tools in conda, not in quay.io

[ypriverol]

Follow-up the the packages in conda (62), that they are active but they don't exist in quay.io.

['scvis_galaxy', 'libdb', 'roprofile', 'pictrust', 'icqsol', 'ngs-sdk', 'perl-bio-db-sam', 'bamkit', 'pyutilib', 'genblasta', 'bayesase', 'r-acidplyr', 'bioconductor-iloreg', 'bioconductor-mafdb.gnomad.r2.1.hs37d5', 'scagaire', 'tatajuba', 'ucsc-ave', 'test-glibc', 'pedagree', 'bioconductor-wpm', 'libffi', 'libsvm', 'fermikit', 'r-crmn', 'r-jpeg', 'r-tximport', 'azure-cli', 'bioconductor-bgx', 'spatyper', 'smashbenchmarking', 'limix', 'cmip', 'perl-sys-info-driver-osx', 'kraken-all', 'bioconductor-pipecomp', 'openms-tools', 'lapack', 'primalscheme', 'gamma', 'eigen', 'argparse', 'niemads', 'r-acidgenomes', 'roprofile.py', 'perl-sanger-allelecount', 'bio-vcf', 'r-dt', 'bioconductor-uncoverapplib', 'ucsc-calc', 'spanki', 'scikit-allel', 'intervalstats', 'xmltodict', 'pmx_biobb', 'hall-lab-svtools', 'perl-mac-systemdirectory', 'gnu-getopt', 'integron_finder', 'bioconductor-msprep', 'cap-mirseq', 'bioconductor-ggtreeextra', 'ghc']

@bgruening

[ypriverol]

Packages in bioconda (1155) repodata.json but not in anaconda Web interface:

['warnings-register', 'phytools', 'inline', 'splitstackshape', 'emdbook', 'fpc', 'module-runtime-conflicts', 'string-random', 'basejump', 'svg', 'gbm', 'digest-perl-md5', 'rematch2', 'config-autoconf', 'rjson', 'whopgenome', 'tap-harness-env', 'sub-attribute', 'futile.options', 'mac-propertylist', 'poppr', 'pod-coverage', 'data-uuid', 'genabel', 'carp', 'fields', 'exception-class', 'pack', 'moosex-nonmoose', 'survey', 'abind', 'rubic', 'compress-bgzf', 'checkpoint', 'net-ftp-recursive', 'list-compare', 'tie-refhash-weak', 'file-sort', 'consensuscore', 'freerange', 'base', 'prefork', 'gwasexacthw', 'cpan-meta-requirements', 'proj4', 'phylobase', 'perlio-gzip', 'text-csv', 'file-fetch', 'perl-osnames', 'dnet', 'module-loaded', 'role-tiny', 'xml-dom-xpath', 'jpeg', 'file-chdir', 'scalar-list-utils', 'env-path', 'file-listing', 'rnacentral', 'error', 'htmltools', 'extutils-cbuilder', 'deoptimr', 'digest-md5', 'mime-base64', 'transformer', 'test2-suite', 'test-deep', 'bio-mlst-check', 'http-cookies', 'alakazam', 'shape', 'math-complex', 'io-uncompress-bunzip2', 'sleuth', 'text-balanced', 'devel-size', 'xml-xpath', 'rgbif', 'appconfig', 'number-format', 'statistics-descriptive', 'sereal', 'ipc-cmd', 'json-maybexs', 'phonr', 'class-singleton', 'optparse', 'moosex-types', 'sub-info', 'purbayes', 'http-daemon', 'levenshtein', 'agricolae', 'pophelper', 'io-stringy', 'devel-stacktrace', 'clone', 'bio-phylo', 'nabor', 'list-someutils', 'graph-readwrite', 'html-entities-numbered', 'extutils-depends', 'xml-regexp', 'extutils-pkgconfig', 'time-piece', 'bio-gff3', 'libxml-perl', 'text-levenshteinxs', 'permute', 'perlio-utf8_strict', 'ngsplotdb-hg38', 'bh', 'findbin-real', 'common-sense', 'gd', 'list-util', 'lwp-mediatypes', 'geomap', 'nanostringnorm', 'geiger', 'pscbs', 'onto-perl', 'deconstructsigs', 'number-misc', 'io-handle', 'funrar', 'extutils-cppguess', 'xmlrpc', 'soap-lite', 'asics', 'extutils-makemaker', 'sereal-decoder', 'som', 'test-simple', 'padwalker', 'forks', 'ade4', 'bio3d', 'class-std', 'plasmidprofiler', 'log-log4perl', 'dorng', 'vars', 'rniftyreg', 'empiricalfdr.deseq2', 'devel-cover', 'genabel.data', 'genenet', 'sub-exporter', 'border-style', 'stringr', 'readbrukerflexdata', 'class-xsaccessor', 'namespace-autoclean', 'termreadkey', 'dpeak', 'pore', 'rbison', 'ggrepel', 'storable', 'compress-raw-bzip2', 'firebrowser', 'aroma.affymetrix', 'runit', 'xml-sax-writer', 'proxy', 'aod', 'snow', 'file-sharedir-install', 'kinship2', 'pod-checker', 'rrcov', 'pod-simple', 'scimpute', 'module-load-conditional', 'class-accessor', 'haplo.stats', 'digest-crc32', 'hpc-runner-command-plugin-logger-sqlite', 'math-bezier', 'bio-eutilities', 'minionqc', 'skellam', 'params-validationcompiler', 'test-eol', 'rlist', 'bundle-bioperl', 'polysat', 'unicode-stringprep', 'fail', 'class-data-inheritable', 'autodie', 'funr', 'adephylo', 'mailtools', 'longitudinal', 'html-parser', 'jsonlite', 'seqinr', 'prroc', 'misctools', 'test-warnings', 'bit64', 'string-approx', 'sub-identify', 'gplots', 'math-random', 'cache-cache', 'extutils-config', 'yaml-libyaml', 'posix', 'grain', 'mime-types', 'rsnps', 'encode', 'xml-libxml', 'graph', 'spdep', 'file-tee', 'class-load', 'test-class-moose', 'text-tabs', 'statistics-caseresampling', 'file-slurp-tiny', 'test-yaml', 'ellipse', 'propcis', 'kaos', 'spocc', 'lncpipereporter', 'extrafont', 'algdesign', 'mailund-newick', 'r.huge', 'batchjobs', 'http-negotiate', 'readonly', 'file-readbackwards', 'env', 'sub-exporter-progressive', 'crypt-rc4', 'rsolnp', 'phangorn', 'git-wrapper', 'time-local', 'data-munge', 'html-tagset', 'yaml', 'test-differences', 'mixin-linewise', 'hook-lexwrap', 'module-implementation', 'par-dist', 'cpan-meta', 'text-wrap', 'genemodel', 'factominer', 'mixomics', 'scope-guard', 'stampp', 'shinyace', 'rentrez', 'sanger-cgp-allelecount', 'ipc-run3', 'sbpiper', 'sub-quote', 'base64', 'blockmodeling', 'file-slurper', 'gam', 'ggrasp', 'ichorcna', 'pegas', 'scales', 'locfdr', 'viridis', 'flashclust', 'text-ansitable', 'bigmemory', 'io-zlib', 'openxlsx', 'tie-hash', 'module-pluggable', 'mba', 'bcbiobase', 'deldir', 'argparser', 'test-output', 'ic10', 'dunn.test', 'histonehmm', 'msgpack', 'test-lectrotest', 'gkmsvm', 'xcell', 'hpc-runner-command', 'venndiagram', 'b-debug', 'algorithm-cluster', 'biganalytics', 'learnbayes', 'test-exception', 'socket', 'r.methodss3', 'text-template-simple', 'xml-namespacesupport', 'car', 'yaml-tiny', 'segmented', 'html-tidy', 'cgi', 'mutoss', 'net-netrc', 'metalonda', 'pod-plaintext', 'pod-usage', 'test-requiresinternet', 'sereal-encoder', 'sigtree', 'locale', 'psych', 'dbi', 'ngsplotdb-hg19', 'graphics-colorobject', 'swamp', 'archive-extract', 'stitch', 'batch', 'gamlss.data', 'net-http', 'dgeclustering', 'svdialogs', 'annotables', 'htscluster', 'flexmix', 'cluster', 'attribute-handlers', 'config-general', 'checkmate', 'estscan1', 'extutils-manifest', 'svgui', 'io-prompt', 'rann', 'taxa', 'test-exec', 'bioverbs', 'par', 'tie-log4perl', 'tsne', 'params', 'lme4qtl', 'module-corelist', 'uri', 'xml-libxslt', 'text-glob', 'version-next', 'tie-ixhash', 'phyext2', 'r.cache', 'term-encoding', 'b', 'diagram', 'module-util', 'bio-db-sam', 'matlab', 'bio-asn1-entrezgene', 'r.oo', 'socket6', 'html-treebuilder-xpath', 'chado', 'listenv', 'filedirutil', 'r2html', 'sanger-cgp-vagrent', 'loose.rock', 'math-cdf', 'wasabi', 'shazam', 'apache-test', 'color-theme', 'test-cpan-meta', 'futile.logger', 'mmgenome', 'extrafontdb', 'module-build', 'qpcr', 'locale-maketext-simple', 'flowr', 'seurat', 'io-scalar', 'giant', 'regexp-common', 'ddrtree', 'rseis', 'tigger', 'drc', 'file-temp', 'date-manip', 'symbol-util', 'sigqc', 'knitrbootstrap', 'multitaper', 'chbutils', 'bioext', 'fda', 'file-share', 'indirect', 'file-remove', 'package-deprecationmanager', 'file-details', 'const-fast', 'sew', 'maldiquant', 'sys-sigaction', 'file-pushd', 'statmod', 'statistics-distributions', 'compute.es', 'spreadsheet-parseexcel', 'json', 'file-util', 'fastmatch', 'rcpptoml', 'cg-pipeline', 'patpro', 'io-tty', 'exporter-tidy', 'clvalid', 'logging', 'gamlss.dist', 'math-round', 'moosex-app-role-log4perl', 'lwp-simple', 'canary-stability', 'list-moreutils', 'moosex-object-pluggable', 'io-interactive', 'unicode-utf8', 'math-spline', 'probmetab', 'text-tabs-wrap', 'loom', 'magrittr', 'jackstraw', 'ada', 'test-subcalls', 'term-progressbar', 'tie-cache', 'pod-parser', 'xnomial', 'config-simple', 'memoize', 'ggdendro', 'shaman', 'spieceasi', 'goeveg', 'heap-simple-xs', 'email-date-format', 'rcppparallel', 'crypt-openssl-random', 'time-hires', 'ipc-sharelite', 'math-combinatorics', 'kmsurv', 'htssip', 'msm', 'test', 'r.filesets', 'params-coerce', 'xml-entities', 'dbd-pg', 'archive-tar-wrapper', 'git-wrapper-plus', 'qlcmatrix', 'pmcmr', 'rsm', 'rgraphics', 'clone-choose', 'ptw', 'inline-c', 'ggally', 'maxlik', 'array-utils', 'pctgcdata', 'samr', 'biodb', 'module-extract-use', 'data-dump', 'http-message', 'autoloader', 'image-exiftool', 'hardyweinberg', 'statistics-lite', 'file-next', 'object-insideout', 'densityclust', 'bcbiornaseq', 'biox-workflow', 'test-nowarnings', 'moose', 'ppi', 'dt', 'sys-info-base', 'test-base', 'getoptlong', 'cghflasso', 'rnexml', 'xml-filter-buffertext', 'io-gzip', 'cnogpro', 'tiff', 'tcr', 'data-match', 'path-class', 'ecodist', 'precrec', 'ahocorasicktrie', 'parent', 'snowfall', 'variable-magic', 'test-trap', 'text-parsewords', 'pamr', 'ic10trainingdata', 'syntactic', 'pcapp', 'heap-simple-perl', 'guilds', 'test-mockmodule', 'grbase', 'globals', 'moosex-role-parameterized', 'rcppgsl', 'cate', 'moosex-role-withoverloading', 'gdtextutil', 'kernlab', 'mcpcounter', 'io-sessiondata', 'sanger-allelecount', 'rphylip', 'ipc-run', 'rblast', 'aliased', 'ggsignif', 'math-bigrat', 'class-load-xs', 'sort-naturally', 'data-visitor', 'findbin-libs', 'extutils-helpers', 'workflowscriptscommon', 'ash', 'kriging', 'truncnorm', 'vegan', 'hash-merge', 'r4cker', 'io-uncompress-rawinflate', 'scatterplot3d', 'graphviz', 'calibrate', 'lyve-set', 'perl-unsafe-signals', 'symbol', 'parallel-iterator', 'term-app-roles', 'test-file', 'params-validate', 'smvar', 'heap', 'xml-writer', 'devel-overloadinfo', 'brio', 'qqman', 'misc3d', 'classdiscovery', 'dplyr', 'data-stag', 'xml-dom', 'ggplot2', 'moo', 'waveslim', 'prettyunits', 'jcode', 'perfmeas', 'class-method-modifiers', 'file-homedir', 'circlize', 'mldbm', 'upsetr', 'argumentcheck', 'googlevis', 'image-info', 'tie-hash-indexed', 'config-tiny', 'bio-tools-phylo-paml', 'test-fork', 'lwp-protocol-https', 'devel-checkbin', 'globaloptions', 'rismed', 'net-ftp', 'sort-versions', 'leaps', 'json-pp', 'db-file', 'file-touch', 'test-longstring', 'breakaway', 'mitools', 'integer', 'types-standard', 'test-prereq', 'tripal', 'statistics-ttest', 'file-compare', 'mutationalpatterns', 'inlinedocs', 'sanger-cgp-battenberg', 'cpan-meta-validator', 'polynom', 'relations', 'orqa', 'module-fromperlver', 'itertools', 'btlib', 'heap-simple', 'exporter-tiny', 'findbin', 'test-utf8', 'pod-elemental', 'devel-assert', 'aptreeshape', 'encode-locale', 'module-build-tiny', 'module-metadata', 'html-tree', 'ore', 'class-inspector', 'cimpl', 'ntlm', 'fateid', 'filesys-df', 'convert-binhex', 'string-rewriteprefix', 'bio-cigar', 'misha', 'super', 'gprofiler', 'gdgraph-histogram', 'rttf2pt1', 'data-utilities', 'downloader', 'math-random-mt-auto', 'importer', 'cpan-meta-check', 'test-leaktrace', 'test-unit-lite', 'xgr', 'ks', 'mmod', 'gdgraph', 'readmzxmldata', 'test-more', 'number-compare', 'math-bigint', 'trimcluster', 'rpmg', 'sql-statement', 'file-slurp', 'file-copy-link', 'extutils-installpaths', 'ggalt', 'image-size', 'klar', 'tibble', 'math-vecstat', 'xml-twig', 'mclust', 'test-xml', 'set-intspan', 'business-isbn', 'relaimpo', 'json-create', 'sub-exporter-formethods', 'hppy', 'fastica', 'isogene', 'test-pod-coverage', 'params-util', 'gmodels', 'test-file-contents', 'array-set', 'r.rsp', 'venn', 'mvr', 'dartr', 'aceperl', 'html-tableextract', 'nleqslv', 'msqrob', 'text-nsp', 'graphics-colornames', 'test-object', 'math-derivative', 'hwriter', 'microseq', 'mixtools', 'bio-tools-run-alignment-clustalw', 'rmysql', 'canopy', 'capture-tiny', 'digest-hmac', 'corpcor', 'png', 'data-optlist', 'text-asciitable', 'tree-dag_node', 'bit', 'compress-raw-zlib', 'biox-seq', 'test-requires', 'pscl', 'postscript', 'phylomeasures', 'font-ttf', 'seqminer', 'micropan', 'slurp', 'smartsva', 'qtl', 'minpack.lm', 'prabclus', 'bit-vector', 'fmsb', 'nam', 'catools', 'experimental', 'bio-samtools', 'archive-zip', 'json-parse', 'moosex-clone', 'logger-simple', 'biosails', 'module-load', 'ldrtools', 'plsgenomics', 'popgenreport', 'enrichr', 'wicket', 'class-std-fast', 'text-levenshtein', 'parallel-forkmanager', 'getopt-argvfile', 'grimport', 'import-into', 'xml-parser', 'tximport', 'algorithm-dependency', 'path-tiny', 'gsmoothr', 'dbchip', 'bc3net', 'parse-recdescent', 'xml-semanticdiff', 'rapidr', 'bbmisc', 'params-check', 'sequenza', 'newick', 'tie-cacher', 'digest', 'www-robotrules', 'momr', 'html-element-extended', 'html-template', 'tie-refhash', 'preseqr', 'bioperl-core', 'moosex-app', 'nhmmfdr', 'rebird', 'd3heatmap', 'geoaxe', 'cpan-meta-yaml', 'biasedurn', 'filter-simple', 'xml-xpathengine', 'pinfsc50', 'progress', 'gwpcr', 'imputelcmd', 'maldiquantforeign', 'math-utils', 'moosex-fileattribute', 'dbm-deep', 'list-uniq', 'mqtl', 'fastqcr', 'test-sys-info', 'types-serialiser', 'cairo', 'spam', 'module-list', 'go-perl', 'specio-exporter', 'spiffy', 'mlgt', 'gsalib', 'bio-automatedannotation', 'xml-sax-base', 'xml-parser-lite', 'devel-symdump', 'discriminer', 'intego', 'text-abbrev', 'nbpseq', 'aroma.core', 'changepoint', 'fftwtools', 'rrbgen', 'pheatmap', 'fakemp', 'idpmisc', 'test-classapi', 'jdk', 'penalized', 'bio-coordinate', 'try-tiny-retry', 'business-isbn-data', 'safe', 'test-without-module', 'version', 'biomark', 'diptest', 'combinat', 'text-diff', 'george', 'template-toolkit', 'eval-closure', 'speedglm', 'hemdag', 'archive-tar', 'blib', 'unicode-normalize', 'rwave', 'text-template', 'datetime-locale', 'file-copy-recursive-reduced', 'cp4p', 'ampliconduo', 'bio-tools-run-alignment-tcoffee', 'ggbiplot', 'bigmemory.sri', 'datetime-format-strptime', 'metama', 'task-weaken', 'rfoc', 'string-truncate', 'rocr', 'traminer', 'mce-shared', 'sys-info-driver-linux', 'coenocliner', 'htmlwidgets', 'statistics-frequency', 'snpassoc', 'crypt-openssl-rsa', 'app-cpanminus', 'file-sharedir', 'lib', 'multicool', 'rmarkdown', 'term-detect-software', 'data-dumper', 'threaded', 'font-afm', 'gmd', 'mess', 'scalar-util-numeric', 'ngsplotdb-mm10', 'http-date', 'devel-globaldestruction', 'imp4p', 'aroma.apd', 'testthat', 'json-xs', 'estscan2', 'ff', 'set-intervaltree', 'role-tiny-with', 'plotrix', 'xsloader', 'io-socket-inet6', 'corbi', 'text-format', 'xml-simple', 'b-hooks-endofscope', 'algorithm-munkres', 'dynamictreecut', 'bio-featureio', 'mro-compat', 'coloc', 'gdtools', 'file-copy-recursive', 'html-form', 'perl-ostype', 'io-all', 'quorts', 'tidygenomics', 'test-script', 'io-html', 'gpca', 'try-tiny', 'io-compress-deflate', 'spreadsheet-writeexcel', 'test-needs', 'tcga2stat', 'clone-pp', 'pracma', 'xml-sax', 'file-path', 'sub-install', 'pegex', 'rappdirs', 'facets', 'metstat', 'class-methodmaker', 'parallel-loops', 'mime-lite', 'mime-quotedprint', 'test-toolbox', 'io-compress', 'svg-graph', 'adegenet', 'matrixeqtl', 'test-builder-tester', 'datetime', 'file-find', 'return-multilevel', 'gamlss', 'wrassp', 'escape-houdini', 'genometricorr', 'number-range', 'probe-perl', 'icluster', 'bbmle', 'maldirppa', 'rvertnet', 'r.utils', 'pod-coverage-trustpod', 'acme-damn', 'docopt', 'bio-viennangs', 'test-memory-cycle', 'nozzle.r1', 'par-packer', 'splancs', 'file-which', 'module-scandeps', 'data-walk', 'statistics-basic', 'missforest', 'test-warn', 'mac-systemdirectory', 'namespace-clean', 'string-escape', 'timedate', 'spp', 'digest-sha', 'nastiseq', 'reshape', 'wgcna', 'http-server-simple', 'local-lib', 'cpan-shell', 'pod-escapes', 'log-any', 'perlio', 'sub-name', 'rbamtools', 'moosex-types-path-tiny', 'term-table', 'file-spec', 'moosex-types-path-class', 'umi4c', 'package-stash-xs', 'raceid', 'test-cleannamespaces', 'dbd-sqlite', 'e1071', 'bloom-faster', 'test-files', 'pod-simple-text', 'test-notabs', 'solarius', 'exactranktests', 'net-ssleay', 'bignum', 'writexls', 'biom', 'sads', 'lambda.r', 'taxonomizr', 'locfit', 'matrixstats', 'number-witherror', 'date-format', 'dbd-mysql', 'knitr', 'r.devices', 'sub-uplevel', 'gpseq', 'getopt-long-descriptive', 'ole-storage_lite', 'robustrankaggreg', 'sendmailr', 'io-socket-ssl', 'algorithm-diff', 'mozilla-ca', 'goalie', 'specio', 'ampvis', 'extutils-parsexs', 'rtfbs', 'biox-workflow-command', 'bedr', 'mldbm-sync', 'hyphy-python', 'sqldf', 'findpython', 'omero', 'vcftools-vcf', 'bipartite', 'hierfstat', 'hdrcde', 'rphast', 'io-string', 'pdf-api2', 'sortedcontainers', 'diffcorr', 'string-util', 'exporter', 'constant', 'tfmpvalue', 'pcap', 'excel-writer-xlsx', 'getopt-long', 'data.table', 'ebimetagenomics', 'ridigbio', 'phewas', 'pma', 'test-inter', 'bma', 'test-fatal', 'km.ci', 'want', 'parse-yapp', 'mixkernel', 'vcfr', 'minems2', 'data-compare', 'future', 'moosex-getopt', 'phylosignal', 'test2', 'gsubfn', 'config-any', 'proc-fork', 'nodiv', 'mime-tools', 'biglm', 'compquadform', 'leapp', 'qiimer', 'dynaloader', 'devel-cycle', 'extutils-constant', 'outliers', 'ncbit', 'carp-clan', 'beanplot', 'rtsne', 'dendextend', 'hivclustering', 'set-scalar', 'perlio-encoding', 'hash-util-fieldhash-compat', 'oai', 'delaporte', 'test-pod', 'sartools', 'exomedepth', 'xml-sax-expat', 'popgenome', 'www-mechanize', 'peer', 'package-stash', 'readr', 'digest-sha1', 'test-harness', 'devel-checkos', 'datetime-timezone', 'isva', 'cellassign', 'file-find-rule', 'dist-checkconflicts', 'fitdistrplus', 'math-base-convert', 'test-most', 'caroline', 'moosex-singleton', 'structssi', 'fnn', 'sets', 'mce', 'pbkdf2-tiny', 'nor1mix', 'treesim', 'unicode-map', 'list-moreutils-xs', 'rcircos', 'perl4-corelibs', 'sparql', 'ipc-system-simple', 'corrplot', 'array-compare', 'bio-db-hts', 'sanger-cgp-vcf', 'metarnaseq', 'type-tiny', 'libwww-perl', 'bio-rna-rnaalisplit', 'module-runtime', 'moosex-types-stringlike', 'tie-toobject', 'signal', 'sys-info-driver-osx', 'html-formatter', 'io-uncompress-gunzip', 'blockfest', 'authen-sasl-saslprep', 'digest-md5-file', 'convert-binary-c', 'sys-info', 'flexclust', 'dumbbench', 'file-grep']

[bgruening]

Follow-up the the packages in conda (62), that they are active but they don't exist in quay.io.

A few of them are available, see here: https://quay.io/repository/biocontainers/bayesase or https://quay.io/repository/biocontainers/bioconductor-mafdb.gnomad.r2.1.hs37d5

A few are very old and have been migrated. This predates our friendship and biocontainers :) I guess we can ignore them.
A few of them where hidden and I fixed them. Please run the scripts again.

[bgruening]

Packages in bioconda (1155) repodata.json but not in anaconda Web interface:

No clue what this is. But most of the packages look really strange and not important.

[ypriverol]

@TMiguelT Most of

Packages in bioconda (1155) repodata.json but not in anaconda Web interface:

No clue what this is. But most of the packages look really strange and not important.

Thanks @bgruening aparenctly the file repodata.json is not updated systematically in anaconda and keep nonsense there. This is realted with the question from @TMiguelT in the biocontainers gitter channel. Good to have this solve.

[ypriverol]

@TMiguelT can I close this issue?

[multimeric]

Thanks for getting back to me. However it seems to me that, while most of these have been explained, it isn't exactly resolved. We have:

• A few quay.io containers that aren't showing up in the API
• The repodata isn't up-to-date

I also have two follow-up questions:

• What does @bgruening mean by "A few are very old and have been migrated". Where have they been migrated to?
• Does channeldata.json have the same issues as repodata? Is it also unreliable?

[ypriverol]

Thanks for getting back to me. However it seems to me that, while most of these have been explained, it isn't exactly resolved. We have:

• A few quay.io containers that aren't showing up in the API

Can you point here which ones! We are updating the API and we need to know who they dare?

• The repodata isn't up-to-date

I think that the repodata.json from conda is not updated weekly, Don't know the mechanism they used to update but as @bgruening mentioned a lot of those packages do not exist even in conda.

I also have two follow-up questions:

• What does @bgruening mean by "A few are very old and have been migrated". Where have they been migrated to?

I can reposnd this one, but @bgruening can double check. But some of the packages has been migrated to conda-forge.

• Does channeldata.json have the same issues as repodata? Is it also unreliable?

To update the information in biocontainers we use two channels conda-forge and bioconda

[bgruening]

What does @bgruening mean by "A few are very old and have been migrated". Where have they been migrated to?

A few very old packages are not included in bioconda anymore and live elsewhere, e.g. conda-forge. So we do not build containers for them automatically.

[ypriverol]

Can I close this issue @TMiguelT ?