": 58, "maf_word_frequency.py": 58, - "mafft": 97, - "mafft-distance": 96, - "mafft-einsi": 96, - "mafft-fftns": 96, - "mafft-fftnsi": 96, - "mafft-ginsi": 96, - "mafft-homologs.rb": 96, - "mafft-linsi": 96, - "mafft-nwns": 96, - "mafft-nwnsi": 96, - "mafft-profile": 96, - "mafft-qinsi": 96, - "mafft-sparsecore.rb": 94, - "mafft-xinsi": 96, + "mafft": 98, + "mafft-distance": 97, + "mafft-einsi": 97, + "mafft-fftns": 97, + "mafft-fftnsi": 97, + "mafft-ginsi": 97, + "mafft-homologs.rb": 97, + "mafft-linsi": 97, + "mafft-nwns": 97, + "mafft-nwnsi": 97, + "mafft-profile": 97, + "mafft-qinsi": 97, + "mafft-sparsecore.rb": 95, + "mafft-xinsi": 97, "mafft.yaml": 1, "mag-improve": 35, "mag2gfa": 1, @@ -15669,7 +15676,7 @@ "main_html_generator.py": 1, "makblk.pl": 4, "makdbs": 4, - "make": 4134, + "make": 4135, "make-barcodes.awk": 1, "make-cluster.R": 1, "make-conf": 1, @@ -15802,7 +15809,7 @@ "make_pp_rst_file.py": 1, "make_prefs_file.py": 1, "make_prg": 2, - "make_pscores.pl": 15, + "make_pscores.pl": 16, "make_qiime_py_file.py": 1, "make_rarefaction_plots.py": 1, "make_rejoin_links.pl": 1, @@ -15819,12 +15826,12 @@ "makeagp2.awk": 1, "makeagp_full.awk": 1, "makeagp_full2.awk": 1, - "makeblastdb": 317, + "makeblastdb": 319, "makecert": 15, "makechimeras.sh": 30, "makeclusterdb": 4, "makecontaminatedgenomes.sh": 30, - "makeconv": 5791, + "makeconv": 5793, "makedtx": 1, "makefasta.awk": 1, "makegeo": 35, @@ -15832,14 +15839,14 @@ "makeglossaries-lite": 1, "makehmmerdb": 173, "makeidx.pl": 4, - "makemat": 29, - "makembindex": 315, + "makemat": 30, + "makembindex": 317, "makenucseq": 24, "makepBAM_genome.sh": 1, "makepBAM_transcriptome.sh": 1, "makeplot.pl": 3, "makepolymers.sh": 30, - "makeprofiledb": 315, + "makeprofiledb": 317, "makeprotseq": 24, "maker": 1, "maker2chado": 1, @@ -16152,7 +16159,7 @@ "mclcm": 23, "mclpipeline": 23, "mcmc_gtb.py": 1, - "mcmctree": 64, + "mcmctree": 65, "mcomp": 4, "mconfig": 15, "mcookie": 13, @@ -16267,7 +16274,7 @@ "mega_reads_assemble_cluster2.sh": 1, "mega_reads_assemble_polish.sh": 1, "mega_reads_assemble_ref.sh": 1, - "megablast": 29, + "megablast": 30, "megadepth": 1, "megagta": 1, "megagta.py": 1, @@ -16831,6 +16838,7 @@ "mob_typer": 1, "mobster": 1, "mobster-to-vcf": 1, + "mobsuiteRepresentativeFasta.pl": 1, "moc": 244, "moc-qt4": 3, "moca": 1, @@ -17021,24 +17029,24 @@ "mseqtools": 1, "msformatter": 1, "msfragger": 2, - "msgattrib": 5264, - "msgcat": 5264, - "msgcmp": 5264, - "msgcomm": 5264, - "msgconv": 5264, - "msgen": 5264, - "msgexec": 5264, + "msgattrib": 5267, + "msgcat": 5267, + "msgcmp": 5267, + "msgcomm": 5267, + "msgconv": 5267, + "msgen": 5267, + "msgexec": 5267, "msgf2pin": 1, "msgf_plus": 3, - "msgfilter": 5264, - "msgfmt": 5264, + "msgfilter": 5267, + "msgfmt": 5267, "msgfplus_search.rb": 1, - "msggrep": 5264, - "msginit": 5264, - "msgmerge": 5264, + "msggrep": 5267, + "msginit": 5267, + "msgmerge": 5267, "msgserv": 1, - "msgunfmt": 5264, - "msguniq": 5264, + "msgunfmt": 5267, + "msguniq": 5267, "msi": 1, "msi_cluster2reads": 1, "msi_clustr2map.pl": 1, @@ -17155,7 +17163,7 @@ "mummerplot": 57, "munge_sumstats.py": 1, "mupbwt": 1, - "muscle": 64, + "muscle": 65, "musixflx": 1, "musixtex": 1, "muspinsim": 1, @@ -17328,9 +17336,9 @@ "ncrf_to_bed": 2, "ncrf_to_bed.py": 2, "ncurses5-config": 565, - "ncurses6-config": 6938, + "ncurses6-config": 6942, "ncursesw5-config": 703, - "ncursesw6-config": 6939, + "ncursesw6-config": 6943, "ndg_httpclient": 2, "ndisasm": 1, "ndmetis": 58, @@ -17420,7 +17428,7 @@ "nf-test": 1, "nfe-umbrella-slice": 6, "ngd": 9, - "ngettext": 5264, + "ngettext": 5267, "ngg_barabasi_albert": 2, "ngg_barbell": 2, "ngg_complete": 2, @@ -17430,9 +17438,9 @@ "ngg_newman_watts_strogatz": 2, "ngg_path": 2, "ngg_ring_lattice": 2, - "nghttp": 4428, - "nghttpd": 4428, - "nghttpx": 4428, + "nghttp": 4431, + "nghttpd": 4431, + "nghttpx": 4431, "ngless": 2, "ngless-wrapped": 1, "nglview": 2, @@ -17466,7 +17474,7 @@ "ngsngs": 1, "ngsplotdb.py": 5, "ngsutils": 1, - "nhance.sh": 7, + "nhance.sh": 9, "nhmmer": 173, "nhmmscan": 173, "nib-conform": 2, @@ -17613,7 +17621,7 @@ "nproc": 82, "npth-config": 2, "npx": 15, - "nquire": 283, + "nquire": 285, "nquire.bak": 1, "nrForwardSplicedReads.pl": 1, "nr_ORFs_gff3.pl": 5, @@ -17704,8 +17712,8 @@ "nw_topology": 2, "nw_trim": 2, "nwalign3": 1, - "nwns": 96, - "nwnsi": 96, + "nwns": 97, + "nwnsi": 97, "nxtrim": 2, "o-bars-for-each-column.R": 1, "o-boxplots.R": 1, @@ -17955,11 +17963,11 @@ "openslide-quickhash1sum": 2, "openslide-show-properties": 2, "openslide-write-png": 2, - "openssl": 7713, + "openssl": 7717, "opentargets_validator": 1, - "opj_compress": 623, - "opj_decompress": 623, - "opj_dump": 623, + "opj_compress": 624, + "opj_decompress": 624, + "opj_dump": 624, "opl2ofm": 1, "opsin": 1, "opt": 6, @@ -18178,7 +18186,7 @@ "paltohdf": 122, "pam": 1, "pamon": 38, - "pamp": 64, + "pamp": 65, "panISa.py": 1, "panX.py": 1, "pan_genome_assembly_statistics": 7, @@ -18219,10 +18227,10 @@ "panfeed-get-kmers": 1, "panfeed-plot": 1, "pangenome_variants_to_treeWAS.pl": 1, - "pango-list": 3993, + "pango-list": 3994, "pango-querymodules": 10, - "pango-segmentation": 2819, - "pango-view": 4796, + "pango-segmentation": 2820, + "pango-view": 4797, "pangoLEARN": 1, "pango_designation": 1, "pangolearn.smk": 1, @@ -18463,14 +18471,14 @@ "pcnt_bezier.lua": 1, "pcoaPlot.py": 2, "pcor": 1, - "pcre-config": 4926, - "pcre2-config": 3687, - "pcre2_jit_test": 3676, - "pcre2grep": 3687, - "pcre2posix_test": 112, - "pcre2test": 3687, - "pcregrep": 4926, - "pcretest": 4926, + "pcre-config": 4928, + "pcre2-config": 3688, + "pcre2_jit_test": 3677, + "pcre2grep": 3688, + "pcre2posix_test": 113, + "pcre2test": 3688, + "pcregrep": 4928, + "pcretest": 4928, "pct2rgb.py": 4, "pctid_ani_sample": 1, "pcz_animate": 1, @@ -18668,7 +18676,7 @@ "perf": 1, "perfect-square": 2, "perform_controls.pl": 1, - "perl": 1672, + "perl": 1674, "perl-doc": 2, "perl-reversion": 9, "perl5.22.0": 54, @@ -18676,12 +18684,12 @@ "perl5.26.2": 369, "perl5.30.3": 5, "perl5.32.0": 64, - "perl5.32.1": 1180, - "perlbug": 1672, - "perldoc": 1672, - "perlivp": 1672, + "perl5.32.1": 1182, + "perlbug": 1674, + "perldoc": 1674, + "perlivp": 1674, "perltex": 1, - "perlthanks": 1672, + "perlthanks": 1674, "permuteGPAT++": 31, "permuteSmooth": 31, "permute_structure.pl": 1, @@ -18821,7 +18829,7 @@ "phonopy-vasp-born": 1, "phonopy-vasp-efe": 1, "photo": 2, - "phrase-search": 281, + "phrase-search": 283, "phsolverserver": 3, "phy2nex": 1, "phykit": 1, @@ -19013,7 +19021,7 @@ "pickle_cat.py": 1, "pickorientation.awk": 1, "pickout": 1, - "piconv": 1672, + "piconv": 1674, "picopore": 1, "picopore-realtime": 1, "picopore-rename": 1, @@ -19052,10 +19060,10 @@ "pints_caller": 1, "pints_normalizer": 1, "pints_visualizer": 1, - "pip": 3617, + "pip": 3619, "pip2": 1, "pip2.7": 1, - "pip3": 2542, + "pip3": 2544, "pipdeptree": 1, "pipelign": 1, "pipeline.py": 1, @@ -19206,13 +19214,13 @@ "pkfix-helper": 1, "pkg-config": 76, "pkg-config.bin": 76, - "pkgdata": 5791, + "pkgdata": 5793, "pkginfo": 10, "pkill": 1, "pktogf": 1, "pktype": 1, "pl2bat.pl": 3, - "pl2pm": 1672, + "pl2pm": 1674, "plaScope.sh": 1, "plac_runner.py": 60, "place_orient1.smk": 1, @@ -19375,11 +19383,11 @@ "pm4ngs-rnaseq-demo": 1, "pm4ngs-server": 1, "pm_which": 2, - "pma2apa": 7, - "pma2pme": 7, + "pma2apa": 9, + "pma2pme": 9, "pmap": 1, - "pmc2bioc": 7, - "pmc2info": 7, + "pmc2bioc": 9, + "pmc2info": 9, "pmd": 1, "pmdtools": 1, "pmemd_mdrun": 1, @@ -19405,21 +19413,21 @@ "pmxmutate": 1, "pn2pdf": 1, "pneumo-typer": 1, - "png-fix-itxt": 5841, + "png-fix-itxt": 5844, "pngcp": 89, - "pngfix": 5841, - "pngtogd": 231, - "pngtogd2": 231, + "pngfix": 5844, + "pngtogd": 232, + "pngtogd2": 232, "pnps-gen": 1, - "poa": 16, + "poa": 17, "pocheck": 1, "poclcc": 3, - "pod2html": 1672, - "pod2man": 1672, - "pod2text": 1672, - "pod2usage": 1672, + "pod2html": 1674, + "pod2man": 1674, + "pod2text": 1674, + "pod2usage": 1674, "pod_cover": 12, - "podchecker": 1672, + "podchecker": 1674, "podselect": 437, "poetry": 6, "pointwise_datasets_concatenator.py": 1, @@ -19465,7 +19473,7 @@ "poppunk_sketch": 1, "poppunk_visualise": 1, "popscle": 1, - "popt": 47, + "popt": 48, "populations": 1, "pore_c": 1, "porechop": 12, @@ -19645,7 +19653,7 @@ "prinseq-graphs-noPCA.pl": 3, "prinseq-graphs.pl": 3, "prinseq-lite.pl": 3, - "print-columns": 195, + "print-columns": 197, "print.pl": 1, "printIcounts": 1, "printScaff": 2, @@ -19738,7 +19746,7 @@ "project.sh.orig": 1, "projectAndStrip": 4, "projectFeatures": 3, - "project_tree_builder": 315, + "project_tree_builder": 317, "projinfo": 38, "projsync": 35, "prokka": 23, @@ -19882,7 +19890,7 @@ "protxml_to_table.rb": 1, "prov-compare": 9, "prov-convert": 9, - "prove": 1672, + "prove": 1674, "provean": 1, "provean.sh": 1, "provis": 1, @@ -19926,10 +19934,10 @@ "psiCalculator.py": 1, "psiPerGene.py": 1, "psibl2seq_unit_test": 5, - "psiblast": 315, + "psiblast": 317, "psiblast_iteration_unit_test": 5, "psiblast_unit_test": 5, - "psicc": 969, + "psicc": 970, "psiclass": 1, "psiphi": 24, "psite": 3, @@ -19981,9 +19989,9 @@ "pt2to3": 73, "ptGAUL.sh": 1, "ptangle": 1, - "ptar": 1672, - "ptardiff": 1672, - "ptargrep": 1672, + "ptar": 1674, + "ptardiff": 1674, + "ptargrep": 1674, "ptdump": 73, "ptest": 1, "ptex": 1, @@ -20159,10 +20167,10 @@ "pydamage": 1, "pydemult": 1, "pydicom": 1, - "pydoc": 3616, - "pydoc3": 3285, - "pydoc3.10": 794, - "pydoc3.11": 262, + "pydoc": 3618, + "pydoc3": 3287, + "pydoc3.10": 795, + "pydoc3.11": 263, "pydoc3.12": 171, "pydoc3.4": 6, "pydoc3.5": 103, @@ -20184,8 +20192,8 @@ "pyflyte-execute": 1, "pyflyte-fast-execute": 1, "pyflyte-map-execute": 1, - "pyftmerge": 376, - "pyftsubset": 376, + "pyftmerge": 377, + "pyftsubset": 377, "pygal_gen.py": 2, "pygenetic_code": 1, "pygmentex": 1, @@ -20287,7 +20295,7 @@ "pytest": 141, "pytest-benchmark": 1, "pythia8-config": 1, - "python": 3617, + "python": 3619, "python-argcomplete-check-easy-install-script": 337, "python-argcomplete-tcsh": 191, "python-build": 2, @@ -20298,13 +20306,13 @@ "python2.5-config": 1, "python2.7": 331, "python2.7-config": 314, - "python3": 3286, - "python3-config": 3285, - "python3.1": 1227, - "python3.10": 794, - "python3.10-config": 794, - "python3.11": 262, - "python3.11-config": 262, + "python3": 3288, + "python3-config": 3287, + "python3.1": 1229, + "python3.10": 795, + "python3.10-config": 795, + "python3.11": 263, + "python3.11-config": 263, "python3.12": 171, "python3.12-config": 171, "python3.4": 6, @@ -20509,7 +20517,7 @@ "quorum": 4, "quorum_create_database": 4, "quorum_error_correct_reads": 4, - "quote-grouped-elements": 7, + "quote-grouped-elements": 9, "qv_to_bqv.py": 58, "qvality": 1, 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"rtc_binner.py": 1, "rtg": 1, @@ -21499,7 +21510,7 @@ "run-htseq-workflow": 1, "run-mummer1": 44, "run-mummer3": 44, - "run-ncbi-converter": 282, + "run-ncbi-converter": 284, "run-ncbi-converter.bak": 1, "run-ntedit": 1, "run-roh.pl": 156, @@ -21702,7 +21713,7 @@ "run_vote.py": 1, "run_voteSpecies.py": 1, "run_vsclust_app.R": 1, - "run_with_lock": 305, + "run_with_lock": 307, "run_workflows.py": 1, "run_x_platform_fuzz_corpus": 37, "runabyss.py": 1, @@ -22073,7 +22084,7 @@ "scitokens-test": 1, "scitokens-test-access": 1, "scitokens-verify": 1, - "sclient": 5760, + "sclient": 5763, "sclust_summary.sh": 1, "scluster": 3, "scmap-cli-post-install-tests.bats": 1, @@ -22092,7 +22103,7 @@ "scn-post-install-tests.sh": 1, "scn-predict.R": 1, "scn-train-model.R": 1, - "scn2xml": 7, + "scn2xml": 9, "scoary": 3, "scoary_GUI": 3, "scompare": 6, @@ -22198,12 +22209,12 @@ "secondary2split.py": 1, "sectosupp": 1, "secutil": 15, - "sed": 3919, + "sed": 3920, "seealso": 24, "seedRand.py": 1, "seedme": 1, "seedme.py": 1, - "seedtop": 77, + "seedtop": 78, "seeker.pl": 1, "seer": 1, "segToGc": 1, @@ -22211,7 +22222,7 @@ "segalign": 1, "segalign_repeat_masker": 1, "segemehl.x": 1, - "segmasker": 315, + "segmasker": 317, "segment-cnv": 1, "segment.py": 1, "segmentFst": 31, @@ -22491,7 +22502,7 @@ "sharq.3": 2, "sharq.3.0.0": 2, "shasta": 1, - "shasum": 1672, + "shasum": 1674, "shed-tools": 2, "shell_utils.py": 1, "shiboken2": 2, @@ -22586,7 +22597,7 @@ "sim-cover2": 2, "sim-shotgun": 2, "sim4db": 3, - "sim_client": 5760, + "sim_client": 5763, "sim_reads": 10, "sim_reads.o": 10, "sim_reads_tran": 10, @@ -22698,7 +22709,7 @@ "sketchy": 1, "skewer": 1, "skg_convert.py": 2, - "skip-if-file-exists": 252, + "skip-if-file-exists": 254, "skip_psl_self.awk": 2, "skip_psl_self_ss.awk": 2, "skip_selfmatches.py": 1, @@ -22821,8 +22832,8 @@ "snp-pileup": 2, "snp-pileup-quickbam": 1, "snp-sites": 13, - "snp2hgvs": 195, - "snp2tbl": 195, + "snp2hgvs": 197, + "snp2tbl": 197, "snpEff": 23, "snpEffAnnotate.py": 3, "snp_diversity.py": 1, @@ -22895,9 +22906,9 @@ "sort-last-maf": 1, "sort-snos": 2, "sort-snos.pl": 2, - "sort-table": 195, - "sort-uniq-count": 283, - "sort-uniq-count-rank": 283, + "sort-table": 197, + "sort-uniq-count": 285, + "sort-uniq-count-rank": 285, "sort2": 2, "sortBed": 269, "sortByRefAndCor.pl": 1, @@ -22974,7 +22985,7 @@ "sparsetable_unittest": 1, "spatypes.txt": 1, "spdi2prod": 12, - "spdi2tbl": 195, + "spdi2tbl": 197, "specialk": 1, "spectra-cluster-cli": 1, "spectral_clustering": 1, @@ -22996,7 +23007,7 @@ "sphinx-quickstart": 39, "spine.pl": 1, "spinner.py": 1, - "splain": 1672, + "splain": 1674, "splash": 1, "splice_site_summary.pl": 1, "spliceai": 1, @@ -23005,7 +23016,7 @@ "splinter.pl": 1, "splinter_scaffolds.pl": 1, "split": 82, - "split-at-intron": 195, + "split-at-intron": 197, "split-bed12-blocks": 3, "split-coverages.py": 1, "split-fasta": 1, @@ -23134,7 +23145,7 @@ "sqlformat": 9, "sqlite.pl": 1, "sqlite3": 2709, - "sqlite3_analyzer": 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+ "toml2xml": 9, "tomlq": 289, "tomsimilarity": 1, "tomtom": 13, @@ -24258,7 +24269,7 @@ "tpp_hostname": 2, "tpp_models.pl": 2, "tpptray.bat": 2, - "tput": 7645, + "tput": 7649, "tqdm": 334, "tr": 82, "trace_comment": 2, @@ -24329,7 +24340,7 @@ "transform_gfa.py": 1, "transformers-cli": 2, "transformseq": 13, - "transicc": 969, + "transicc": 970, "transit": 1, "transition_counter": 1, "transl": 1, @@ -24345,8 +24356,8 @@ "translate_reduced_reads.pl": 1, "translatorx": 1, "translatorx_vLocal.pl": 1, - "transmute": 281, - "transmute.Linux": 195, + "transmute": 283, + "transmute.Linux": 197, "transposcope": 1, "transpose.pl": 1, "transpose.pl.bak": 1, @@ -24481,7 +24492,7 @@ "tryptic.py": 1, "ts": 3, "tsebra.py": 3, - "tset": 7645, + "tset": 7649, "tskit": 6, "tsort": 82, "tsp": 2, @@ -24516,7 +24527,7 @@ "tth-hash": 11, "ttree": 66, "tts": 5, - "ttx": 376, + "ttx": 377, "tty": 82, "turbocor": 1, "tutorial_eqtlbma.R": 1, @@ -24631,7 +24642,7 @@ "uniprot_sprot_to_sqlite3.py": 2, 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@@ -25860,10 +25872,10 @@ "zrun": 3, "zsh": 3, "zsh-5.8": 3, - "zstd": 5150, - "zstdcat": 5150, - "zstdgrep": 4948, - "zstdless": 4948, - "zstdmt": 5150, + "zstd": 5154, + "zstdcat": 5154, + "zstdgrep": 4952, + "zstdless": 4952, + "zstdmt": 5154, "ztr_dump": 2 } \ No newline at end of file diff --git a/quay.io/biocontainers/i/impg:0.2.0--h4349ce8_0.json b/quay.io/biocontainers/i/impg:0.2.0--h4349ce8_0.json new file mode 100644 index 0000000..162b181 --- /dev/null +++ b/quay.io/biocontainers/i/impg:0.2.0--h4349ce8_0.json @@ -0,0 +1,4 @@ +{ + "impg": "/usr/local/bin/impg", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/k/kalamari:5.3.2--pl5321h031d066_0.json b/quay.io/biocontainers/k/kalamari:5.3.2--pl5321h031d066_0.json new file mode 100644 index 0000000..2d75b88 --- /dev/null +++ b/quay.io/biocontainers/k/kalamari:5.3.2--pl5321h031d066_0.json @@ -0,0 +1,284 @@ +{ + "accn-at-a-time": "/usr/local/bin/accn-at-a-time", + "adig": 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"/usr/local/bin/pcretest", + "perl": "/usr/local/bin/perl", + "perl5.32.1": "/usr/local/bin/perl5.32.1", + "perlbug": "/usr/local/bin/perlbug", + "perldoc": "/usr/local/bin/perldoc", + "perlivp": "/usr/local/bin/perlivp", + "perlthanks": "/usr/local/bin/perlthanks", + "phrase-search": "/usr/local/bin/phrase-search", + "piconv": "/usr/local/bin/piconv", + "pl2pm": "/usr/local/bin/pl2pm", + "pma2apa": "/usr/local/bin/pma2apa", + "pma2pme": "/usr/local/bin/pma2pme", + "pmc2bioc": "/usr/local/bin/pmc2bioc", + "pmc2info": "/usr/local/bin/pmc2info", + "pod2html": "/usr/local/bin/pod2html", + "pod2man": "/usr/local/bin/pod2man", + "pod2text": "/usr/local/bin/pod2text", + "pod2usage": "/usr/local/bin/pod2usage", + "podchecker": "/usr/local/bin/podchecker", + "print-columns": "/usr/local/bin/print-columns", + "project_tree_builder": "/usr/local/bin/project_tree_builder", + "prove": "/usr/local/bin/prove", + "psiblast": "/usr/local/bin/psiblast", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "quote-grouped-elements": "/usr/local/bin/quote-grouped-elements", + "rchive": "/usr/local/bin/rchive", + "rchive.Linux": "/usr/local/bin/rchive.Linux", + "recode-sr-latin": "/usr/local/bin/recode-sr-latin", + "ref2pmid": "/usr/local/bin/ref2pmid", + "refseq-nm-cds": "/usr/local/bin/refseq-nm-cds", + "reorder-columns": "/usr/local/bin/reorder-columns", + "reset": "/usr/local/bin/reset", + "rpsblast": "/usr/local/bin/rpsblast", + "rpsbproc": "/usr/local/bin/rpsbproc", + "rpstblastn": "/usr/local/bin/rpstblastn", + "rsync": "/usr/local/bin/rsync", + "rsync-ssl": "/usr/local/bin/rsync-ssl", + "run-ncbi-converter": "/usr/local/bin/run-ncbi-converter", + "run_with_lock": "/usr/local/bin/run_with_lock", + "sclient": "/usr/local/bin/sclient", + "scn2xml": "/usr/local/bin/scn2xml", + "segmasker": "/usr/local/bin/segmasker", + "shasum": "/usr/local/bin/shasum", + "sim_client": "/usr/local/bin/sim_client", + "skip-if-file-exists": "/usr/local/bin/skip-if-file-exists", + "snp2hgvs": "/usr/local/bin/snp2hgvs", + "snp2tbl": "/usr/local/bin/snp2tbl", + "sort-table": "/usr/local/bin/sort-table", + "sort-uniq-count": "/usr/local/bin/sort-uniq-count", + "sort-uniq-count-rank": "/usr/local/bin/sort-uniq-count-rank", + "spdi2tbl": "/usr/local/bin/spdi2tbl", + "splain": "/usr/local/bin/splain", + "split-at-intron": "/usr/local/bin/split-at-intron", + "stream-local": "/usr/local/bin/stream-local", + "stream-pubmed": "/usr/local/bin/stream-pubmed", + "streamzip": "/usr/local/bin/streamzip", + "tabs": "/usr/local/bin/tabs", + "tar": "/usr/local/bin/tar", + "tbl2prod": "/usr/local/bin/tbl2prod", + "tbl2xml": "/usr/local/bin/tbl2xml", + "tblastn": "/usr/local/bin/tblastn", + "tblastn_vdb": "/usr/local/bin/tblastn_vdb", + "tblastx": "/usr/local/bin/tblastx", + "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", + "unlz4": "/usr/local/bin/unlz4", + "unzstd": "/usr/local/bin/unzstd", + "update_blastdb.pl": "/usr/local/bin/update_blastdb.pl", + "update_blastdb.pl.bak": "/usr/local/bin/update_blastdb.pl.bak", + "uuclient": "/usr/local/bin/uuclient", + "validateTaxonomy.pl": "/usr/local/bin/validateTaxonomy.pl", + "wget": "/usr/local/bin/wget", + "windowmasker": "/usr/local/bin/windowmasker", + "windowmasker_2.2.22_adapter.py": "/usr/local/bin/windowmasker_2.2.22_adapter.py", + "word-at-a-time": "/usr/local/bin/word-at-a-time", + "xgettext": "/usr/local/bin/xgettext", + "xml2fsa": "/usr/local/bin/xml2fsa", + "xml2json": "/usr/local/bin/xml2json", + "xml2tbl": "/usr/local/bin/xml2tbl", + "xsubpp": "/usr/local/bin/xsubpp", + "xtract": "/usr/local/bin/xtract", + "xtract.Linux": "/usr/local/bin/xtract.Linux", + "xxh128sum": "/usr/local/bin/xxh128sum", + "xxh32sum": "/usr/local/bin/xxh32sum", + "xxh64sum": "/usr/local/bin/xxh64sum", + "xxhsum": "/usr/local/bin/xxhsum", + "yaml2xml": "/usr/local/bin/yaml2xml", + "zipdetails": "/usr/local/bin/zipdetails", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/r/r-dsb:1.0.3--r43h3121a25_0.json b/quay.io/biocontainers/r/r-dsb:1.0.3--r43h3121a25_0.json new file mode 100644 index 0000000..b3f78aa --- /dev/null +++ b/quay.io/biocontainers/r/r-dsb:1.0.3--r43h3121a25_0.json @@ -0,0 +1,232 @@ +{ + "R": "/usr/local/bin/R", + "Rscript": "/usr/local/bin/Rscript", + "adig": "/usr/local/bin/adig", + "ahost": "/usr/local/bin/ahost", + "autopoint": "/usr/local/bin/autopoint", + "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", + "curl": "/usr/local/bin/curl", + "curl-config": "/usr/local/bin/curl-config", + "derb": "/usr/local/bin/derb", + "djpeg": "/usr/local/bin/djpeg", + "envsubst": "/usr/local/bin/envsubst", + "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", + "fribidi": "/usr/local/bin/fribidi", + "genbrk": "/usr/local/bin/genbrk", + "gencfu": "/usr/local/bin/gencfu", + "gencnval": "/usr/local/bin/gencnval", + "gendict": "/usr/local/bin/gendict", + "genrb": "/usr/local/bin/genrb", + "gettext": "/usr/local/bin/gettext", + "gettext.sh": "/usr/local/bin/gettext.sh", + "gettextize": "/usr/local/bin/gettextize", + "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", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "jpegtran": "/usr/local/bin/jpegtran", + "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", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "make": "/usr/local/bin/make", + "makeconv": "/usr/local/bin/makeconv", + "msgattrib": "/usr/local/bin/msgattrib", + "msgcat": "/usr/local/bin/msgcat", + "msgcmp": "/usr/local/bin/msgcmp", + "msgcomm": "/usr/local/bin/msgcomm", + "msgconv": "/usr/local/bin/msgconv", + "msgen": "/usr/local/bin/msgen", + "msgexec": "/usr/local/bin/msgexec", + "msgfilter": "/usr/local/bin/msgfilter", + "msgfmt": "/usr/local/bin/msgfmt", + "msggrep": "/usr/local/bin/msggrep", + "msginit": "/usr/local/bin/msginit", + "msgmerge": "/usr/local/bin/msgmerge", + "msgunfmt": "/usr/local/bin/msgunfmt", + "msguniq": "/usr/local/bin/msguniq", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "ngettext": "/usr/local/bin/ngettext", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "openssl": "/usr/local/bin/openssl", + "pango-list": "/usr/local/bin/pango-list", + "pango-segmentation": "/usr/local/bin/pango-segmentation", + "pango-view": "/usr/local/bin/pango-view", + "pcre2-config": "/usr/local/bin/pcre2-config", + "pcre2_jit_test": "/usr/local/bin/pcre2_jit_test", + "pcre2grep": "/usr/local/bin/pcre2grep", + "pcre2posix_test": "/usr/local/bin/pcre2posix_test", + "pcre2test": "/usr/local/bin/pcre2test", + "pkgdata": "/usr/local/bin/pkgdata", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "recode-sr-latin": "/usr/local/bin/recode-sr-latin", + "reset": "/usr/local/bin/reset", + "sclient": "/usr/local/bin/sclient", + "sed": "/usr/local/bin/sed", + "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", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tjbench": "/usr/local/bin/tjbench", + "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", + "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-addr2line": "/usr/local/bin/x86_64-conda-linux-gnu-addr2line", + "x86_64-conda-linux-gnu-ar": "/usr/local/bin/x86_64-conda-linux-gnu-ar", + "x86_64-conda-linux-gnu-as": "/usr/local/bin/x86_64-conda-linux-gnu-as", + "x86_64-conda-linux-gnu-c++": "/usr/local/bin/x86_64-conda-linux-gnu-c++", + "x86_64-conda-linux-gnu-c++filt": "/usr/local/bin/x86_64-conda-linux-gnu-c++filt", + "x86_64-conda-linux-gnu-c89": "/usr/local/bin/x86_64-conda-linux-gnu-c89", + "x86_64-conda-linux-gnu-c99": "/usr/local/bin/x86_64-conda-linux-gnu-c99", + "x86_64-conda-linux-gnu-cc": "/usr/local/bin/x86_64-conda-linux-gnu-cc", + "x86_64-conda-linux-gnu-cpp": "/usr/local/bin/x86_64-conda-linux-gnu-cpp", + "x86_64-conda-linux-gnu-dwp": "/usr/local/bin/x86_64-conda-linux-gnu-dwp", + "x86_64-conda-linux-gnu-elfedit": "/usr/local/bin/x86_64-conda-linux-gnu-elfedit", + "x86_64-conda-linux-gnu-f95": "/usr/local/bin/x86_64-conda-linux-gnu-f95", + "x86_64-conda-linux-gnu-g++": "/usr/local/bin/x86_64-conda-linux-gnu-g++", + "x86_64-conda-linux-gnu-gcc": "/usr/local/bin/x86_64-conda-linux-gnu-gcc", + "x86_64-conda-linux-gnu-gcc-ar": "/usr/local/bin/x86_64-conda-linux-gnu-gcc-ar", + "x86_64-conda-linux-gnu-gcc-nm": "/usr/local/bin/x86_64-conda-linux-gnu-gcc-nm", + "x86_64-conda-linux-gnu-gcc-ranlib": "/usr/local/bin/x86_64-conda-linux-gnu-gcc-ranlib", + "x86_64-conda-linux-gnu-gcov": "/usr/local/bin/x86_64-conda-linux-gnu-gcov", + "x86_64-conda-linux-gnu-gcov-dump": "/usr/local/bin/x86_64-conda-linux-gnu-gcov-dump", + "x86_64-conda-linux-gnu-gcov-tool": "/usr/local/bin/x86_64-conda-linux-gnu-gcov-tool", + "x86_64-conda-linux-gnu-gfortran": "/usr/local/bin/x86_64-conda-linux-gnu-gfortran", + "x86_64-conda-linux-gnu-gprof": "/usr/local/bin/x86_64-conda-linux-gnu-gprof", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda-linux-gnu-ld.bfd": "/usr/local/bin/x86_64-conda-linux-gnu-ld.bfd", + "x86_64-conda-linux-gnu-ld.gold": "/usr/local/bin/x86_64-conda-linux-gnu-ld.gold", + "x86_64-conda-linux-gnu-nm": "/usr/local/bin/x86_64-conda-linux-gnu-nm", + "x86_64-conda-linux-gnu-objcopy": "/usr/local/bin/x86_64-conda-linux-gnu-objcopy", + "x86_64-conda-linux-gnu-objdump": "/usr/local/bin/x86_64-conda-linux-gnu-objdump", + "x86_64-conda-linux-gnu-ranlib": "/usr/local/bin/x86_64-conda-linux-gnu-ranlib", + "x86_64-conda-linux-gnu-readelf": "/usr/local/bin/x86_64-conda-linux-gnu-readelf", + "x86_64-conda-linux-gnu-size": "/usr/local/bin/x86_64-conda-linux-gnu-size", + "x86_64-conda-linux-gnu-strings": "/usr/local/bin/x86_64-conda-linux-gnu-strings", + "x86_64-conda-linux-gnu-strip": "/usr/local/bin/x86_64-conda-linux-gnu-strip", + "x86_64-conda_cos6-linux-gnu-addr2line": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-addr2line", + "x86_64-conda_cos6-linux-gnu-ar": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ar", + "x86_64-conda_cos6-linux-gnu-as": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-as", + "x86_64-conda_cos6-linux-gnu-c++": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-c++", + "x86_64-conda_cos6-linux-gnu-c++filt": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-c++filt", + "x86_64-conda_cos6-linux-gnu-c89": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-c89", + "x86_64-conda_cos6-linux-gnu-c99": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-c99", + "x86_64-conda_cos6-linux-gnu-cc": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-cc", + "x86_64-conda_cos6-linux-gnu-cpp": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-cpp", + "x86_64-conda_cos6-linux-gnu-dwp": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-dwp", + "x86_64-conda_cos6-linux-gnu-elfedit": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-elfedit", + "x86_64-conda_cos6-linux-gnu-f95": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-f95", + "x86_64-conda_cos6-linux-gnu-g++": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-g++", + "x86_64-conda_cos6-linux-gnu-gcc": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-gcc", + "x86_64-conda_cos6-linux-gnu-gcc-ar": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-gcc-ar", + "x86_64-conda_cos6-linux-gnu-gcc-nm": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-gcc-nm", + "x86_64-conda_cos6-linux-gnu-gcc-ranlib": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib", + "x86_64-conda_cos6-linux-gnu-gcov": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-gcov", + "x86_64-conda_cos6-linux-gnu-gcov-dump": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-gcov-dump", + "x86_64-conda_cos6-linux-gnu-gcov-tool": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-gcov-tool", + "x86_64-conda_cos6-linux-gnu-gfortran": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-gfortran", + "x86_64-conda_cos6-linux-gnu-gprof": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-gprof", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld.bfd": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld.bfd", + "x86_64-conda_cos6-linux-gnu-ld.gold": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld.gold", + "x86_64-conda_cos6-linux-gnu-nm": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-nm", + "x86_64-conda_cos6-linux-gnu-objcopy": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-objcopy", + "x86_64-conda_cos6-linux-gnu-objdump": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-objdump", + "x86_64-conda_cos6-linux-gnu-ranlib": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ranlib", + "x86_64-conda_cos6-linux-gnu-readelf": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-readelf", + "x86_64-conda_cos6-linux-gnu-size": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-size", + "x86_64-conda_cos6-linux-gnu-strings": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-strings", + "x86_64-conda_cos6-linux-gnu-strip": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-strip", + "xgettext": "/usr/local/bin/xgettext", + "xmlwf": "/usr/local/bin/xmlwf", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/r/ripcal:2.0--hdfd78af_0.json b/quay.io/biocontainers/r/ripcal:2.0--hdfd78af_0.json new file mode 100644 index 0000000..3a37296 --- /dev/null +++ b/quay.io/biocontainers/r/ripcal:2.0--hdfd78af_0.json @@ -0,0 +1,524 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.10": "/usr/local/bin/2to3-3.10", + "AnalyseDists": "/usr/local/bin/AnalyseDists", + "AnalyseSeqs": "/usr/local/bin/AnalyseSeqs", + "Kinfold": "/usr/local/bin/Kinfold", + "RNA2Dfold": "/usr/local/bin/RNA2Dfold", + "RNALalifold": "/usr/local/bin/RNALalifold", + "RNALfold": "/usr/local/bin/RNALfold", + "RNAPKplex": "/usr/local/bin/RNAPKplex", + "RNAaliduplex": "/usr/local/bin/RNAaliduplex", + "RNAalifold": "/usr/local/bin/RNAalifold", + "RNAcofold": "/usr/local/bin/RNAcofold", + "RNAdistance": "/usr/local/bin/RNAdistance", + "RNAdos": "/usr/local/bin/RNAdos", + "RNAduplex": "/usr/local/bin/RNAduplex", + "RNAeval": "/usr/local/bin/RNAeval", + "RNAfold": "/usr/local/bin/RNAfold", + "RNAforester": "/usr/local/bin/RNAforester", + "RNAheat": "/usr/local/bin/RNAheat", + "RNAinverse": "/usr/local/bin/RNAinverse", + "RNAlocmin": "/usr/local/bin/RNAlocmin", + "RNAmultifold": "/usr/local/bin/RNAmultifold", + "RNApaln": "/usr/local/bin/RNApaln", + "RNAparconv": "/usr/local/bin/RNAparconv", + "RNApdist": "/usr/local/bin/RNApdist", + "RNAplex": "/usr/local/bin/RNAplex", + "RNAplfold": "/usr/local/bin/RNAplfold", + "RNAplot": "/usr/local/bin/RNAplot", + "RNApvmin": "/usr/local/bin/RNApvmin", + "RNAsnoop": "/usr/local/bin/RNAsnoop", + "RNAsubopt": "/usr/local/bin/RNAsubopt", + "RNAup": "/usr/local/bin/RNAup", + "TMalign": "/usr/local/bin/TMalign", + "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", + "annotate": "/usr/local/bin/annotate", + "archive-ncbinlp": "/usr/local/bin/archive-ncbinlp", + "archive-nihocc": "/usr/local/bin/archive-nihocc", + "archive-nmcds": "/usr/local/bin/archive-nmcds", + "archive-pmc": "/usr/local/bin/archive-pmc", + "archive-pubmed": "/usr/local/bin/archive-pubmed", + "archive-taxonomy": "/usr/local/bin/archive-taxonomy", + "args2slice": "/usr/local/bin/args2slice", + "asn2ref": "/usr/local/bin/asn2ref", + "asn2xml": "/usr/local/bin/asn2xml", + "autopoint": "/usr/local/bin/autopoint", + "awk": "/usr/local/bin/awk", + "b2ct": "/usr/local/bin/b2ct", + "bamToGBrowse.pl": "/usr/local/bin/bamToGBrowse.pl", + "baseml": "/usr/local/bin/baseml", + "basemlg": "/usr/local/bin/basemlg", + "bdf2gdfont.pl": "/usr/local/bin/bdf2gdfont.pl", + "bdftogd": "/usr/local/bin/bdftogd", + "between-two-genes": "/usr/local/bin/between-two-genes", + "bl2seq": "/usr/local/bin/bl2seq", + "blast_formatter": "/usr/local/bin/blast_formatter", + "blastall": "/usr/local/bin/blastall", + "blastclust": "/usr/local/bin/blastclust", + "blastdb_aliastool": "/usr/local/bin/blastdb_aliastool", + "blastdbcheck": "/usr/local/bin/blastdbcheck", + "blastdbcmd": "/usr/local/bin/blastdbcmd", + "blastn": "/usr/local/bin/blastn", + "blastn_vdb": "/usr/local/bin/blastn_vdb", + "blastp": "/usr/local/bin/blastp", + "blastpgp": "/usr/local/bin/blastpgp", + "blastx": "/usr/local/bin/blastx", + "blst2gm": "/usr/local/bin/blst2gm", + "blst2tkns": "/usr/local/bin/blst2tkns", + "bp_aacomp": "/usr/local/bin/bp_aacomp", + "bp_bioflat_index": "/usr/local/bin/bp_bioflat_index", + "bp_biogetseq": "/usr/local/bin/bp_biogetseq", + "bp_dbsplit": "/usr/local/bin/bp_dbsplit", + "bp_extract_feature_seq": "/usr/local/bin/bp_extract_feature_seq", + "bp_fastam9_to_table": "/usr/local/bin/bp_fastam9_to_table", + "bp_fetch": "/usr/local/bin/bp_fetch", + "bp_filter_search": "/usr/local/bin/bp_filter_search", + "bp_find-blast-matches": "/usr/local/bin/bp_find-blast-matches", + "bp_gccalc": "/usr/local/bin/bp_gccalc", + "bp_genbank2gff3": "/usr/local/bin/bp_genbank2gff3", + "bp_hmmer_to_table.pl": "/usr/local/bin/bp_hmmer_to_table.pl", + "bp_index": "/usr/local/bin/bp_index", + "bp_local_taxonomydb_query": "/usr/local/bin/bp_local_taxonomydb_query", + "bp_make_mrna_protein": "/usr/local/bin/bp_make_mrna_protein", + "bp_mask_by_search": "/usr/local/bin/bp_mask_by_search", + "bp_mrtrans": "/usr/local/bin/bp_mrtrans", + "bp_mutate": "/usr/local/bin/bp_mutate", + "bp_nexus2nh": "/usr/local/bin/bp_nexus2nh", + "bp_nrdb": "/usr/local/bin/bp_nrdb", + "bp_oligo_count": "/usr/local/bin/bp_oligo_count", + "bp_pairwise_kaks": "/usr/local/bin/bp_pairwise_kaks", + "bp_parse_hmmsearch.pl": "/usr/local/bin/bp_parse_hmmsearch.pl", + "bp_process_gadfly": "/usr/local/bin/bp_process_gadfly", + "bp_process_sgd": "/usr/local/bin/bp_process_sgd", + "bp_revtrans-motif": "/usr/local/bin/bp_revtrans-motif", + "bp_search2alnblocks": "/usr/local/bin/bp_search2alnblocks", + "bp_search2gff": "/usr/local/bin/bp_search2gff", + "bp_search2table": "/usr/local/bin/bp_search2table", + "bp_search2tribe": "/usr/local/bin/bp_search2tribe", + "bp_seq_length": "/usr/local/bin/bp_seq_length", + "bp_seqconvert": "/usr/local/bin/bp_seqconvert", + "bp_seqcut": "/usr/local/bin/bp_seqcut", + "bp_seqpart": "/usr/local/bin/bp_seqpart", + "bp_seqret": "/usr/local/bin/bp_seqret", + "bp_seqretsplit": "/usr/local/bin/bp_seqretsplit", + "bp_split_seq": "/usr/local/bin/bp_split_seq", + "bp_sreformat": "/usr/local/bin/bp_sreformat", + "bp_taxid4species": "/usr/local/bin/bp_taxid4species", + "bp_taxonomy2tree": "/usr/local/bin/bp_taxonomy2tree", + "bp_translate_seq": "/usr/local/bin/bp_translate_seq", + "bp_tree2pag": "/usr/local/bin/bp_tree2pag", + "bp_unflatten_seq": "/usr/local/bin/bp_unflatten_seq", + "bunzip2": "/usr/local/bin/bunzip2", + "bzcat": "/usr/local/bin/bzcat", + "bzcmp": "/usr/local/bin/bzcmp", + "bzdiff": "/usr/local/bin/bzdiff", + "bzegrep": "/usr/local/bin/bzegrep", + "bzfgrep": "/usr/local/bin/bzfgrep", + "bzgrep": "/usr/local/bin/bzgrep", + "bzip2": "/usr/local/bin/bzip2", + "bzip2recover": "/usr/local/bin/bzip2recover", + "bzless": "/usr/local/bin/bzless", + "bzmore": "/usr/local/bin/bzmore", + "c_rehash": "/usr/local/bin/c_rehash", + "captoinfo": "/usr/local/bin/captoinfo", + "chi2": "/usr/local/bin/chi2", + "chrom_sizes.pl": "/usr/local/bin/chrom_sizes.pl", + "cit2pmid": "/usr/local/bin/cit2pmid", + "cjpeg": "/usr/local/bin/cjpeg", + "cleanup-blastdb-volumes.py": "/usr/local/bin/cleanup-blastdb-volumes.py", + "clear": "/usr/local/bin/clear", + "clustalo": "/usr/local/bin/clustalo", + "clustalw": "/usr/local/bin/clustalw", + "clustalw2": "/usr/local/bin/clustalw2", + "codeml": "/usr/local/bin/codeml", + "combine-uid-lists": "/usr/local/bin/combine-uid-lists", + "compile_et": "/usr/local/bin/compile_et", + "config_data": "/usr/local/bin/config_data", + "convert2blastmask": "/usr/local/bin/convert2blastmask", + "copymat": "/usr/local/bin/copymat", + "corelist": "/usr/local/bin/corelist", + "cpan": "/usr/local/bin/cpan", + "csv2xml": "/usr/local/bin/csv2xml", + "ct2db": "/usr/local/bin/ct2db", + "curl": "/usr/local/bin/curl", + "curl-config": "/usr/local/bin/curl-config", + "cwebp": "/usr/local/bin/cwebp", + "datatool": "/usr/local/bin/datatool", + "db_archive": "/usr/local/bin/db_archive", + "db_checkpoint": "/usr/local/bin/db_checkpoint", + "db_convert": "/usr/local/bin/db_convert", + "db_deadlock": "/usr/local/bin/db_deadlock", + "db_dump": "/usr/local/bin/db_dump", + "db_hotbackup": "/usr/local/bin/db_hotbackup", + "db_load": "/usr/local/bin/db_load", + "db_log_verify": "/usr/local/bin/db_log_verify", + "db_printlog": "/usr/local/bin/db_printlog", + "db_recover": "/usr/local/bin/db_recover", + "db_replicate": "/usr/local/bin/db_replicate", + "db_stat": "/usr/local/bin/db_stat", + "db_tuner": "/usr/local/bin/db_tuner", + "db_upgrade": "/usr/local/bin/db_upgrade", + "db_verify": "/usr/local/bin/db_verify", + "deltablast": "/usr/local/bin/deltablast", + "derb": "/usr/local/bin/derb", + "deripcal": "/usr/local/bin/deripcal", + "difference-uid-lists": "/usr/local/bin/difference-uid-lists", + "disambiguate-nucleotides": "/usr/local/bin/disambiguate-nucleotides", + "djpeg": "/usr/local/bin/djpeg", + "download-ncbi-data": "/usr/local/bin/download-ncbi-data", + "download-ncbi-software": "/usr/local/bin/download-ncbi-software", + "download-pmc": "/usr/local/bin/download-pmc", + "download-pubmed": "/usr/local/bin/download-pubmed", + "download-sequence": "/usr/local/bin/download-sequence", + "ds2pme": "/usr/local/bin/ds2pme", + "dustmasker": "/usr/local/bin/dustmasker", + "dwebp": "/usr/local/bin/dwebp", + "ecommon.sh": "/usr/local/bin/ecommon.sh", + "efetch": "/usr/local/bin/efetch", + "efilter": "/usr/local/bin/efilter", + "einfo": "/usr/local/bin/einfo", + "einsi": "/usr/local/bin/einsi", + "elink": "/usr/local/bin/elink", + "enc2xs": "/usr/local/bin/enc2xs", + "encguess": "/usr/local/bin/encguess", + "envsubst": "/usr/local/bin/envsubst", + "epost": "/usr/local/bin/epost", + "esample": "/usr/local/bin/esample", + "esearch": "/usr/local/bin/esearch", + "esummary": "/usr/local/bin/esummary", + "evolver": "/usr/local/bin/evolver", + "exclude-uid-lists": "/usr/local/bin/exclude-uid-lists", + "expand-current": "/usr/local/bin/expand-current", + "fastacmd": "/usr/local/bin/fastacmd", + "fc-cache": "/usr/local/bin/fc-cache", + "fc-cat": "/usr/local/bin/fc-cat", + "fc-conflist": "/usr/local/bin/fc-conflist", + "fc-list": "/usr/local/bin/fc-list", + "fc-match": "/usr/local/bin/fc-match", + "fc-pattern": "/usr/local/bin/fc-pattern", + "fc-query": "/usr/local/bin/fc-query", + "fc-scan": "/usr/local/bin/fc-scan", + "fc-validate": "/usr/local/bin/fc-validate", + "fetch-local": "/usr/local/bin/fetch-local", + "fetch-nmcds": "/usr/local/bin/fetch-nmcds", + "fetch-pmc": "/usr/local/bin/fetch-pmc", + "fetch-pubmed": "/usr/local/bin/fetch-pubmed", + "fetch-taxonomy": "/usr/local/bin/fetch-taxonomy", + "fftns": "/usr/local/bin/fftns", + "fftnsi": "/usr/local/bin/fftnsi", + "filter-columns": "/usr/local/bin/filter-columns", + "filter-genbank": "/usr/local/bin/filter-genbank", + "filter-record": "/usr/local/bin/filter-record", + "filter-stop-words": "/usr/local/bin/filter-stop-words", + "find-in-gene": "/usr/local/bin/find-in-gene", + "formatdb": "/usr/local/bin/formatdb", + "formatrpsdb": "/usr/local/bin/formatrpsdb", + "freetype-config": "/usr/local/bin/freetype-config", + "fuse-ranges": "/usr/local/bin/fuse-ranges", + "fuse-segments": "/usr/local/bin/fuse-segments", + "gawk": "/usr/local/bin/gawk", + "gawk-5.3.0": "/usr/local/bin/gawk-5.3.0", + "gawkbug": "/usr/local/bin/gawkbug", + "gbf2fsa": "/usr/local/bin/gbf2fsa", + "gbf2ref": "/usr/local/bin/gbf2ref", + "gbf2xml": "/usr/local/bin/gbf2xml", + "gd2copypal": "/usr/local/bin/gd2copypal", + "gd2togif": "/usr/local/bin/gd2togif", + "gd2topng": "/usr/local/bin/gd2topng", + "gdcmpgif": "/usr/local/bin/gdcmpgif", + "gdparttopng": "/usr/local/bin/gdparttopng", + "gdtopng": "/usr/local/bin/gdtopng", + "genbrk": "/usr/local/bin/genbrk", + "gencfu": "/usr/local/bin/gencfu", + "gencnval": "/usr/local/bin/gencnval", + "gendict": "/usr/local/bin/gendict", + "gene2range": "/usr/local/bin/gene2range", + "genomeCoverageBed.pl": "/usr/local/bin/genomeCoverageBed.pl", + "genrb": "/usr/local/bin/genrb", + "get_species_taxids.sh": "/usr/local/bin/get_species_taxids.sh", + "get_species_taxids.sh.bak": "/usr/local/bin/get_species_taxids.sh.bak", + "gettext": "/usr/local/bin/gettext", + "gettext.sh": "/usr/local/bin/gettext.sh", + "gettextize": "/usr/local/bin/gettextize", + "gif2rgb": "/usr/local/bin/gif2rgb", + "gif2webp": "/usr/local/bin/gif2webp", + "gifbuild": "/usr/local/bin/gifbuild", + "gifclrmp": "/usr/local/bin/gifclrmp", + "giffix": "/usr/local/bin/giffix", + "giftext": "/usr/local/bin/giftext", + "giftogd2": "/usr/local/bin/giftogd2", + "giftool": "/usr/local/bin/giftool", + "ginsi": "/usr/local/bin/ginsi", + "gm2ranges": "/usr/local/bin/gm2ranges", + "gm2segs": "/usr/local/bin/gm2segs", + "gss-client": "/usr/local/bin/gss-client", + "h2ph": "/usr/local/bin/h2ph", + "h2xs": "/usr/local/bin/h2xs", + "hgvs2spdi": "/usr/local/bin/hgvs2spdi", + "icu-config": "/usr/local/bin/icu-config", + "icuexportdata": "/usr/local/bin/icuexportdata", + "icuinfo": "/usr/local/bin/icuinfo", + "idle3": "/usr/local/bin/idle3", + "idle3.10": "/usr/local/bin/idle3.10", + "idn2": "/usr/local/bin/idn2", + "img2webp": "/usr/local/bin/img2webp", + "impala": "/usr/local/bin/impala", + "infinitesites": "/usr/local/bin/infinitesites", + "infocmp": "/usr/local/bin/infocmp", + "infotocap": "/usr/local/bin/infotocap", + "ini2xml": "/usr/local/bin/ini2xml", + "instmodsh": "/usr/local/bin/instmodsh", + "intersect-uid-lists": "/usr/local/bin/intersect-uid-lists", + "join-into-groups-of": "/usr/local/bin/join-into-groups-of", + "jpegtran": "/usr/local/bin/jpegtran", + "json2xml": "/usr/local/bin/json2xml", + "json_pp": "/usr/local/bin/json_pp", + "json_xs": "/usr/local/bin/json_xs", + "jsonl2xml": "/usr/local/bin/jsonl2xml", + "just-first-key": "/usr/local/bin/just-first-key", + "k5srvutil": "/usr/local/bin/k5srvutil", + "kadmin": "/usr/local/bin/kadmin", + "kdestroy": "/usr/local/bin/kdestroy", + "keyctl": "/usr/local/bin/keyctl", + "kinit": "/usr/local/bin/kinit", + "kinwalker": "/usr/local/bin/kinwalker", + "klist": "/usr/local/bin/klist", + "kpasswd": "/usr/local/bin/kpasswd", + "krb5-config": "/usr/local/bin/krb5-config", + "ksu": "/usr/local/bin/ksu", + "kswitch": "/usr/local/bin/kswitch", + "ktutil": "/usr/local/bin/ktutil", + "kvno": "/usr/local/bin/kvno", + "legacy_blast.pl": "/usr/local/bin/legacy_blast.pl", + "libdeflate-gunzip": "/usr/local/bin/libdeflate-gunzip", + "libdeflate-gzip": "/usr/local/bin/libdeflate-gzip", + "libnetcfg": "/usr/local/bin/libnetcfg", + "libpng-config": "/usr/local/bin/libpng-config", + "libpng16-config": "/usr/local/bin/libpng16-config", + "linsi": "/usr/local/bin/linsi", + "lwp-download": "/usr/local/bin/lwp-download", + "lwp-dump": "/usr/local/bin/lwp-dump", + "lwp-mirror": "/usr/local/bin/lwp-mirror", + "lwp-request": "/usr/local/bin/lwp-request", + "lzcat": "/usr/local/bin/lzcat", + "lzcmp": "/usr/local/bin/lzcmp", + "lzdiff": "/usr/local/bin/lzdiff", + "lzegrep": "/usr/local/bin/lzegrep", + "lzfgrep": "/usr/local/bin/lzfgrep", + "lzgrep": "/usr/local/bin/lzgrep", + "lzless": "/usr/local/bin/lzless", + "lzma": "/usr/local/bin/lzma", + "lzmadec": "/usr/local/bin/lzmadec", + "lzmainfo": "/usr/local/bin/lzmainfo", + "lzmore": "/usr/local/bin/lzmore", + "mafft": "/usr/local/bin/mafft", + "mafft-distance": "/usr/local/bin/mafft-distance", + "mafft-einsi": "/usr/local/bin/mafft-einsi", + "mafft-fftns": "/usr/local/bin/mafft-fftns", + "mafft-fftnsi": "/usr/local/bin/mafft-fftnsi", + "mafft-ginsi": "/usr/local/bin/mafft-ginsi", + "mafft-homologs.rb": "/usr/local/bin/mafft-homologs.rb", + "mafft-linsi": "/usr/local/bin/mafft-linsi", + "mafft-nwns": "/usr/local/bin/mafft-nwns", + "mafft-nwnsi": "/usr/local/bin/mafft-nwnsi", + "mafft-profile": "/usr/local/bin/mafft-profile", + "mafft-qinsi": "/usr/local/bin/mafft-qinsi", + "mafft-sparsecore.rb": "/usr/local/bin/mafft-sparsecore.rb", + "mafft-xinsi": "/usr/local/bin/mafft-xinsi", + "make_pscores.pl": "/usr/local/bin/make_pscores.pl", + "makeblastdb": "/usr/local/bin/makeblastdb", + "makeconv": "/usr/local/bin/makeconv", + "makemat": "/usr/local/bin/makemat", + "makembindex": "/usr/local/bin/makembindex", + "makeprofiledb": "/usr/local/bin/makeprofiledb", + "mcmctree": "/usr/local/bin/mcmctree", + "megablast": "/usr/local/bin/megablast", + "msgattrib": "/usr/local/bin/msgattrib", + "msgcat": "/usr/local/bin/msgcat", + "msgcmp": "/usr/local/bin/msgcmp", + "msgcomm": "/usr/local/bin/msgcomm", + "msgconv": "/usr/local/bin/msgconv", + "msgen": "/usr/local/bin/msgen", + "msgexec": "/usr/local/bin/msgexec", + "msgfilter": "/usr/local/bin/msgfilter", + "msgfmt": "/usr/local/bin/msgfmt", + "msggrep": "/usr/local/bin/msggrep", + "msginit": "/usr/local/bin/msginit", + "msgmerge": "/usr/local/bin/msgmerge", + "msgunfmt": "/usr/local/bin/msgunfmt", + "msguniq": "/usr/local/bin/msguniq", + "muscle": "/usr/local/bin/muscle", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-config", + "ngettext": "/usr/local/bin/ngettext", + "nghttp": "/usr/local/bin/nghttp", + "nghttpd": "/usr/local/bin/nghttpd", + "nghttpx": "/usr/local/bin/nghttpx", + "nhance.sh": "/usr/local/bin/nhance.sh", + "nquire": "/usr/local/bin/nquire", + "nwns": "/usr/local/bin/nwns", + "nwnsi": "/usr/local/bin/nwnsi", + "openssl": "/usr/local/bin/openssl", + "pamp": "/usr/local/bin/pamp", + "pcre-config": "/usr/local/bin/pcre-config", + "pcregrep": "/usr/local/bin/pcregrep", + "pcretest": "/usr/local/bin/pcretest", + "perl": "/usr/local/bin/perl", + "perl5.32.1": "/usr/local/bin/perl5.32.1", + "perlbug": "/usr/local/bin/perlbug", + "perldoc": "/usr/local/bin/perldoc", + "perlivp": "/usr/local/bin/perlivp", + "perlthanks": "/usr/local/bin/perlthanks", + "phrase-search": "/usr/local/bin/phrase-search", + "piconv": "/usr/local/bin/piconv", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "pkgdata": "/usr/local/bin/pkgdata", + "pl2pm": "/usr/local/bin/pl2pm", + "pma2apa": "/usr/local/bin/pma2apa", + "pma2pme": "/usr/local/bin/pma2pme", + "pmc2bioc": "/usr/local/bin/pmc2bioc", + "pmc2info": "/usr/local/bin/pmc2info", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "pngtogd": "/usr/local/bin/pngtogd", + "pngtogd2": "/usr/local/bin/pngtogd2", + "poa": "/usr/local/bin/poa", + "pod2html": "/usr/local/bin/pod2html", + "pod2man": "/usr/local/bin/pod2man", + "pod2text": "/usr/local/bin/pod2text", + "pod2usage": "/usr/local/bin/pod2usage", + "podchecker": "/usr/local/bin/podchecker", + "popt": "/usr/local/bin/popt", + "print-columns": "/usr/local/bin/print-columns", + "project_tree_builder": "/usr/local/bin/project_tree_builder", + "prove": "/usr/local/bin/prove", + "psiblast": "/usr/local/bin/psiblast", + "ptar": "/usr/local/bin/ptar", + "ptardiff": "/usr/local/bin/ptardiff", + "ptargrep": "/usr/local/bin/ptargrep", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.10": "/usr/local/bin/pydoc3.10", + "python": "/usr/local/bin/python", + "python3": "/usr/local/bin/python3", + "python3-config": "/usr/local/bin/python3-config", + "python3.1": "/usr/local/bin/python3.1", + "python3.10": "/usr/local/bin/python3.10", + "python3.10-config": "/usr/local/bin/python3.10-config", + "quote-grouped-elements": "/usr/local/bin/quote-grouped-elements", + "rchive": "/usr/local/bin/rchive", + "rchive.Linux": "/usr/local/bin/rchive.Linux", + "rdjpgcom": "/usr/local/bin/rdjpgcom", + "recode-sr-latin": "/usr/local/bin/recode-sr-latin", + "ref2pmid": "/usr/local/bin/ref2pmid", + "refseq-nm-cds": "/usr/local/bin/refseq-nm-cds", + "reorder-columns": "/usr/local/bin/reorder-columns", + "reset": "/usr/local/bin/reset", + "ripcal": "/usr/local/bin/ripcal", + "ripcal.bak": "/usr/local/bin/ripcal.bak", + "ripcal_summarise": "/usr/local/bin/ripcal_summarise", + "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", + "seedtop": "/usr/local/bin/seedtop", + "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", + "t_coffee": "/usr/local/bin/t_coffee", + "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", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "toml2xml": "/usr/local/bin/toml2xml", + "tput": "/usr/local/bin/tput", + "transmute": "/usr/local/bin/transmute", + "transmute.Linux": "/usr/local/bin/transmute.Linux", + "tset": "/usr/local/bin/tset", + "uniq-table": "/usr/local/bin/uniq-table", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "update_blastdb.pl": "/usr/local/bin/update_blastdb.pl", + "update_blastdb.pl.bak": "/usr/local/bin/update_blastdb.pl.bak", + "uuclient": "/usr/local/bin/uuclient", + "webpinfo": "/usr/local/bin/webpinfo", + "webpmux": "/usr/local/bin/webpmux", + "webpng": "/usr/local/bin/webpng", + "wget": "/usr/local/bin/wget", + "wheel": "/usr/local/bin/wheel", + "windowmasker": "/usr/local/bin/windowmasker", + "windowmasker_2.2.22_adapter.py": "/usr/local/bin/windowmasker_2.2.22_adapter.py", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "word-at-a-time": "/usr/local/bin/word-at-a-time", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xgettext": "/usr/local/bin/xgettext", + "xml2fsa": "/usr/local/bin/xml2fsa", + "xml2json": "/usr/local/bin/xml2json", + "xml2tbl": "/usr/local/bin/xml2tbl", + "xmlwf": "/usr/local/bin/xmlwf", + "xsubpp": "/usr/local/bin/xsubpp", + "xtract": "/usr/local/bin/xtract", + "xtract.Linux": "/usr/local/bin/xtract.Linux", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "yaml2xml": "/usr/local/bin/yaml2xml", + "yn00": "/usr/local/bin/yn00", + "zipdetails": "/usr/local/bin/zipdetails", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file diff --git a/quay.io/biocontainers/s/sigprofilermatrixgenerator:1.2.26--pyhdfd78af_0.json b/quay.io/biocontainers/s/sigprofilermatrixgenerator:1.2.26--pyhdfd78af_0.json new file mode 100644 index 0000000..fc23aaf --- /dev/null +++ b/quay.io/biocontainers/s/sigprofilermatrixgenerator:1.2.26--pyhdfd78af_0.json @@ -0,0 +1,114 @@ +{ + "2to3": "/usr/local/bin/2to3", + "2to3-3.11": "/usr/local/bin/2to3-3.11", + "SigProfilerMatrixGenerator": "/usr/local/bin/SigProfilerMatrixGenerator", + "SigProfilerPlotting": "/usr/local/bin/SigProfilerPlotting", + "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", + "fonttools": "/usr/local/bin/fonttools", + "freetype-config": "/usr/local/bin/freetype-config", + "idle3": "/usr/local/bin/idle3", + "idle3.11": "/usr/local/bin/idle3.11", + "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", + "ncurses6-config": "/usr/local/bin/ncurses6-config", + "ncursesw6-config": "/usr/local/bin/ncursesw6-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", + "pip": "/usr/local/bin/pip", + "pip3": "/usr/local/bin/pip3", + "png-fix-itxt": "/usr/local/bin/png-fix-itxt", + "pngfix": "/usr/local/bin/pngfix", + "psicc": "/usr/local/bin/psicc", + "pydoc": "/usr/local/bin/pydoc", + "pydoc3": "/usr/local/bin/pydoc3", + "pydoc3.11": "/usr/local/bin/pydoc3.11", + "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", + "python3.11": "/usr/local/bin/python3.11", + "python3.11-config": "/usr/local/bin/python3.11-config", + "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", + "tiffcp": "/usr/local/bin/tiffcp", + "tiffdump": "/usr/local/bin/tiffdump", + "tiffinfo": "/usr/local/bin/tiffinfo", + "tiffset": "/usr/local/bin/tiffset", + "tiffsplit": "/usr/local/bin/tiffsplit", + "tificc": "/usr/local/bin/tificc", + "tjbench": "/usr/local/bin/tjbench", + "toe": "/usr/local/bin/toe", + "tput": "/usr/local/bin/tput", + "transicc": "/usr/local/bin/transicc", + "tset": "/usr/local/bin/tset", + "ttx": "/usr/local/bin/ttx", + "unlzma": "/usr/local/bin/unlzma", + "unxz": "/usr/local/bin/unxz", + "unzstd": "/usr/local/bin/unzstd", + "wheel": "/usr/local/bin/wheel", + "wish": "/usr/local/bin/wish", + "wish8.6": "/usr/local/bin/wish8.6", + "wrjpgcom": "/usr/local/bin/wrjpgcom", + "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld", + "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld", + "xz": "/usr/local/bin/xz", + "xzcat": "/usr/local/bin/xzcat", + "xzcmp": "/usr/local/bin/xzcmp", + "xzdec": "/usr/local/bin/xzdec", + "xzdiff": "/usr/local/bin/xzdiff", + "xzegrep": "/usr/local/bin/xzegrep", + "xzfgrep": "/usr/local/bin/xzfgrep", + "xzgrep": "/usr/local/bin/xzgrep", + "xzless": "/usr/local/bin/xzless", + "xzmore": "/usr/local/bin/xzmore", + "zstd": "/usr/local/bin/zstd", + "zstdcat": "/usr/local/bin/zstdcat", + "zstdgrep": "/usr/local/bin/zstdgrep", + "zstdless": "/usr/local/bin/zstdless", + "zstdmt": "/usr/local/bin/zstdmt", + "env-execute": "/usr/local/env-execute" +} \ No newline at end of file