From e0af7fdafe0d1430b96ba36342f8c165c60e60a1 Mon Sep 17 00:00:00 2001
From: github-actions <github-actions@users.noreply.github.com>
Date: Mon, 6 May 2024 00:42:23 +0000
Subject: [PATCH] Automated deployment with updated cache 2024-05-06

---
 counts.json                                   | 688 +++++++++---------
 .../c/crocodeel:1.0.2--pyhdfd78af_0.json      | 114 +++
 .../s/sccmec:1.0.0--hdfd78af_0.json           | 315 ++++++++
 3 files changed, 775 insertions(+), 342 deletions(-)
 create mode 100644 quay.io/biocontainers/c/crocodeel:1.0.2--pyhdfd78af_0.json
 create mode 100644 quay.io/biocontainers/s/sccmec:1.0.0--hdfd78af_0.json

diff --git a/counts.json b/counts.json
index b19ea91..0df920a 100644
--- a/counts.json
+++ b/counts.json
@@ -2326,10 +2326,10 @@
     "2csfastq_1csfastq": 1,
     "2ft": 2,
     "2ndscore": 1,
-    "2to3": 3618,
+    "2to3": 3620,
     "2to3-3.10": 795,
     "2to3-3.11": 263,
-    "2to3-3.12": 171,
+    "2to3-3.12": 173,
     "2to3-3.4": 6,
     "2to3-3.5": 103,
     "2to3-3.6": 342,
@@ -4895,7 +4895,7 @@
     "abyss-tofastq": 17,
     "ac-diamond": 1,
     "accession_retrieve": 1,
-    "accn-at-a-time": 254,
+    "accn-at-a-time": 255,
     "accurate_bkp.py": 1,
     "acdc": 25,
     "acdc-filter-fasta-by-name.awk": 1,
@@ -4997,7 +4997,7 @@
     "addtit.pl": 2,
     "adf_checker.pl": 1,
     "adhocfilelist": 1,
-    "adig": 4481,
+    "adig": 4482,
     "adjustPeakFile.pl": 5,
     "adjustRedunGroupFile.pl": 5,
     "adjustScanRankerScoreByGroup": 2,
@@ -5113,7 +5113,7 @@
     "agrvate": 1,
     "agtsampleinforw.dll": 2,
     "ahmm-s": 1,
-    "ahost": 4481,
+    "ahost": 4482,
     "airr-tools": 5,
     "akita_data.py": 1,
     "akita_data_read.py": 1,
@@ -5156,7 +5156,7 @@
     "align-cache.2.11.0": 9,
     "align-cache.3": 2,
     "align-cache.3.0.0": 2,
-    "align-columns": 197,
+    "align-columns": 198,
     "align-ema.smk": 1,
     "align-families.py": 1,
     "align-info": 21,
@@ -5279,7 +5279,7 @@
     "amdgpu-arch": 1,
     "ame": 13,
     "amgr": 1,
-    "amino-acid-composition": 285,
+    "amino-acid-composition": 286,
     "aminoextract": 2,
     "amk_ccc": 2,
     "amk_fft2": 2,
@@ -5709,12 +5709,12 @@
     "arcasHLA": 1,
     "archer": 1,
     "architeuthis": 1,
-    "archive-ncbinlp": 9,
-    "archive-nihocc": 9,
-    "archive-nmcds": 9,
-    "archive-pmc": 9,
-    "archive-pubmed": 284,
-    "archive-taxonomy": 9,
+    "archive-ncbinlp": 10,
+    "archive-nihocc": 10,
+    "archive-nmcds": 10,
+    "archive-pmc": 10,
+    "archive-pubmed": 285,
+    "archive-taxonomy": 10,
     "archive_directory.py": 2,
     "archosv": 2,
     "archspec": 6,
@@ -5725,7 +5725,7 @@
     "argnorm": 1,
     "argparse2tool": 1,
     "argparse2tool_check_path": 1,
-    "args2slice": 9,
+    "args2slice": 10,
     "args_oap": 1,
     "aria2c": 17,
     "ariba": 3,
@@ -5802,8 +5802,8 @@
     "asn2ff": 1,
     "asn2gb": 2,
     "asn2idx": 1,
-    "asn2ref": 9,
-    "asn2xml": 198,
+    "asn2ref": 10,
+    "asn2xml": 199,
     "asndhuff": 1,
     "asntool": 1,
     "asp-cp": 87,
@@ -5905,7 +5905,7 @@
     "autometa-taxonomy-majority-vote": 2,
     "autometa-unclustered-recruitment": 2,
     "autometa-update-databases": 2,
-    "autopoint": 5267,
+    "autopoint": 5268,
     "autoreconf.bak": 10,
     "autoscan.bak": 10,
     "autoupdate.bak": 10,
@@ -6498,7 +6498,7 @@
     "beta_diversity.py": 4,
     "beta_diversity_through_plots.py": 1,
     "beta_significance.py": 1,
-    "between-two-genes": 285,
+    "between-two-genes": 286,
     "bf.sh": 1,
     "bfc": 1,
     "bfconvert": 1,
@@ -6706,7 +6706,7 @@
     "blast_check_pair.pl": 1,
     "blast_filter.pl": 1,
     "blast_format_unit_test": 5,
-    "blast_formatter": 317,
+    "blast_formatter": 318,
     "blast_names_mapping.tsv": 1,
     "blast_outfmt6_replace_trans_id_w_gene_symbol.pl": 1,
     "blast_report": 20,
@@ -6721,12 +6721,12 @@
     "blastbesties": 1,
     "blastcl3": 1,
     "blastclust": 30,
-    "blastdb_aliastool": 317,
+    "blastdb_aliastool": 318,
     "blastdb_convert": 20,
     "blastdb_format_unit_test": 5,
     "blastdb_path": 20,
-    "blastdbcheck": 317,
-    "blastdbcmd": 317,
+    "blastdbcheck": 318,
+    "blastdbcmd": 318,
     "blastdbcp": 52,
     "blastdiag_unit_test": 5,
     "blastengine_unit_test": 5,
@@ -6734,13 +6734,13 @@
     "blastfilter_unit_test": 5,
     "blasthits_unit_test": 5,
     "blastinput_unit_test": 5,
-    "blastn": 317,
-    "blastn_vdb": 32,
+    "blastn": 318,
+    "blastn_vdb": 33,
     "blastoptions_unit_test": 5,
-    "blastp": 317,
+    "blastp": 318,
     "blastpgp": 30,
     "blastsetup_unit_test": 5,
-    "blastx": 317,
+    "blastx": 318,
     "blastzWrapper": 1,
     "blat": 19,
     "blat2gbrowse.pl": 14,
@@ -6763,8 +6763,8 @@
     "blossom5": 1,
     "blossom_randGraph.py": 1,
     "blosum62.fas": 2,
-    "blst2gm": 9,
-    "blst2tkns": 197,
+    "blst2gm": 10,
+    "blst2tkns": 198,
     "bmaToLinks.pl": 1,
     "bmfilter": 4,
     "bmge": 1,
@@ -6982,7 +6982,7 @@
     "broad_utils.py": 1,
     "brockman_pipeline": 1,
     "brooklyn_plot": 1,
-    "brotli": 403,
+    "brotli": 404,
     "browse": 18,
     "bs_call": 2,
     "bs_seeker2-align.py": 1,
@@ -7079,7 +7079,7 @@
     "bundlelinks": 1,
     "bundler": 18,
     "bunwarpj": 4,
-    "bunzip2": 6568,
+    "bunzip2": 6570,
     "burden_test_vase": 1,
     "burst_linux_DB12": 1,
     "burst_linux_DB15": 1,
@@ -7130,16 +7130,16 @@
     "bxStats.py": 1,
     "bxcl_seqqc": 1,
     "bxtools": 1,
-    "bzcat": 6568,
-    "bzcmp": 6568,
-    "bzdiff": 6568,
-    "bzegrep": 6568,
-    "bzfgrep": 6568,
-    "bzgrep": 6568,
-    "bzip2": 6568,
-    "bzip2recover": 6568,
-    "bzless": 6568,
-    "bzmore": 6568,
+    "bzcat": 6570,
+    "bzcmp": 6570,
+    "bzdiff": 6570,
+    "bzegrep": 6570,
+    "bzfgrep": 6570,
+    "bzgrep": 6570,
+    "bzip2": 6570,
+    "bzip2recover": 6570,
+    "bzless": 6570,
+    "bzmore": 6570,
     "c++": 5,
     "c++filt": 8,
     "c-index-test": 8,
@@ -7156,7 +7156,7 @@
     "cPecanLibTests": 1,
     "cPecanModifyHmm": 1,
     "cPecanRealign": 1,
-    "c_rehash": 7717,
+    "c_rehash": 7719,
     "ca2ace.pl": 3,
     "ca2ctg": 2,
     "ca2mates": 2,
@@ -7296,7 +7296,9 @@
     "callvariants.sh": 30,
     "callvariants2.sh": 30,
     "cameo": 4,
-    "camlhmp": 1,
+    "camlhmp": 2,
+    "camlhmp-blast": 1,
+    "camlhmp-extract": 1,
     "campyagainst": 1,
     "campygstyper": 1,
     "canal": 2,
@@ -7330,7 +7332,7 @@
     "capnpc-c++": 52,
     "capnpc-capnp": 52,
     "capnpc-cython": 1,
-    "captoinfo": 7649,
+    "captoinfo": 7651,
     "captus_assembly": 1,
     "caqc.pl": 3,
     "caqc_help.ini": 3,
@@ -7763,10 +7765,10 @@
     "circulocov": 1,
     "cirdna": 24,
     "cirtap": 1,
-    "cit2pmid": 9,
+    "cit2pmid": 10,
     "civicpy": 1,
     "cjk-gs-integrate": 1,
-    "cjpeg": 5730,
+    "cjpeg": 5731,
     "ckeygen": 1,
     "cksum": 82,
     "claMLST": 1,
@@ -7868,11 +7870,11 @@
     "cleanmap.awk": 1,
     "cleanme.pl": 1,
     "cleanpp.sh": 3,
-    "cleanup-blastdb-volumes.py": 246,
+    "cleanup-blastdb-volumes.py": 247,
     "cleanup-coverage.py": 2,
     "cleanup-stale-gcp-resources.py": 1,
     "cleanup.py": 1,
-    "clear": 7649,
+    "clear": 7651,
     "clearCNV": 1,
     "clearcut": 1,
     "cleric": 1,
@@ -8107,7 +8109,7 @@
     "colorcet": 3,
     "colord": 1,
     "colored-matrix": 2,
-    "coloredlogs": 72,
+    "coloredlogs": 73,
     "colorinterpolate": 1,
     "colorrna.pl": 1,
     "colrm": 13,
@@ -8122,7 +8124,7 @@
     "combine": 4,
     "combine-assembled-files.sh": 1,
     "combine-subexons": 1,
-    "combine-uid-lists": 9,
+    "combine-uid-lists": 10,
     "combineAndAnnotateReferences.pl": 1,
     "combineFile": 2,
     "combineFragandDBGraph_fastg.py": 1,
@@ -8224,7 +8226,7 @@
     "compileSpliceCands": 12,
     "compile_STARE_Linux.sh": 1,
     "compile_STARE_macOS.sh": 1,
-    "compile_et": 5763,
+    "compile_et": 5764,
     "compiled_table.py": 1,
     "compleasm": 1,
     "complementBed": 269,
@@ -8407,7 +8409,7 @@
     "convert2bed-float128": 14,
     "convert2bed-megarow": 14,
     "convert2bed-typical": 14,
-    "convert2blastmask": 317,
+    "convert2blastmask": 318,
     "convert2snns": 2,
     "convertCoordinates.pl": 5,
     "convertFastaQualToFastQ.rb": 1,
@@ -8523,7 +8525,7 @@
     "core_diversity_analyses.py": 1,
     "core_methods.py": 1,
     "core_overlap_plot.py": 1,
-    "corelist": 1674,
+    "corelist": 1675,
     "corepack": 11,
     "coreprocess.pl": 3,
     "coresnpfilter": 1,
@@ -8627,7 +8629,7 @@
     "cp2k_run": 1,
     "cp2k_shell.ssmp": 1,
     "cpack": 11,
-    "cpan": 1674,
+    "cpan": 1675,
     "cpancover": 6,
     "cpanm": 242,
     "cpat.py": 1,
@@ -8766,6 +8768,7 @@
     "crlupdate": 15,
     "crnsimulator": 2,
     "croco-0.6-config": 8,
+    "crocodeel": 1,
     "cromshell": 1,
     "cromwell": 2,
     "cromwell-tools": 1,
@@ -8819,7 +8822,7 @@
     "csv2rdf": 32,
     "csv2tsv": 1,
     "csv2xlsx": 1,
-    "csv2xml": 197,
+    "csv2xml": 198,
     "csvExtractBorders": 1,
     "csvFrags2text": 1,
     "csv_to_tsv": 1,
@@ -8865,8 +8868,8 @@
     "curate_database.py": 1,
     "curate_universe": 1,
     "curesim": 2,
-    "curl": 5085,
-    "curl-config": 5879,
+    "curl": 5086,
+    "curl-config": 5880,
     "curlywhirly": 1,
     "curve_keygen": 68,
     "cusp": 24,
@@ -9014,7 +9017,7 @@
     "dataset_manager.py": 1,
     "datasets": 2,
     "datasets-cli": 2,
-    "datatool": 317,
+    "datatool": 318,
     "datavzrd": 2,
     "date": 82,
     "datma.py": 1,
@@ -9251,7 +9254,7 @@
     "deltaBS.pl": 1,
     "delta_filter_wrapper.py": 5,
     "delta_unit_test": 5,
-    "deltablast": 317,
+    "deltablast": 318,
     "deltapd": 1,
     "demes": 4,
     "demesdraw": 1,
@@ -9386,7 +9389,7 @@
     "diff_iso_usage": 1,
     "diff_motif": 1,
     "diffacto": 1,
-    "difference-uid-lists": 9,
+    "difference-uid-lists": 10,
     "difference_from_first_TSS_script_mordor.r": 1,
     "difference_from_first_TSS_script_mordor_chrom_wide.r": 1,
     "differentialBindingAffinity_multipleSNPs": 1,
@@ -9425,7 +9428,7 @@
     "dirmngr-client": 2,
     "dirname": 82,
     "dirseq": 2,
-    "disambiguate-nucleotides": 197,
+    "disambiguate-nucleotides": 198,
     "disco": 17,
     "disco.cfg": 1,
     "disco_2.cfg": 1,
@@ -9465,7 +9468,7 @@
     "django-admin": 4,
     "django-admin.py": 3,
     "django-admin.pyc": 1,
-    "djpeg": 5730,
+    "djpeg": 5731,
     "dkfzbiasfilter.py": 1,
     "dkfzbiasfilter_summarize.py": 1,
     "dlcoal_to_dlcpar": 1,
@@ -9576,15 +9579,15 @@
     "download-db.sh": 9,
     "download-dfam.py": 1,
     "download-entities.pl": 2,
-    "download-ncbi-data": 270,
+    "download-ncbi-data": 271,
     "download-ncbi-genomes": 1,
-    "download-ncbi-software": 197,
+    "download-ncbi-software": 198,
     "download-ncbi-taxa.sh": 1,
     "download-ncbi-taxmaps": 1,
     "download-ncbi-taxonomy": 1,
-    "download-pmc": 9,
-    "download-pubmed": 284,
-    "download-sequence": 284,
+    "download-pmc": 10,
+    "download-pubmed": 285,
+    "download-sequence": 285,
     "download-spatypes.sh": 1,
     "download-srr-files": 3,
     "download-taxonomy.sh": 1,
@@ -9684,7 +9687,7 @@
     "drtext": 24,
     "drttest": 1,
     "drugbank": 1,
-    "ds2pme": 9,
+    "ds2pme": 10,
     "dsCompareCurves": 1,
     "dsComputeBEDDensity": 1,
     "dsComputeGCCoverage": 1,
@@ -9821,7 +9824,7 @@
     "dupre": 1,
     "dupsifter": 1,
     "dust": 13,
-    "dustmasker": 317,
+    "dustmasker": 318,
     "dv_call_variants.py": 1,
     "dv_make_examples.py": 1,
     "dv_postprocess_variants.py": 1,
@@ -9910,7 +9913,7 @@
     "ecodbtaxstat": 1,
     "ecofind": 1,
     "ecogrep": 1,
-    "ecommon.sh": 197,
+    "ecommon.sh": 198,
     "econtact": 88,
     "ecotag": 1,
     "ecotaxspecificity": 1,
@@ -9946,9 +9949,9 @@
     "edonr256-hash": 9,
     "edonr512-hash": 9,
     "eel": 1,
-    "efetch": 285,
+    "efetch": 286,
     "effectivet3": 1,
-    "efilter": 285,
+    "efilter": 286,
     "efishent": 1,
     "efn": 1,
     "efn2": 5,
@@ -9964,7 +9967,7 @@
     "eigenstrat_database_tools": 1,
     "eigenstrat_rename_snps": 1,
     "eigenstrat_snp_coverage": 1,
-    "einfo": 285,
+    "einfo": 286,
     "einsi": 97,
     "einverted": 24,
     "eject": 13,
@@ -9993,7 +9996,7 @@
     "elfedit": 8,
     "elgato_report.py": 1,
     "eliminateBadSuperReadsUsingList": 1,
-    "elink": 285,
+    "elink": 286,
     "elm2meme": 13,
     "elprep": 1,
     "elsize": 6,
@@ -10028,8 +10031,8 @@
     "enano": 1,
     "enasearch": 1,
     "enc": 1,
-    "enc2xs": 1674,
-    "encguess": 1674,
+    "enc2xs": 1675,
+    "encguess": 1675,
     "encode2var": 1,
     "encode_dir": 1,
     "encode_exclude_loci": 1,
@@ -10061,7 +10064,7 @@
     "enumall": 1,
     "enumerate_paths.py": 1,
     "env": 82,
-    "env-execute": 6812,
+    "env-execute": 6814,
     "env.yml": 1,
     "env_parallel": 99,
     "env_parallel.ash": 99,
@@ -10078,7 +10081,7 @@
     "environment.yml": 1,
     "envpath": 3,
     "envset.cmd": 1,
-    "envsubst": 5267,
+    "envsubst": 5268,
     "eoulsan.sh": 1,
     "epa-ng": 4,
     "epestfind": 24,
@@ -10094,7 +10097,7 @@
     "epimuller-define": 1,
     "epimuller-draw": 1,
     "epimuller-parse": 1,
-    "epost": 285,
+    "epost": 286,
     "eprimer3": 24,
     "eprimer32": 24,
     "eproxy": 88,
@@ -10129,11 +10132,11 @@
     "errno": 3,
     "errorEstimate": 6,
     "error_corrected2frg": 1,
-    "esample": 270,
+    "esample": 271,
     "esbuild": 1,
     "esd2esi": 10,
     "esdcompat": 12,
-    "esearch": 285,
+    "esearch": 286,
     "esh": 1,
     "esimsa": 1,
     "esl-afetch": 163,
@@ -10192,7 +10195,7 @@
     "estscan": 1,
     "estwise": 3,
     "estwisedb": 3,
-    "esummary": 285,
+    "esummary": 286,
     "etandem": 24,
     "ete": 2,
     "ete3": 56,
@@ -10247,7 +10250,7 @@
     "excise_precursors.pl": 1,
     "excise_precursors_iterative_final.pl": 1,
     "excl_seqs": 2,
-    "exclude-uid-lists": 270,
+    "exclude-uid-lists": 271,
     "exclude_N": 1,
     "exclude_loci": 1,
     "exclude_loci_backup": 1,
@@ -10258,7 +10261,7 @@
     "exec-plugins.sh": 1,
     "exec_annotation": 2,
     "executeTestCGP.py": 9,
-    "executor": 10,
+    "executor": 11,
     "exiftool": 1,
     "existDB": 5,
     "exomiser-rest-prioritiser": 1,
@@ -10273,7 +10276,7 @@
     "expam": 1,
     "expam_limit": 1,
     "expand": 82,
-    "expand-current": 270,
+    "expand-current": 271,
     "expandCols": 269,
     "expand_fastq": 1,
     "expand_links.pl": 7,
@@ -10442,7 +10445,7 @@
     "ezez4makefile_v4.pl": 1,
     "ezez4qsub_vx1.pl": 1,
     "ezez_vx1.pl": 1,
-    "f2py": 2016,
+    "f2py": 2018,
     "f2py2": 135,
     "f2py2.7": 135,
     "f2py3": 1591,
@@ -10984,12 +10987,12 @@
     "fermi2.pl": 2,
     "fetch": 4,
     "fetch-extras": 73,
-    "fetch-local": 9,
-    "fetch-nmcds": 9,
-    "fetch-pmc": 9,
-    "fetch-pubmed": 284,
+    "fetch-local": 10,
+    "fetch-nmcds": 10,
+    "fetch-pmc": 10,
+    "fetch-pubmed": 285,
     "fetch-tax.pl": 1,
-    "fetch-taxonomy": 9,
+    "fetch-taxonomy": 10,
     "fetchChromSizes": 5,
     "fetchEnaLibraryFastqs.sh": 1,
     "fetchFastq.sh": 1,
@@ -11068,18 +11071,18 @@
     "filter-alignments.py": 1,
     "filter-bam": 2,
     "filter-bam-by-ids": 3,
-    "filter-columns": 185,
-    "filter-genbank": 9,
+    "filter-columns": 186,
+    "filter-genbank": 10,
     "filter-gff": 1,
     "filter-nonunique-peptide-matches": 2,
     "filter-positions.pl": 1,
     "filter-ppx.pl": 14,
-    "filter-record": 9,
+    "filter-record": 10,
     "filter-sort": 1,
     "filter-stage-1.prl": 4,
     "filter-stage-2.prl": 4,
     "filter-stats.pl": 1,
-    "filter-stop-words": 285,
+    "filter-stop-words": 286,
     "filter-stoptags.py": 7,
     "filter-table": 12,
     "filter-variations": 2,
@@ -11255,7 +11258,7 @@
     "find-all-symbols": 2,
     "find-compounds.pl": 1,
     "find-duplicate-reads": 2,
-    "find-in-gene": 197,
+    "find-in-gene": 198,
     "find-knots.py": 7,
     "find-mango-assembly.sh": 1,
     "find-mango-home": 1,
@@ -11464,7 +11467,7 @@
     "font-awesome-to-png": 2,
     "font2c": 3,
     "fontinst": 1,
-    "fonttools": 377,
+    "fonttools": 378,
     "fop": 1,
     "forceOneClusterPerPairMem.py": 1,
     "forest.py": 1,
@@ -11551,7 +11554,7 @@
     "freec": 1,
     "freec2bed.pl": 1,
     "freec2circos.pl": 1,
-    "freetype-config": 5792,
+    "freetype-config": 5793,
     "freeze_graph": 25,
     "freq2group.pl": 5,
     "frequency.py": 1,
@@ -11695,8 +11698,8 @@
     "funr": 1,
     "funzip": 25,
     "fuse": 1,
-    "fuse-ranges": 197,
-    "fuse-segments": 185,
+    "fuse-ranges": 198,
+    "fuse-segments": 186,
     "fuse.sh": 30,
     "fusion-bloom": 1,
     "fusion-bloom.makefile": 1,
@@ -11975,9 +11978,9 @@
     "gb2fasta": 1,
     "gbSmallDNA2gff.pl": 14,
     "gbase": 2,
-    "gbf2fsa": 9,
-    "gbf2ref": 9,
-    "gbf2xml": 284,
+    "gbf2fsa": 10,
+    "gbf2ref": 10,
+    "gbf2xml": 285,
     "gbf2xml.bak": 1,
     "gbfalncut": 2,
     "gbfcut": 2,
@@ -12144,7 +12147,7 @@
     "gendict": 5793,
     "gendist": 10,
     "gene2protein.db3": 2,
-    "gene2range": 185,
+    "gene2range": 186,
     "gene2xml": 1,
     "geneAssociationZscore.py": 1,
     "geneBody_coverage.py": 3,
@@ -12492,8 +12495,8 @@
     "get_sequence_type": 1,
     "get_sequences_for_meme.py": 1,
     "get_simple_cycs.py": 1,
-    "get_species_taxids.sh": 284,
-    "get_species_taxids.sh.bak": 279,
+    "get_species_taxids.sh": 285,
+    "get_species_taxids.sh.bak": 280,
     "get_standard_headers": 1,
     "get_stats_summary.pl": 1,
     "get_subontology_from.pl": 1,
@@ -12563,9 +12566,9 @@
     "getscu": 1,
     "getsize": 13,
     "getsnvfreq_by_interval": 1,
-    "gettext": 5267,
-    "gettext.sh": 5267,
-    "gettextize": 5267,
+    "gettext": 5268,
+    "gettext.sh": 5268,
+    "gettextize": 5268,
     "getuniqgenomealign": 1,
     "getuniqgenomealign_interval": 1,
     "getuniqgenomealign_sample_names": 1,
@@ -12741,8 +12744,8 @@
     "glpsol": 224,
     "glsearch36": 7,
     "gm": 2,
-    "gm2ranges": 9,
-    "gm2segs": 9,
+    "gm2ranges": 10,
+    "gm2segs": 10,
     "gmap": 13,
     "gmap.nosimd": 8,
     "gmap.sse42": 11,
@@ -13071,7 +13074,7 @@
     "gsnapl.sse42": 11,
     "gsnd": 104,
     "gsort": 5,
-    "gss-client": 5763,
+    "gss-client": 5764,
     "gss-server": 2,
     "gst-completion-helper": 1,
     "gst-device-monitor-1.0": 227,
@@ -13292,8 +13295,8 @@
     "h264dec": 9,
     "h264enc": 9,
     "h2load": 3929,
-    "h2ph": 1674,
-    "h2xs": 1674,
+    "h2ph": 1675,
+    "h2xs": 1675,
     "h4_ncdump": 122,
     "h4_ncgen": 122,
     "h4cc": 122,
@@ -13523,7 +13526,7 @@
     "hexdump": 13,
     "hgGcPercent": 3,
     "hgvs-shell": 1,
-    "hgvs2spdi": 197,
+    "hgvs2spdi": 198,
     "hhalign": 4,
     "hhalign_omp": 4,
     "hhblits": 4,
@@ -13786,7 +13789,7 @@
     "huge-split.pl": 1,
     "huggingface-cli": 2,
     "hulk": 1,
-    "humanfriendly": 101,
+    "humanfriendly": 102,
     "humann": 1,
     "humann2": 2,
     "humann2_associate": 1,
@@ -13948,10 +13951,10 @@
     "idfetch": 1,
     "idiag-socket-details": 8,
     "idle": 332,
-    "idle3": 3287,
+    "idle3": 3289,
     "idle3.10": 795,
     "idle3.11": 263,
-    "idle3.12": 171,
+    "idle3.12": 173,
     "idle3.4": 6,
     "idle3.5": 103,
     "idle3.6": 342,
@@ -13961,7 +13964,7 @@
     "idlj": 117,
     "idmatrix.sh": 30,
     "idn": 30,
-    "idn2": 255,
+    "idn2": 256,
     "idpAssemble": 2,
     "idpQonvert": 2,
     "idpQuery": 2,
@@ -14165,12 +14168,12 @@
     "infoalign": 24,
     "infoassembly": 24,
     "infobase": 24,
-    "infocmp": 7649,
+    "infocmp": 7651,
     "inforesidue": 24,
     "informant.py": 1,
     "infoseq": 24,
-    "infotocap": 7649,
-    "ini2xml": 9,
+    "infotocap": 7651,
+    "ini2xml": 10,
     "init_Trinotate_sqlite_db.pl": 1,
     "init_db.sh": 1,
     "initdb": 45,
@@ -14228,7 +14231,7 @@
     "installpackages.R": 1,
     "installvst": 15,
     "instance_events": 29,
-    "instmodsh": 1674,
+    "instmodsh": 1675,
     "int_seqs_to_char_strings.py": 58,
     "intake": 1,
     "intake-server": 1,
@@ -14263,7 +14266,7 @@
     "interprophet.rb": 1,
     "interproscan.sh": 1,
     "intersect": 5,
-    "intersect-uid-lists": 283,
+    "intersect-uid-lists": 284,
     "intersectBed": 269,
     "intersectFiles.py": 2,
     "intersectGenomicSets.py": 1,
@@ -14540,7 +14543,7 @@
     "jobTreeStatus": 2,
     "jobTreeTest_Dependencies.py": 1,
     "join": 82,
-    "join-into-groups-of": 285,
+    "join-into-groups-of": 286,
     "join-long-chromosomes": 3,
     "join.pl": 1,
     "join.pl.bak": 1,
@@ -14564,8 +14567,8 @@
     "jp.py": 100,
     "jpackage": 114,
     "jpeg2hdf": 122,
-    "jpegtran": 5730,
-    "jpgicc": 970,
+    "jpegtran": 5731,
+    "jpgicc": 971,
     "jpredapi": 1,
     "jps": 533,
     "jq": 300,
@@ -14577,12 +14580,12 @@
     "jsearch": 1,
     "jshell": 424,
     "json2gff": 1,
-    "json2xml": 197,
+    "json2xml": 198,
     "json_collect_data_source.py": 1,
-    "json_pp": 1674,
-    "json_xs": 343,
+    "json_pp": 1675,
+    "json_xs": 344,
     "jsondiff": 8,
-    "jsonl2xml": 9,
+    "jsonl2xml": 10,
     "jsonpatch": 8,
     "jsonpointer": 10,
     "jsonschema": 206,
@@ -14634,17 +14637,17 @@
     "jupyter-serverextension": 37,
     "jupyter-troubleshoot": 143,
     "jupyter-trust": 136,
-    "just-first-key": 9,
+    "just-first-key": 10,
     "just_blast_test.pl": 1,
     "jwebserver": 32,
-    "k5srvutil": 5763,
+    "k5srvutil": 5764,
     "k8": 159,
     "k8-Linux": 1,
     "k_means": 1,
     "k_means_coefficient": 1,
     "k_neighbors": 1,
     "k_neighbors_coefficient": 1,
-    "kadmin": 5763,
+    "kadmin": 5764,
     "kadmin.local": 2,
     "kadmind": 2,
     "kaiju": 4,
@@ -14738,7 +14741,7 @@
     "kdbmeta.3.0.0": 2,
     "kdbmeta.3.0.3": 1,
     "kdbmeta.3.1.0": 1,
-    "kdestroy": 5763,
+    "kdestroy": 5764,
     "kea-config": 35,
     "keep-header": 1,
     "keep-ribo-periodic": 1,
@@ -14748,7 +14751,7 @@
     "keggcharter.py": 1,
     "keggpathway_map.py": 1,
     "keyFreq": 1,
-    "keyctl": 2393,
+    "keyctl": 2394,
     "keygen": 1,
     "keyring": 10,
     "keytool": 533,
@@ -14779,7 +14782,7 @@
     "kinSimRiboswitch": 1,
     "king": 1,
     "kingfisher": 1,
-    "kinit": 5763,
+    "kinit": 5764,
     "kinship-read": 1,
     "kinshipDecompose": 1,
     "kinwalker": 48,
@@ -14792,7 +14795,7 @@
     "kitsch": 10,
     "kitsune": 1,
     "kleborate": 1,
-    "klist": 5763,
+    "klist": 5764,
     "kma": 18,
     "kma_index": 18,
     "kma_shm": 18,
@@ -14877,7 +14880,7 @@
     "kp1mer_to_kmer.py": 1,
     "kp2np.py": 1,
     "kpal": 2,
-    "kpasswd": 5763,
+    "kpasswd": 5764,
     "kpileup.py": 1,
     "kprop": 2,
     "kpropd": 2,
@@ -14924,7 +14927,7 @@
     "krakenuniq-report": 1,
     "krakenuniq-translate": 1,
     "krakmeopen": 1,
-    "krb5-config": 5763,
+    "krb5-config": 5764,
     "krb5-send-pr": 2,
     "krb5kdc": 2,
     "kreport2krona.py": 3,
@@ -14940,9 +14943,9 @@
     "kseq_split": 1,
     "ksnp": 1,
     "kssd": 1,
-    "ksu": 5763,
+    "ksu": 5764,
     "ksw": 1,
-    "kswitch": 5763,
+    "kswitch": 5764,
     "ktClassifyBLAST": 16,
     "ktClassifyHits": 12,
     "ktGetContigMagnitudes": 16,
@@ -14973,12 +14976,12 @@
     "ktserver": 2,
     "kttimedmgr": 2,
     "kttimedtest": 2,
-    "ktutil": 5763,
+    "ktutil": 5764,
     "ktutilmgr": 2,
     "ktutilserv": 2,
     "ktutiltest": 2,
     "kubectl": 1,
-    "kvno": 5763,
+    "kvno": 5764,
     "kwip": 2,
     "kwip-stats": 2,
     "l4p-tmpl": 32,
@@ -15096,7 +15099,7 @@
     "lefse_plot_features.py": 1,
     "lefse_plot_res.py": 1,
     "lefse_run.py": 1,
-    "legacy_blast.pl": 317,
+    "legacy_blast.pl": 318,
     "legsta": 1,
     "lemon-0.x-to-1.x.sh": 4,
     "lemur": 1,
@@ -15130,8 +15133,8 @@
     "libclair3.cpython-36m-x86_64-linux-gnu.so": 1,
     "libclair3.o": 1,
     "libclair3.so": 1,
-    "libdeflate-gunzip": 4092,
-    "libdeflate-gzip": 4092,
+    "libdeflate-gunzip": 4093,
+    "libdeflate-gzip": 4093,
     "libdrawgram.so": 5,
     "libdrawtree.so": 5,
     "libfile.pl": 1,
@@ -15140,9 +15143,9 @@
     "libiomp5md.dll": 1,
     "liblist.pl": 1,
     "liblist.pl.bak": 1,
-    "libnetcfg": 1674,
-    "libpng-config": 5844,
-    "libpng16-config": 5844,
+    "libnetcfg": 1675,
+    "libpng-config": 5845,
+    "libpng16-config": 5845,
     "libpypy-c.so": 1,
     "libpypy-c.so.debug": 1,
     "libpypy3-c.so.debug": 3,
@@ -15198,7 +15201,7 @@
     "link_ssv.py": 1,
     "linkage2allegro": 1,
     "linkhsp_unit_test": 5,
-    "linkicc": 970,
+    "linkicc": 971,
     "linknets": 2,
     "links2sql.pl": 7,
     "linksBed": 269,
@@ -15505,17 +15508,17 @@
     "lz4_decompress": 2,
     "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,
+    "lzcat": 7477,
+    "lzcmp": 7477,
+    "lzdiff": 7477,
+    "lzegrep": 7477,
+    "lzfgrep": 7477,
+    "lzgrep": 7477,
+    "lzless": 7477,
+    "lzma": 7477,
+    "lzmadec": 7477,
+    "lzmainfo": 7477,
+    "lzmore": 7477,
     "lzop_build_offset_table.py": 58,
     "m-party": 1,
     "m-tx": 1,
@@ -15826,7 +15829,7 @@
     "makeagp2.awk": 1,
     "makeagp_full.awk": 1,
     "makeagp_full2.awk": 1,
-    "makeblastdb": 319,
+    "makeblastdb": 320,
     "makecert": 15,
     "makechimeras.sh": 30,
     "makeclusterdb": 4,
@@ -15840,13 +15843,13 @@
     "makehmmerdb": 173,
     "makeidx.pl": 4,
     "makemat": 30,
-    "makembindex": 317,
+    "makembindex": 318,
     "makenucseq": 24,
     "makepBAM_genome.sh": 1,
     "makepBAM_transcriptome.sh": 1,
     "makeplot.pl": 3,
     "makepolymers.sh": 30,
-    "makeprofiledb": 317,
+    "makeprofiledb": 318,
     "makeprotseq": 24,
     "maker": 1,
     "maker2chado": 1,
@@ -15957,7 +15960,7 @@
     "mark_partial_genes.py": 2,
     "mark_productivity": 1,
     "mark_prophage_features.py": 2,
-    "markdown-it": 44,
+    "markdown-it": 45,
     "markdown_py": 117,
     "markdups": 1,
     "markermagu": 1,
@@ -17029,24 +17032,24 @@
     "mseqtools": 1,
     "msformatter": 1,
     "msfragger": 2,
-    "msgattrib": 5267,
-    "msgcat": 5267,
-    "msgcmp": 5267,
-    "msgcomm": 5267,
-    "msgconv": 5267,
-    "msgen": 5267,
-    "msgexec": 5267,
+    "msgattrib": 5268,
+    "msgcat": 5268,
+    "msgcmp": 5268,
+    "msgcomm": 5268,
+    "msgconv": 5268,
+    "msgen": 5268,
+    "msgexec": 5268,
     "msgf2pin": 1,
     "msgf_plus": 3,
-    "msgfilter": 5267,
-    "msgfmt": 5267,
+    "msgfilter": 5268,
+    "msgfmt": 5268,
     "msgfplus_search.rb": 1,
-    "msggrep": 5267,
-    "msginit": 5267,
-    "msgmerge": 5267,
+    "msggrep": 5268,
+    "msginit": 5268,
+    "msgmerge": 5268,
     "msgserv": 1,
-    "msgunfmt": 5267,
-    "msguniq": 5267,
+    "msgunfmt": 5268,
+    "msguniq": 5268,
     "msi": 1,
     "msi_cluster2reads": 1,
     "msi_clustr2map.pl": 1,
@@ -17336,9 +17339,9 @@
     "ncrf_to_bed": 2,
     "ncrf_to_bed.py": 2,
     "ncurses5-config": 565,
-    "ncurses6-config": 6942,
+    "ncurses6-config": 6944,
     "ncursesw5-config": 703,
-    "ncursesw6-config": 6943,
+    "ncursesw6-config": 6945,
     "ndg_httpclient": 2,
     "ndisasm": 1,
     "ndmetis": 58,
@@ -17428,7 +17431,7 @@
     "nf-test": 1,
     "nfe-umbrella-slice": 6,
     "ngd": 9,
-    "ngettext": 5267,
+    "ngettext": 5268,
     "ngg_barabasi_albert": 2,
     "ngg_barbell": 2,
     "ngg_complete": 2,
@@ -17438,9 +17441,9 @@
     "ngg_newman_watts_strogatz": 2,
     "ngg_path": 2,
     "ngg_ring_lattice": 2,
-    "nghttp": 4431,
-    "nghttpd": 4431,
-    "nghttpx": 4431,
+    "nghttp": 4432,
+    "nghttpd": 4432,
+    "nghttpx": 4432,
     "ngless": 2,
     "ngless-wrapped": 1,
     "nglview": 2,
@@ -17474,7 +17477,7 @@
     "ngsngs": 1,
     "ngsplotdb.py": 5,
     "ngsutils": 1,
-    "nhance.sh": 9,
+    "nhance.sh": 10,
     "nhmmer": 173,
     "nhmmscan": 173,
     "nib-conform": 2,
@@ -17621,7 +17624,7 @@
     "nproc": 82,
     "npth-config": 2,
     "npx": 15,
-    "nquire": 285,
+    "nquire": 286,
     "nquire.bak": 1,
     "nrForwardSplicedReads.pl": 1,
     "nr_ORFs_gff3.pl": 5,
@@ -17963,11 +17966,11 @@
     "openslide-quickhash1sum": 2,
     "openslide-show-properties": 2,
     "openslide-write-png": 2,
-    "openssl": 7717,
+    "openssl": 7719,
     "opentargets_validator": 1,
-    "opj_compress": 624,
-    "opj_decompress": 624,
-    "opj_dump": 624,
+    "opj_compress": 625,
+    "opj_decompress": 625,
+    "opj_dump": 625,
     "opl2ofm": 1,
     "opsin": 1,
     "opt": 6,
@@ -18471,14 +18474,14 @@
     "pcnt_bezier.lua": 1,
     "pcoaPlot.py": 2,
     "pcor": 1,
-    "pcre-config": 4928,
+    "pcre-config": 4929,
     "pcre2-config": 3688,
     "pcre2_jit_test": 3677,
     "pcre2grep": 3688,
     "pcre2posix_test": 113,
     "pcre2test": 3688,
-    "pcregrep": 4928,
-    "pcretest": 4928,
+    "pcregrep": 4929,
+    "pcretest": 4929,
     "pct2rgb.py": 4,
     "pctid_ani_sample": 1,
     "pcz_animate": 1,
@@ -18676,7 +18679,7 @@
     "perf": 1,
     "perfect-square": 2,
     "perform_controls.pl": 1,
-    "perl": 1674,
+    "perl": 1675,
     "perl-doc": 2,
     "perl-reversion": 9,
     "perl5.22.0": 54,
@@ -18684,12 +18687,12 @@
     "perl5.26.2": 369,
     "perl5.30.3": 5,
     "perl5.32.0": 64,
-    "perl5.32.1": 1182,
-    "perlbug": 1674,
-    "perldoc": 1674,
-    "perlivp": 1674,
+    "perl5.32.1": 1183,
+    "perlbug": 1675,
+    "perldoc": 1675,
+    "perlivp": 1675,
     "perltex": 1,
-    "perlthanks": 1674,
+    "perlthanks": 1675,
     "permuteGPAT++": 31,
     "permuteSmooth": 31,
     "permute_structure.pl": 1,
@@ -18829,7 +18832,7 @@
     "phonopy-vasp-born": 1,
     "phonopy-vasp-efe": 1,
     "photo": 2,
-    "phrase-search": 283,
+    "phrase-search": 284,
     "phsolverserver": 3,
     "phy2nex": 1,
     "phykit": 1,
@@ -19021,7 +19024,7 @@
     "pickle_cat.py": 1,
     "pickorientation.awk": 1,
     "pickout": 1,
-    "piconv": 1674,
+    "piconv": 1675,
     "picopore": 1,
     "picopore-realtime": 1,
     "picopore-rename": 1,
@@ -19029,7 +19032,7 @@
     "picrust2_pipeline.py": 1,
     "pidof": 1,
     "pigeon": 1,
-    "pigz": 113,
+    "pigz": 114,
     "pilconvert.py": 23,
     "pildriver.py": 23,
     "pilercr": 7,
@@ -19060,10 +19063,10 @@
     "pints_caller": 1,
     "pints_normalizer": 1,
     "pints_visualizer": 1,
-    "pip": 3619,
+    "pip": 3621,
     "pip2": 1,
     "pip2.7": 1,
-    "pip3": 2544,
+    "pip3": 2546,
     "pipdeptree": 1,
     "pipelign": 1,
     "pipeline.py": 1,
@@ -19220,7 +19223,7 @@
     "pktogf": 1,
     "pktype": 1,
     "pl2bat.pl": 3,
-    "pl2pm": 1674,
+    "pl2pm": 1675,
     "plaScope.sh": 1,
     "plac_runner.py": 60,
     "place_orient1.smk": 1,
@@ -19383,11 +19386,11 @@
     "pm4ngs-rnaseq-demo": 1,
     "pm4ngs-server": 1,
     "pm_which": 2,
-    "pma2apa": 9,
-    "pma2pme": 9,
+    "pma2apa": 10,
+    "pma2pme": 10,
     "pmap": 1,
-    "pmc2bioc": 9,
-    "pmc2info": 9,
+    "pmc2bioc": 10,
+    "pmc2info": 10,
     "pmd": 1,
     "pmdtools": 1,
     "pmemd_mdrun": 1,
@@ -19413,21 +19416,21 @@
     "pmxmutate": 1,
     "pn2pdf": 1,
     "pneumo-typer": 1,
-    "png-fix-itxt": 5844,
+    "png-fix-itxt": 5845,
     "pngcp": 89,
-    "pngfix": 5844,
+    "pngfix": 5845,
     "pngtogd": 232,
     "pngtogd2": 232,
     "pnps-gen": 1,
     "poa": 17,
     "pocheck": 1,
     "poclcc": 3,
-    "pod2html": 1674,
-    "pod2man": 1674,
-    "pod2text": 1674,
-    "pod2usage": 1674,
+    "pod2html": 1675,
+    "pod2man": 1675,
+    "pod2text": 1675,
+    "pod2usage": 1675,
     "pod_cover": 12,
-    "podchecker": 1674,
+    "podchecker": 1675,
     "podselect": 437,
     "poetry": 6,
     "pointwise_datasets_concatenator.py": 1,
@@ -19653,7 +19656,7 @@
     "prinseq-graphs-noPCA.pl": 3,
     "prinseq-graphs.pl": 3,
     "prinseq-lite.pl": 3,
-    "print-columns": 197,
+    "print-columns": 198,
     "print.pl": 1,
     "printIcounts": 1,
     "printScaff": 2,
@@ -19746,7 +19749,7 @@
     "project.sh.orig": 1,
     "projectAndStrip": 4,
     "projectFeatures": 3,
-    "project_tree_builder": 317,
+    "project_tree_builder": 318,
     "projinfo": 38,
     "projsync": 35,
     "prokka": 23,
@@ -19890,7 +19893,7 @@
     "protxml_to_table.rb": 1,
     "prov-compare": 9,
     "prov-convert": 9,
-    "prove": 1674,
+    "prove": 1675,
     "provean": 1,
     "provean.sh": 1,
     "provis": 1,
@@ -19934,10 +19937,10 @@
     "psiCalculator.py": 1,
     "psiPerGene.py": 1,
     "psibl2seq_unit_test": 5,
-    "psiblast": 317,
+    "psiblast": 318,
     "psiblast_iteration_unit_test": 5,
     "psiblast_unit_test": 5,
-    "psicc": 970,
+    "psicc": 971,
     "psiclass": 1,
     "psiphi": 24,
     "psite": 3,
@@ -19989,9 +19992,9 @@
     "pt2to3": 73,
     "ptGAUL.sh": 1,
     "ptangle": 1,
-    "ptar": 1674,
-    "ptardiff": 1674,
-    "ptargrep": 1674,
+    "ptar": 1675,
+    "ptardiff": 1675,
+    "ptargrep": 1675,
     "ptdump": 73,
     "ptest": 1,
     "ptex": 1,
@@ -20167,11 +20170,11 @@
     "pydamage": 1,
     "pydemult": 1,
     "pydicom": 1,
-    "pydoc": 3618,
-    "pydoc3": 3287,
+    "pydoc": 3620,
+    "pydoc3": 3289,
     "pydoc3.10": 795,
     "pydoc3.11": 263,
-    "pydoc3.12": 171,
+    "pydoc3.12": 173,
     "pydoc3.4": 6,
     "pydoc3.5": 103,
     "pydoc3.6": 342,
@@ -20192,12 +20195,12 @@
     "pyflyte-execute": 1,
     "pyflyte-fast-execute": 1,
     "pyflyte-map-execute": 1,
-    "pyftmerge": 377,
-    "pyftsubset": 377,
+    "pyftmerge": 378,
+    "pyftsubset": 378,
     "pygal_gen.py": 2,
     "pygenetic_code": 1,
     "pygmentex": 1,
-    "pygmentize": 241,
+    "pygmentize": 242,
     "pygmes": 1,
     "pygrun": 1,
     "pygtail": 2,
@@ -20295,7 +20298,7 @@
     "pytest": 141,
     "pytest-benchmark": 1,
     "pythia8-config": 1,
-    "python": 3619,
+    "python": 3621,
     "python-argcomplete-check-easy-install-script": 337,
     "python-argcomplete-tcsh": 191,
     "python-build": 2,
@@ -20306,15 +20309,15 @@
     "python2.5-config": 1,
     "python2.7": 331,
     "python2.7-config": 314,
-    "python3": 3288,
-    "python3-config": 3287,
-    "python3.1": 1229,
+    "python3": 3290,
+    "python3-config": 3289,
+    "python3.1": 1231,
     "python3.10": 795,
     "python3.10-config": 795,
     "python3.11": 263,
     "python3.11-config": 263,
-    "python3.12": 171,
-    "python3.12-config": 171,
+    "python3.12": 173,
+    "python3.12-config": 173,
     "python3.4": 6,
     "python3.4-config": 6,
     "python3.4m": 6,
@@ -20517,7 +20520,7 @@
     "quorum": 4,
     "quorum_create_database": 4,
     "quorum_error_correct_reads": 4,
-    "quote-grouped-elements": 9,
+    "quote-grouped-elements": 10,
     "qv_to_bqv.py": 58,
     "qvality": 1,
     "qvalue": 13,
@@ -20686,8 +20689,8 @@
     "rcexplain.3.0.3": 1,
     "rcexplain.3.1.0": 1,
     "rcf": 1,
-    "rchive": 284,
-    "rchive.Linux": 284,
+    "rchive": 285,
+    "rchive.Linux": 285,
     "rchive.go": 14,
     "rcl": 1,
     "rcl-dot-resmap.pl": 1,
@@ -20703,7 +20706,7 @@
     "rdfgraphisomorphism": 32,
     "rdfpipe": 32,
     "rdfs2dot": 32,
-    "rdjpgcom": 5730,
+    "rdjpgcom": 5731,
     "rdkit2fps": 1,
     "rdma_client": 19,
     "rdma_server": 19,
@@ -20795,7 +20798,7 @@
     "recgraph": 1,
     "reciprocal_blast_local": 1,
     "reciprocal_blast_local.py": 1,
-    "recode-sr-latin": 5267,
+    "recode-sr-latin": 5268,
     "recode_dir": 1,
     "recode_dir_legacy": 1,
     "recoder": 24,
@@ -20841,7 +20844,7 @@
     "ref-variation.3": 2,
     "ref-variation.3.0.3": 1,
     "ref-variation.3.1.0": 1,
-    "ref2pmid": 9,
+    "ref2pmid": 10,
     "refFinder": 1,
     "ref_map.pl": 1,
     "ref_seqs_from_bam": 1,
@@ -20877,7 +20880,7 @@
     "refresh-versioned": 1,
     "refseq-download": 1,
     "refseq-extract": 1,
-    "refseq-nm-cds": 9,
+    "refseq-nm-cds": 10,
     "refseq_masher": 1,
     "refseqget": 24,
     "refseqsplit.py": 2,
@@ -21091,7 +21094,7 @@
     "renumberRMFiles.pl": 3,
     "renumber_structure": 1,
     "reorder": 1,
-    "reorder-columns": 285,
+    "reorder-columns": 286,
     "reorder-fasta": 3,
     "reorder.smk": 1,
     "reorient_sequences_by_id.py": 2,
@@ -21157,7 +21160,7 @@
     "rescue_fusion.py": 1,
     "reseq": 1,
     "reseq-prepare-names.py": 1,
-    "reset": 7649,
+    "reset": 7651,
     "resetFragLibrary": 2,
     "reset_array.pl": 1,
     "reset_experiment.pl": 1,
@@ -21262,7 +21265,7 @@
     "ribotin-ref": 1,
     "ribotin-verkko": 1,
     "ribotish": 1,
-    "rich-click": 15,
+    "rich-click": 16,
     "riostream": 19,
     "ripcal": 1,
     "ripcal.bak": 1,
@@ -21418,9 +21421,9 @@
     "rpkmforgenes.py": 1,
     "rppr": 17,
     "rps_unit_test": 5,
-    "rpsblast": 326,
-    "rpsbproc": 245,
-    "rpstblastn": 317,
+    "rpsblast": 327,
+    "rpsbproc": 246,
+    "rpstblastn": 318,
     "rqcfilter.sh": 30,
     "rqcfilter2.sh": 29,
     "rqw": 1,
@@ -21510,7 +21513,7 @@
     "run-htseq-workflow": 1,
     "run-mummer1": 44,
     "run-mummer3": 44,
-    "run-ncbi-converter": 284,
+    "run-ncbi-converter": 285,
     "run-ncbi-converter.bak": 1,
     "run-ntedit": 1,
     "run-roh.pl": 156,
@@ -21713,7 +21716,7 @@
     "run_vote.py": 1,
     "run_voteSpecies.py": 1,
     "run_vsclust_app.R": 1,
-    "run_with_lock": 307,
+    "run_with_lock": 308,
     "run_workflows.py": 1,
     "run_x_platform_fuzz_corpus": 37,
     "runabyss.py": 1,
@@ -22055,6 +22058,7 @@
     "sccaf-regress-out": 1,
     "sccaller": 1,
     "sccmap": 198,
+    "sccmec": 1,
     "scelestial": 1,
     "scelestial-synthesis": 1,
     "scelvis": 1,
@@ -22084,7 +22088,7 @@
     "scitokens-test": 1,
     "scitokens-test-access": 1,
     "scitokens-verify": 1,
-    "sclient": 5763,
+    "sclient": 5764,
     "sclust_summary.sh": 1,
     "scluster": 3,
     "scmap-cli-post-install-tests.bats": 1,
@@ -22103,7 +22107,7 @@
     "scn-post-install-tests.sh": 1,
     "scn-predict.R": 1,
     "scn-train-model.R": 1,
-    "scn2xml": 9,
+    "scn2xml": 10,
     "scoary": 3,
     "scoary_GUI": 3,
     "scompare": 6,
@@ -22222,7 +22226,7 @@
     "segalign": 1,
     "segalign_repeat_masker": 1,
     "segemehl.x": 1,
-    "segmasker": 317,
+    "segmasker": 318,
     "segment-cnv": 1,
     "segment.py": 1,
     "segmentFst": 31,
@@ -22502,7 +22506,7 @@
     "sharq.3": 2,
     "sharq.3.0.0": 2,
     "shasta": 1,
-    "shasum": 1674,
+    "shasum": 1675,
     "shed-tools": 2,
     "shell_utils.py": 1,
     "shiboken2": 2,
@@ -22597,7 +22601,7 @@
     "sim-cover2": 2,
     "sim-shotgun": 2,
     "sim4db": 3,
-    "sim_client": 5763,
+    "sim_client": 5764,
     "sim_reads": 10,
     "sim_reads.o": 10,
     "sim_reads_tran": 10,
@@ -22709,7 +22713,7 @@
     "sketchy": 1,
     "skewer": 1,
     "skg_convert.py": 2,
-    "skip-if-file-exists": 254,
+    "skip-if-file-exists": 255,
     "skip_psl_self.awk": 2,
     "skip_psl_self_ss.awk": 2,
     "skip_selfmatches.py": 1,
@@ -22832,8 +22836,8 @@
     "snp-pileup": 2,
     "snp-pileup-quickbam": 1,
     "snp-sites": 13,
-    "snp2hgvs": 197,
-    "snp2tbl": 197,
+    "snp2hgvs": 198,
+    "snp2tbl": 198,
     "snpEff": 23,
     "snpEffAnnotate.py": 3,
     "snp_diversity.py": 1,
@@ -22906,9 +22910,9 @@
     "sort-last-maf": 1,
     "sort-snos": 2,
     "sort-snos.pl": 2,
-    "sort-table": 197,
-    "sort-uniq-count": 285,
-    "sort-uniq-count-rank": 285,
+    "sort-table": 198,
+    "sort-uniq-count": 286,
+    "sort-uniq-count-rank": 286,
     "sort2": 2,
     "sortBed": 269,
     "sortByRefAndCor.pl": 1,
@@ -22985,7 +22989,7 @@
     "sparsetable_unittest": 1,
     "spatypes.txt": 1,
     "spdi2prod": 12,
-    "spdi2tbl": 197,
+    "spdi2tbl": 198,
     "specialk": 1,
     "spectra-cluster-cli": 1,
     "spectral_clustering": 1,
@@ -23007,7 +23011,7 @@
     "sphinx-quickstart": 39,
     "spine.pl": 1,
     "spinner.py": 1,
-    "splain": 1674,
+    "splain": 1675,
     "splash": 1,
     "splice_site_summary.pl": 1,
     "spliceai": 1,
@@ -23016,7 +23020,7 @@
     "splinter.pl": 1,
     "splinter_scaffolds.pl": 1,
     "split": 82,
-    "split-at-intron": 197,
+    "split-at-intron": 198,
     "split-bed12-blocks": 3,
     "split-coverages.py": 1,
     "split-fasta": 1,
@@ -23145,7 +23149,7 @@
     "sqlformat": 9,
     "sqlite.pl": 1,
     "sqlite3": 2709,
-    "sqlite3_analyzer": 7059,
+    "sqlite3_analyzer": 7061,
     "sqlitebrowser": 1,
     "sqlmetal": 15,
     "sqlsharp": 15,
@@ -23472,15 +23476,15 @@
     "strainscan_build": 1,
     "stranger": 1,
     "stream": 76,
-    "stream-local": 9,
-    "stream-pubmed": 283,
+    "stream-local": 10,
+    "stream-pubmed": 284,
     "stream_atac": 1,
     "stream_run_test": 1,
     "streamer_1d": 22,
     "streamlit": 6,
     "streamlit.cmd": 6,
     "streamsam.sh": 30,
-    "streamzip": 1246,
+    "streamzip": 1247,
     "streme": 6,
     "streme_xml_to_html": 6,
     "stress-ng": 1,
@@ -23745,7 +23749,7 @@
     "tableproxy64": 1,
     "tableschema": 1,
     "tablet": 1,
-    "tabs": 7649,
+    "tabs": 7651,
     "tabulate": 126,
     "tabulate.py": 1,
     "tabulator": 1,
@@ -23901,20 +23905,20 @@
     "tba": 1,
     "tbl2asn": 29,
     "tbl2asn-test": 12,
-    "tbl2prod": 185,
-    "tbl2xml": 197,
-    "tblastn": 317,
-    "tblastn_vdb": 32,
-    "tblastx": 317,
+    "tbl2prod": 186,
+    "tbl2xml": 198,
+    "tblastn": 318,
+    "tblastn_vdb": 33,
+    "tblastx": 318,
     "tblite": 1,
     "tbox-scan": 1,
     "tbpore": 1,
     "tbtamr": 1,
     "tbvcfreport": 1,
     "tcdemux": 1,
-    "tclsh": 7296,
+    "tclsh": 7298,
     "tclsh8.5": 473,
-    "tclsh8.6": 7059,
+    "tclsh8.6": 7061,
     "tcode": 24,
     "tcsh": 3,
     "td_bignet": 2,
@@ -23951,12 +23955,12 @@
     "test-download": 2,
     "test-download.3": 2,
     "test-download.3.0.0": 2,
-    "test-edirect": 254,
-    "test-eutils": 283,
+    "test-edirect": 255,
+    "test-eutils": 284,
     "test-gzip": 1,
     "test-merStream": 5,
-    "test-pmc-index": 9,
-    "test-pubmed-index": 283,
+    "test-pmc-index": 10,
+    "test-pubmed-index": 284,
     "test-read-write-cursor": 2,
     "test-read-write-cursor.3": 2,
     "test-read-write-cursor.3.0.0": 2,
@@ -24007,7 +24011,7 @@
     "test_install.bak": 1,
     "test_miso": 1,
     "test_musicc.py": 2,
-    "test_pcre": 78,
+    "test_pcre": 79,
     "test_proton.bam": 1,
     "test_proton.bam.bai": 1,
     "test_regexp": 1,
@@ -24110,7 +24114,7 @@
     "thumbpdf": 1,
     "tiara": 2,
     "tiara-test": 2,
-    "tic": 7649,
+    "tic": 7651,
     "tiddit": 1,
     "tides": 1,
     "tidk": 1,
@@ -24125,16 +24129,16 @@
     "tiff2rgba": 5293,
     "tiffcmp": 5293,
     "tiffcomment": 18,
-    "tiffcp": 5483,
+    "tiffcp": 5484,
     "tiffcrop": 5293,
     "tiffdither": 5293,
-    "tiffdump": 5483,
+    "tiffdump": 5484,
     "tifffile": 21,
-    "tiffinfo": 5483,
+    "tiffinfo": 5484,
     "tiffmedian": 5293,
-    "tiffset": 5483,
-    "tiffsplit": 5483,
-    "tificc": 970,
+    "tiffset": 5484,
+    "tiffsplit": 5484,
+    "tificc": 971,
     "tigStore": 3,
     "tiger-hash": 11,
     "tigge_check": 1,
@@ -24188,7 +24192,7 @@
     "titan-gc-prepare.py": 1,
     "titan.py": 1,
     "titration": 2,
-    "tjbench": 357,
+    "tjbench": 358,
     "tkconch": 1,
     "tkpp": 1,
     "tksm": 1,
@@ -24219,14 +24223,14 @@
     "to_upper_case.pl.bak": 1,
     "toco": 75,
     "toco_from_protos": 75,
-    "toe": 7649,
+    "toe": 7651,
     "tohnsw": 1,
     "toil": 3,
     "toil-cwl-runner": 3,
     "toil-wdl-runner": 2,
     "tolkein": 1,
     "tombo": 2,
-    "toml2xml": 9,
+    "toml2xml": 10,
     "tomlq": 289,
     "tomsimilarity": 1,
     "tomtom": 13,
@@ -24269,8 +24273,8 @@
     "tpp_hostname": 2,
     "tpp_models.pl": 2,
     "tpptray.bat": 2,
-    "tput": 7649,
-    "tqdm": 334,
+    "tput": 7651,
+    "tqdm": 335,
     "tr": 82,
     "trace_comment": 2,
     "trace_comments": 2,
@@ -24340,7 +24344,7 @@
     "transform_gfa.py": 1,
     "transformers-cli": 2,
     "transformseq": 13,
-    "transicc": 970,
+    "transicc": 971,
     "transit": 1,
     "transition_counter": 1,
     "transl": 1,
@@ -24356,8 +24360,8 @@
     "translate_reduced_reads.pl": 1,
     "translatorx": 1,
     "translatorx_vLocal.pl": 1,
-    "transmute": 283,
-    "transmute.Linux": 197,
+    "transmute": 284,
+    "transmute.Linux": 198,
     "transposcope": 1,
     "transpose.pl": 1,
     "transpose.pl.bak": 1,
@@ -24492,7 +24496,7 @@
     "tryptic.py": 1,
     "ts": 3,
     "tsebra.py": 3,
-    "tset": 7649,
+    "tset": 7651,
     "tskit": 6,
     "tsort": 82,
     "tsp": 2,
@@ -24527,7 +24531,7 @@
     "tth-hash": 11,
     "ttree": 66,
     "tts": 5,
-    "ttx": 377,
+    "ttx": 378,
     "tty": 82,
     "turbocor": 1,
     "tutorial_eqtlbma.R": 1,
@@ -24642,7 +24646,7 @@
     "uniprot_sprot_to_sqlite3.py": 2,
     "uniprot_support.py": 1,
     "uniq": 83,
-    "uniq-table": 185,
+    "uniq-table": 186,
     "uniqLine.pl": 1,
     "uniqPolishes": 3,
     "uniqscan": 1,
@@ -24669,14 +24673,14 @@
     "unix2mac": 1,
     "unlink": 82,
     "unlz4": 3498,
-    "unlzma": 7475,
+    "unlzma": 7477,
     "unmapped2anchors.py": 1,
     "unmerge": 1,
     "unmerge-paired-reads.sh": 2,
     "unnaf": 1,
     "unpack200": 421,
     "unpickle.py": 1,
-    "unpigz": 113,
+    "unpigz": 114,
     "unquip": 1,
     "unshare": 13,
     "unsquashfs": 3,
@@ -24686,7 +24690,7 @@
     "unstarch-typical": 14,
     "untangle": 2,
     "unweight_fasta.py": 1,
-    "unxz": 7700,
+    "unxz": 7702,
     "unzip": 32,
     "unzip.sh": 29,
     "unziphdf5": 1,
@@ -24694,7 +24698,7 @@
     "unzipont": 1,
     "unzipont_dir": 1,
     "unzipsfx": 25,
-    "unzstd": 5154,
+    "unzstd": 5156,
     "update-blastdb.py": 2,
     "update-serotypefinder-db": 1,
     "update-sort-bed-migrate-candidates": 14,
@@ -24714,8 +24718,8 @@
     "updateDeltaClr": 2,
     "updateLibSizes": 2,
     "update_alias.py": 1,
-    "update_blastdb.pl": 317,
-    "update_blastdb.pl.bak": 288,
+    "update_blastdb.pl": 318,
+    "update_blastdb.pl.bak": 289,
     "update_database": 1,
     "update_info.py": 3,
     "update_selected_column9_values.py": 2,
@@ -24765,7 +24769,7 @@
     "utmpdump": 13,
     "utrgff2gbrowse.pl": 14,
     "utrrnaseq": 12,
-    "uuclient": 5763,
+    "uuclient": 5764,
     "uuid": 36,
     "uuid-config": 36,
     "uuidgen": 13,
@@ -25440,7 +25444,7 @@
     "wg-blimp": 1,
     "wgMLST": 1,
     "wgdi": 1,
-    "wget": 413,
+    "wget": 414,
     "wgetdir": 1,
     "wgmlst": 1,
     "wgs2ncbi": 1,
@@ -25449,7 +25453,7 @@
     "wham": 1,
     "whamg": 1,
     "whatshap": 14,
-    "wheel": 3618,
+    "wheel": 3620,
     "wheezy.template": 2,
     "whereis": 13,
     "which": 1,
@@ -25486,15 +25490,15 @@
     "window-acgt": 2,
     "windowBed": 269,
     "windowMaker": 269,
-    "windowmasker": 317,
-    "windowmasker_2.2.22_adapter.py": 317,
+    "windowmasker": 318,
+    "windowmasker_2.2.22_adapter.py": 318,
     "winextract": 1,
     "winnowmap": 3,
     "wiq.py": 1,
     "wisestork": 1,
-    "wish": 7296,
+    "wish": 7298,
     "wish8.5": 473,
-    "wish8.6": 7059,
+    "wish8.6": 7061,
     "wkhtmltoimage": 2,
     "wkhtmltopdf": 2,
     "wlmscpfs": 1,
@@ -25504,7 +25508,7 @@
     "woltka": 1,
     "womtool": 4,
     "wopl2ofm": 1,
-    "word-at-a-time": 285,
+    "word-at-a-time": 286,
     "word-square": 2,
     "word_enrich.pl": 1,
     "wordcloud_cli": 1,
@@ -25543,7 +25547,7 @@
     "write_strain_fasta.py": 1,
     "writedb_entry": 1,
     "writedb_unit_test": 5,
-    "wrjpgcom": 5730,
+    "wrjpgcom": 5731,
     "ws": 2,
     "wsdl": 15,
     "wsdl2": 15,
@@ -25609,7 +25613,7 @@
     "x86_64-conda-linux-gnu-gfortran": 3326,
     "x86_64-conda-linux-gnu-gfortran.bin": 575,
     "x86_64-conda-linux-gnu-gprof": 3362,
-    "x86_64-conda-linux-gnu-ld": 5446,
+    "x86_64-conda-linux-gnu-ld": 5448,
     "x86_64-conda-linux-gnu-ld.bfd": 3362,
     "x86_64-conda-linux-gnu-ld.gold": 3362,
     "x86_64-conda-linux-gnu-nm": 3362,
@@ -25645,7 +25649,7 @@
     "x86_64-conda_cos6-linux-gnu-gfortran": 4095,
     "x86_64-conda_cos6-linux-gnu-gfortran.bin": 1344,
     "x86_64-conda_cos6-linux-gnu-gprof": 4129,
-    "x86_64-conda_cos6-linux-gnu-ld": 6280,
+    "x86_64-conda_cos6-linux-gnu-ld": 6282,
     "x86_64-conda_cos6-linux-gnu-ld.bfd": 4129,
     "x86_64-conda_cos6-linux-gnu-ld.gold": 4129,
     "x86_64-conda_cos6-linux-gnu-nm": 4129,
@@ -25684,7 +25688,7 @@
     "xgboost": 27,
     "xgboost.dll": 1,
     "xgboost.lib": 1,
-    "xgettext": 5267,
+    "xgettext": 5268,
     "xgui": 2,
     "xhmm": 1,
     "xinteract": 2,
@@ -25702,9 +25706,9 @@
     "xml2-config.bak": 34,
     "xml2dcm": 1,
     "xml2dsr": 1,
-    "xml2fsa": 197,
-    "xml2json": 197,
-    "xml2tbl": 270,
+    "xml2fsa": 198,
+    "xml2json": 198,
+    "xml2tbl": 271,
     "xml_grep": 64,
     "xml_merge": 64,
     "xml_pp": 64,
@@ -25755,7 +25759,7 @@
     "xsltproc_lite": 7,
     "xstreme": 2,
     "xstreme_html_to_tsv": 2,
-    "xsubpp": 1674,
+    "xsubpp": 1675,
     "xsv": 1,
     "xtandem": 3,
     "xtb": 1,
@@ -25763,8 +25767,8 @@
     "xtea_hg19": 1,
     "xtea_long": 1,
     "xtermcolor": 2,
-    "xtract": 285,
-    "xtract.Linux": 197,
+    "xtract": 286,
+    "xtract.Linux": 198,
     "xtract.go": 15,
     "xtract.pl": 1,
     "xtractcol": 1,
@@ -25777,16 +25781,16 @@
     "xxhsum": 31,
     "xy-plot": 88,
     "xyalign": 1,
-    "xz": 7700,
-    "xzcat": 7475,
-    "xzcmp": 7475,
-    "xzdec": 7475,
-    "xzdiff": 7475,
-    "xzegrep": 7475,
-    "xzfgrep": 7475,
-    "xzgrep": 7475,
-    "xzless": 7475,
-    "xzmore": 7475,
+    "xz": 7702,
+    "xzcat": 7477,
+    "xzcmp": 7477,
+    "xzdec": 7477,
+    "xzdiff": 7477,
+    "xzegrep": 7477,
+    "xzfgrep": 7477,
+    "xzgrep": 7477,
+    "xzless": 7477,
+    "xzmore": 7477,
     "y2racc": 7,
     "yacc": 4,
     "yacht": 1,
@@ -25797,7 +25801,7 @@
     "yak": 2,
     "yaml2gff.1.4.pl": 14,
     "yaml2obj": 4,
-    "yaml2xml": 9,
+    "yaml2xml": 10,
     "yamllint": 1,
     "yamlpp5-events": 4,
     "yamlpp5-highlight": 4,
@@ -25847,7 +25851,7 @@
     "zipHomerResults.pl": 5,
     "zipcloak": 2,
     "zipcmp": 90,
-    "zipdetails": 1674,
+    "zipdetails": 1675,
     "zipgrep": 25,
     "zipinfo": 25,
     "zipmerge": 90,
@@ -25872,10 +25876,10 @@
     "zrun": 3,
     "zsh": 3,
     "zsh-5.8": 3,
-    "zstd": 5154,
-    "zstdcat": 5154,
-    "zstdgrep": 4952,
-    "zstdless": 4952,
-    "zstdmt": 5154,
+    "zstd": 5156,
+    "zstdcat": 5156,
+    "zstdgrep": 4954,
+    "zstdless": 4954,
+    "zstdmt": 5156,
     "ztr_dump": 2
 }
\ No newline at end of file
diff --git a/quay.io/biocontainers/c/crocodeel:1.0.2--pyhdfd78af_0.json b/quay.io/biocontainers/c/crocodeel:1.0.2--pyhdfd78af_0.json
new file mode 100644
index 0000000..4962639
--- /dev/null
+++ b/quay.io/biocontainers/c/crocodeel:1.0.2--pyhdfd78af_0.json
@@ -0,0 +1,114 @@
+{
+    "2to3": "/usr/local/bin/2to3",
+    "2to3-3.12": "/usr/local/bin/2to3-3.12",
+    "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",
+    "crocodeel": "/usr/local/bin/crocodeel",
+    "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",
+    "idle3.12": "/usr/local/bin/idle3.12",
+    "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",
+    "pydoc3.12": "/usr/local/bin/pydoc3.12",
+    "pyftmerge": "/usr/local/bin/pyftmerge",
+    "pyftsubset": "/usr/local/bin/pyftsubset",
+    "python": "/usr/local/bin/python",
+    "python3": "/usr/local/bin/python3",
+    "python3-config": "/usr/local/bin/python3-config",
+    "python3.1": "/usr/local/bin/python3.1",
+    "python3.12": "/usr/local/bin/python3.12",
+    "python3.12-config": "/usr/local/bin/python3.12-config",
+    "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",
+    "tqdm": "/usr/local/bin/tqdm",
+    "transicc": "/usr/local/bin/transicc",
+    "tset": "/usr/local/bin/tset",
+    "ttx": "/usr/local/bin/ttx",
+    "unlzma": "/usr/local/bin/unlzma",
+    "unxz": "/usr/local/bin/unxz",
+    "unzstd": "/usr/local/bin/unzstd",
+    "wheel": "/usr/local/bin/wheel",
+    "wish": "/usr/local/bin/wish",
+    "wish8.6": "/usr/local/bin/wish8.6",
+    "wrjpgcom": "/usr/local/bin/wrjpgcom",
+    "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld",
+    "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld",
+    "xz": "/usr/local/bin/xz",
+    "xzcat": "/usr/local/bin/xzcat",
+    "xzcmp": "/usr/local/bin/xzcmp",
+    "xzdec": "/usr/local/bin/xzdec",
+    "xzdiff": "/usr/local/bin/xzdiff",
+    "xzegrep": "/usr/local/bin/xzegrep",
+    "xzfgrep": "/usr/local/bin/xzfgrep",
+    "xzgrep": "/usr/local/bin/xzgrep",
+    "xzless": "/usr/local/bin/xzless",
+    "xzmore": "/usr/local/bin/xzmore",
+    "zstd": "/usr/local/bin/zstd",
+    "zstdcat": "/usr/local/bin/zstdcat",
+    "zstdgrep": "/usr/local/bin/zstdgrep",
+    "zstdless": "/usr/local/bin/zstdless",
+    "zstdmt": "/usr/local/bin/zstdmt",
+    "env-execute": "/usr/local/env-execute"
+}
\ No newline at end of file
diff --git a/quay.io/biocontainers/s/sccmec:1.0.0--hdfd78af_0.json b/quay.io/biocontainers/s/sccmec:1.0.0--hdfd78af_0.json
new file mode 100644
index 0000000..da3cd6f
--- /dev/null
+++ b/quay.io/biocontainers/s/sccmec:1.0.0--hdfd78af_0.json
@@ -0,0 +1,315 @@
+{
+    "2to3": "/usr/local/bin/2to3",
+    "2to3-3.12": "/usr/local/bin/2to3-3.12",
+    "accn-at-a-time": "/usr/local/bin/accn-at-a-time",
+    "adig": "/usr/local/bin/adig",
+    "ahost": "/usr/local/bin/ahost",
+    "align-columns": "/usr/local/bin/align-columns",
+    "amino-acid-composition": "/usr/local/bin/amino-acid-composition",
+    "archive-ncbinlp": "/usr/local/bin/archive-ncbinlp",
+    "archive-nihocc": "/usr/local/bin/archive-nihocc",
+    "archive-nmcds": "/usr/local/bin/archive-nmcds",
+    "archive-pmc": "/usr/local/bin/archive-pmc",
+    "archive-pubmed": "/usr/local/bin/archive-pubmed",
+    "archive-taxonomy": "/usr/local/bin/archive-taxonomy",
+    "args2slice": "/usr/local/bin/args2slice",
+    "asn2ref": "/usr/local/bin/asn2ref",
+    "asn2xml": "/usr/local/bin/asn2xml",
+    "autopoint": "/usr/local/bin/autopoint",
+    "between-two-genes": "/usr/local/bin/between-two-genes",
+    "blast_formatter": "/usr/local/bin/blast_formatter",
+    "blastdb_aliastool": "/usr/local/bin/blastdb_aliastool",
+    "blastdbcheck": "/usr/local/bin/blastdbcheck",
+    "blastdbcmd": "/usr/local/bin/blastdbcmd",
+    "blastn": "/usr/local/bin/blastn",
+    "blastn_vdb": "/usr/local/bin/blastn_vdb",
+    "blastp": "/usr/local/bin/blastp",
+    "blastx": "/usr/local/bin/blastx",
+    "blst2gm": "/usr/local/bin/blst2gm",
+    "blst2tkns": "/usr/local/bin/blst2tkns",
+    "bunzip2": "/usr/local/bin/bunzip2",
+    "bzcat": "/usr/local/bin/bzcat",
+    "bzcmp": "/usr/local/bin/bzcmp",
+    "bzdiff": "/usr/local/bin/bzdiff",
+    "bzegrep": "/usr/local/bin/bzegrep",
+    "bzfgrep": "/usr/local/bin/bzfgrep",
+    "bzgrep": "/usr/local/bin/bzgrep",
+    "bzip2": "/usr/local/bin/bzip2",
+    "bzip2recover": "/usr/local/bin/bzip2recover",
+    "bzless": "/usr/local/bin/bzless",
+    "bzmore": "/usr/local/bin/bzmore",
+    "c_rehash": "/usr/local/bin/c_rehash",
+    "camlhmp": "/usr/local/bin/camlhmp",
+    "camlhmp-blast": "/usr/local/bin/camlhmp-blast",
+    "camlhmp-extract": "/usr/local/bin/camlhmp-extract",
+    "captoinfo": "/usr/local/bin/captoinfo",
+    "cit2pmid": "/usr/local/bin/cit2pmid",
+    "cleanup-blastdb-volumes.py": "/usr/local/bin/cleanup-blastdb-volumes.py",
+    "clear": "/usr/local/bin/clear",
+    "coloredlogs": "/usr/local/bin/coloredlogs",
+    "combine-uid-lists": "/usr/local/bin/combine-uid-lists",
+    "compile_et": "/usr/local/bin/compile_et",
+    "convert2blastmask": "/usr/local/bin/convert2blastmask",
+    "corelist": "/usr/local/bin/corelist",
+    "cpan": "/usr/local/bin/cpan",
+    "csv2xml": "/usr/local/bin/csv2xml",
+    "curl": "/usr/local/bin/curl",
+    "curl-config": "/usr/local/bin/curl-config",
+    "datatool": "/usr/local/bin/datatool",
+    "deltablast": "/usr/local/bin/deltablast",
+    "difference-uid-lists": "/usr/local/bin/difference-uid-lists",
+    "disambiguate-nucleotides": "/usr/local/bin/disambiguate-nucleotides",
+    "download-ncbi-data": "/usr/local/bin/download-ncbi-data",
+    "download-ncbi-software": "/usr/local/bin/download-ncbi-software",
+    "download-pmc": "/usr/local/bin/download-pmc",
+    "download-pubmed": "/usr/local/bin/download-pubmed",
+    "download-sequence": "/usr/local/bin/download-sequence",
+    "ds2pme": "/usr/local/bin/ds2pme",
+    "dustmasker": "/usr/local/bin/dustmasker",
+    "ecommon.sh": "/usr/local/bin/ecommon.sh",
+    "efetch": "/usr/local/bin/efetch",
+    "efilter": "/usr/local/bin/efilter",
+    "einfo": "/usr/local/bin/einfo",
+    "elink": "/usr/local/bin/elink",
+    "enc2xs": "/usr/local/bin/enc2xs",
+    "encguess": "/usr/local/bin/encguess",
+    "envsubst": "/usr/local/bin/envsubst",
+    "epost": "/usr/local/bin/epost",
+    "esample": "/usr/local/bin/esample",
+    "esearch": "/usr/local/bin/esearch",
+    "esummary": "/usr/local/bin/esummary",
+    "exclude-uid-lists": "/usr/local/bin/exclude-uid-lists",
+    "executor": "/usr/local/bin/executor",
+    "expand-current": "/usr/local/bin/expand-current",
+    "f2py": "/usr/local/bin/f2py",
+    "fetch-local": "/usr/local/bin/fetch-local",
+    "fetch-nmcds": "/usr/local/bin/fetch-nmcds",
+    "fetch-pmc": "/usr/local/bin/fetch-pmc",
+    "fetch-pubmed": "/usr/local/bin/fetch-pubmed",
+    "fetch-taxonomy": "/usr/local/bin/fetch-taxonomy",
+    "filter-columns": "/usr/local/bin/filter-columns",
+    "filter-genbank": "/usr/local/bin/filter-genbank",
+    "filter-record": "/usr/local/bin/filter-record",
+    "filter-stop-words": "/usr/local/bin/filter-stop-words",
+    "find-in-gene": "/usr/local/bin/find-in-gene",
+    "fuse-ranges": "/usr/local/bin/fuse-ranges",
+    "fuse-segments": "/usr/local/bin/fuse-segments",
+    "gbf2fsa": "/usr/local/bin/gbf2fsa",
+    "gbf2ref": "/usr/local/bin/gbf2ref",
+    "gbf2xml": "/usr/local/bin/gbf2xml",
+    "gene2range": "/usr/local/bin/gene2range",
+    "get_species_taxids.sh": "/usr/local/bin/get_species_taxids.sh",
+    "get_species_taxids.sh.bak": "/usr/local/bin/get_species_taxids.sh.bak",
+    "gettext": "/usr/local/bin/gettext",
+    "gettext.sh": "/usr/local/bin/gettext.sh",
+    "gettextize": "/usr/local/bin/gettextize",
+    "gm2ranges": "/usr/local/bin/gm2ranges",
+    "gm2segs": "/usr/local/bin/gm2segs",
+    "gss-client": "/usr/local/bin/gss-client",
+    "h2ph": "/usr/local/bin/h2ph",
+    "h2xs": "/usr/local/bin/h2xs",
+    "hgvs2spdi": "/usr/local/bin/hgvs2spdi",
+    "humanfriendly": "/usr/local/bin/humanfriendly",
+    "idle3": "/usr/local/bin/idle3",
+    "idle3.12": "/usr/local/bin/idle3.12",
+    "idn2": "/usr/local/bin/idn2",
+    "infocmp": "/usr/local/bin/infocmp",
+    "infotocap": "/usr/local/bin/infotocap",
+    "ini2xml": "/usr/local/bin/ini2xml",
+    "instmodsh": "/usr/local/bin/instmodsh",
+    "intersect-uid-lists": "/usr/local/bin/intersect-uid-lists",
+    "join-into-groups-of": "/usr/local/bin/join-into-groups-of",
+    "json2xml": "/usr/local/bin/json2xml",
+    "json_pp": "/usr/local/bin/json_pp",
+    "json_xs": "/usr/local/bin/json_xs",
+    "jsonl2xml": "/usr/local/bin/jsonl2xml",
+    "just-first-key": "/usr/local/bin/just-first-key",
+    "k5srvutil": "/usr/local/bin/k5srvutil",
+    "kadmin": "/usr/local/bin/kadmin",
+    "kdestroy": "/usr/local/bin/kdestroy",
+    "keyctl": "/usr/local/bin/keyctl",
+    "kinit": "/usr/local/bin/kinit",
+    "klist": "/usr/local/bin/klist",
+    "kpasswd": "/usr/local/bin/kpasswd",
+    "krb5-config": "/usr/local/bin/krb5-config",
+    "ksu": "/usr/local/bin/ksu",
+    "kswitch": "/usr/local/bin/kswitch",
+    "ktutil": "/usr/local/bin/ktutil",
+    "kvno": "/usr/local/bin/kvno",
+    "legacy_blast.pl": "/usr/local/bin/legacy_blast.pl",
+    "libnetcfg": "/usr/local/bin/libnetcfg",
+    "lzcat": "/usr/local/bin/lzcat",
+    "lzcmp": "/usr/local/bin/lzcmp",
+    "lzdiff": "/usr/local/bin/lzdiff",
+    "lzegrep": "/usr/local/bin/lzegrep",
+    "lzfgrep": "/usr/local/bin/lzfgrep",
+    "lzgrep": "/usr/local/bin/lzgrep",
+    "lzless": "/usr/local/bin/lzless",
+    "lzma": "/usr/local/bin/lzma",
+    "lzmadec": "/usr/local/bin/lzmadec",
+    "lzmainfo": "/usr/local/bin/lzmainfo",
+    "lzmore": "/usr/local/bin/lzmore",
+    "makeblastdb": "/usr/local/bin/makeblastdb",
+    "makembindex": "/usr/local/bin/makembindex",
+    "makeprofiledb": "/usr/local/bin/makeprofiledb",
+    "markdown-it": "/usr/local/bin/markdown-it",
+    "msgattrib": "/usr/local/bin/msgattrib",
+    "msgcat": "/usr/local/bin/msgcat",
+    "msgcmp": "/usr/local/bin/msgcmp",
+    "msgcomm": "/usr/local/bin/msgcomm",
+    "msgconv": "/usr/local/bin/msgconv",
+    "msgen": "/usr/local/bin/msgen",
+    "msgexec": "/usr/local/bin/msgexec",
+    "msgfilter": "/usr/local/bin/msgfilter",
+    "msgfmt": "/usr/local/bin/msgfmt",
+    "msggrep": "/usr/local/bin/msggrep",
+    "msginit": "/usr/local/bin/msginit",
+    "msgmerge": "/usr/local/bin/msgmerge",
+    "msgunfmt": "/usr/local/bin/msgunfmt",
+    "msguniq": "/usr/local/bin/msguniq",
+    "ncurses6-config": "/usr/local/bin/ncurses6-config",
+    "ncursesw6-config": "/usr/local/bin/ncursesw6-config",
+    "ngettext": "/usr/local/bin/ngettext",
+    "nghttp": "/usr/local/bin/nghttp",
+    "nghttpd": "/usr/local/bin/nghttpd",
+    "nghttpx": "/usr/local/bin/nghttpx",
+    "nhance.sh": "/usr/local/bin/nhance.sh",
+    "nquire": "/usr/local/bin/nquire",
+    "openssl": "/usr/local/bin/openssl",
+    "pcre-config": "/usr/local/bin/pcre-config",
+    "pcregrep": "/usr/local/bin/pcregrep",
+    "pcretest": "/usr/local/bin/pcretest",
+    "perl": "/usr/local/bin/perl",
+    "perl5.32.1": "/usr/local/bin/perl5.32.1",
+    "perlbug": "/usr/local/bin/perlbug",
+    "perldoc": "/usr/local/bin/perldoc",
+    "perlivp": "/usr/local/bin/perlivp",
+    "perlthanks": "/usr/local/bin/perlthanks",
+    "phrase-search": "/usr/local/bin/phrase-search",
+    "piconv": "/usr/local/bin/piconv",
+    "pigz": "/usr/local/bin/pigz",
+    "pip": "/usr/local/bin/pip",
+    "pip3": "/usr/local/bin/pip3",
+    "pl2pm": "/usr/local/bin/pl2pm",
+    "pma2apa": "/usr/local/bin/pma2apa",
+    "pma2pme": "/usr/local/bin/pma2pme",
+    "pmc2bioc": "/usr/local/bin/pmc2bioc",
+    "pmc2info": "/usr/local/bin/pmc2info",
+    "pod2html": "/usr/local/bin/pod2html",
+    "pod2man": "/usr/local/bin/pod2man",
+    "pod2text": "/usr/local/bin/pod2text",
+    "pod2usage": "/usr/local/bin/pod2usage",
+    "podchecker": "/usr/local/bin/podchecker",
+    "print-columns": "/usr/local/bin/print-columns",
+    "project_tree_builder": "/usr/local/bin/project_tree_builder",
+    "prove": "/usr/local/bin/prove",
+    "psiblast": "/usr/local/bin/psiblast",
+    "ptar": "/usr/local/bin/ptar",
+    "ptardiff": "/usr/local/bin/ptardiff",
+    "ptargrep": "/usr/local/bin/ptargrep",
+    "pydoc": "/usr/local/bin/pydoc",
+    "pydoc3": "/usr/local/bin/pydoc3",
+    "pydoc3.12": "/usr/local/bin/pydoc3.12",
+    "pygmentize": "/usr/local/bin/pygmentize",
+    "python": "/usr/local/bin/python",
+    "python3": "/usr/local/bin/python3",
+    "python3-config": "/usr/local/bin/python3-config",
+    "python3.1": "/usr/local/bin/python3.1",
+    "python3.12": "/usr/local/bin/python3.12",
+    "python3.12-config": "/usr/local/bin/python3.12-config",
+    "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",
+    "rich-click": "/usr/local/bin/rich-click",
+    "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",
+    "sccmec": "/usr/local/bin/sccmec",
+    "sclient": "/usr/local/bin/sclient",
+    "scn2xml": "/usr/local/bin/scn2xml",
+    "segmasker": "/usr/local/bin/segmasker",
+    "shasum": "/usr/local/bin/shasum",
+    "sim_client": "/usr/local/bin/sim_client",
+    "skip-if-file-exists": "/usr/local/bin/skip-if-file-exists",
+    "snp2hgvs": "/usr/local/bin/snp2hgvs",
+    "snp2tbl": "/usr/local/bin/snp2tbl",
+    "sort-table": "/usr/local/bin/sort-table",
+    "sort-uniq-count": "/usr/local/bin/sort-uniq-count",
+    "sort-uniq-count-rank": "/usr/local/bin/sort-uniq-count-rank",
+    "spdi2tbl": "/usr/local/bin/spdi2tbl",
+    "splain": "/usr/local/bin/splain",
+    "split-at-intron": "/usr/local/bin/split-at-intron",
+    "sqlite3_analyzer": "/usr/local/bin/sqlite3_analyzer",
+    "stream-local": "/usr/local/bin/stream-local",
+    "stream-pubmed": "/usr/local/bin/stream-pubmed",
+    "streamzip": "/usr/local/bin/streamzip",
+    "tabs": "/usr/local/bin/tabs",
+    "tbl2prod": "/usr/local/bin/tbl2prod",
+    "tbl2xml": "/usr/local/bin/tbl2xml",
+    "tblastn": "/usr/local/bin/tblastn",
+    "tblastn_vdb": "/usr/local/bin/tblastn_vdb",
+    "tblastx": "/usr/local/bin/tblastx",
+    "tclsh": "/usr/local/bin/tclsh",
+    "tclsh8.6": "/usr/local/bin/tclsh8.6",
+    "test-edirect": "/usr/local/bin/test-edirect",
+    "test-eutils": "/usr/local/bin/test-eutils",
+    "test-pmc-index": "/usr/local/bin/test-pmc-index",
+    "test-pubmed-index": "/usr/local/bin/test-pubmed-index",
+    "test_pcre": "/usr/local/bin/test_pcre",
+    "tic": "/usr/local/bin/tic",
+    "toe": "/usr/local/bin/toe",
+    "toml2xml": "/usr/local/bin/toml2xml",
+    "tput": "/usr/local/bin/tput",
+    "transmute": "/usr/local/bin/transmute",
+    "transmute.Linux": "/usr/local/bin/transmute.Linux",
+    "tset": "/usr/local/bin/tset",
+    "uniq-table": "/usr/local/bin/uniq-table",
+    "unlzma": "/usr/local/bin/unlzma",
+    "unpigz": "/usr/local/bin/unpigz",
+    "unxz": "/usr/local/bin/unxz",
+    "unzstd": "/usr/local/bin/unzstd",
+    "update_blastdb.pl": "/usr/local/bin/update_blastdb.pl",
+    "update_blastdb.pl.bak": "/usr/local/bin/update_blastdb.pl.bak",
+    "uuclient": "/usr/local/bin/uuclient",
+    "wget": "/usr/local/bin/wget",
+    "wheel": "/usr/local/bin/wheel",
+    "windowmasker": "/usr/local/bin/windowmasker",
+    "windowmasker_2.2.22_adapter.py": "/usr/local/bin/windowmasker_2.2.22_adapter.py",
+    "wish": "/usr/local/bin/wish",
+    "wish8.6": "/usr/local/bin/wish8.6",
+    "word-at-a-time": "/usr/local/bin/word-at-a-time",
+    "x86_64-conda-linux-gnu-ld": "/usr/local/bin/x86_64-conda-linux-gnu-ld",
+    "x86_64-conda_cos6-linux-gnu-ld": "/usr/local/bin/x86_64-conda_cos6-linux-gnu-ld",
+    "xgettext": "/usr/local/bin/xgettext",
+    "xml2fsa": "/usr/local/bin/xml2fsa",
+    "xml2json": "/usr/local/bin/xml2json",
+    "xml2tbl": "/usr/local/bin/xml2tbl",
+    "xsubpp": "/usr/local/bin/xsubpp",
+    "xtract": "/usr/local/bin/xtract",
+    "xtract.Linux": "/usr/local/bin/xtract.Linux",
+    "xz": "/usr/local/bin/xz",
+    "xzcat": "/usr/local/bin/xzcat",
+    "xzcmp": "/usr/local/bin/xzcmp",
+    "xzdec": "/usr/local/bin/xzdec",
+    "xzdiff": "/usr/local/bin/xzdiff",
+    "xzegrep": "/usr/local/bin/xzegrep",
+    "xzfgrep": "/usr/local/bin/xzfgrep",
+    "xzgrep": "/usr/local/bin/xzgrep",
+    "xzless": "/usr/local/bin/xzless",
+    "xzmore": "/usr/local/bin/xzmore",
+    "yaml2xml": "/usr/local/bin/yaml2xml",
+    "zipdetails": "/usr/local/bin/zipdetails",
+    "zstd": "/usr/local/bin/zstd",
+    "zstdcat": "/usr/local/bin/zstdcat",
+    "zstdgrep": "/usr/local/bin/zstdgrep",
+    "zstdless": "/usr/local/bin/zstdless",
+    "zstdmt": "/usr/local/bin/zstdmt",
+    "env-execute": "/usr/local/env-execute"
+}
\ No newline at end of file