[Blends-commit] [Git][blends-team/med][master] 2 commits: Update dependency information and changelog

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
1f156456 by Andreas Tille at 2023-02-08T11:04:23+01:00
Update dependency information and changelog

- - - - -
9d22a4c9 by Andreas Tille at 2023-02-08T11:05:32+01:00
Upload to unstable

- - - - -


2 changed files:

- debian/changelog
- + dependency_data/debian-med_3.8.json


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,50 @@
-debian-med (3.7.4) UNRELEASED; urgency=medium
+debian-med (3.8) unstable; urgency=medium
 
   * nifti2dicom, qnifti2dicom, libsimpleitk1-dev, python3-simpleitk removed
     from Debian thus removed from tasks
   * Suggests: libgatk-native-bindings-java
   * Replace: msxpertsuite by massxpert, minexpert2 (see #1024780)
 
- -- Andreas Tille <tille at debian.org>  Mon, 07 Nov 2022 07:27:02 +0100
+  * start of automatic changelog entry * 
+  
+  * Changes in metapackage dependencies
+   -med-bio
+    added:
+      Recommends:  minexpert2, snippy, metaeuk, any2fasta, btllib-tools,
+                   savvy-util, comet-ms, muscle3, pyfastx, seqan-needle,
+                   seqan-raptor, massxpert
+    removed:
+      Recommends:  sequenceconverter.app, msxpertsuite
+   -med-bio-dev
+    added:
+      Recommends:  libbio-db-seqfeature-perl, python3-pyfastx,
+                   libbiojava6-java, python3-bioframe
+      Suggests:    libsavvy-dev, libgatk-native-bindings-java, libbtllib-dev,
+                   python3-cgelib, python3-conda-package-streaming
+    removed:
+      Recommends:  libbiojava5-java
+   -med-bio-phylogeny
+    added:
+      Recommends:  muscle3
+   -med-cloud
+    added:
+      Recommends:  muscle3
+   -med-covid-19
+    added:
+      Recommends:  muscle3
+   -med-imaging
+    removed:
+      Recommends:  qnifti2dicom, nifti2dicom
+   -med-imaging-dev
+    added:
+      Recommends:  python3-bioxtasraw
+    removed:
+      Recommends:  python3-simpleitk, libsimpleitk1-dev
+   -med-psychology
+    added:
+      Recommends:  python3-bioxtasraw
+
+ -- Andreas Tille <tille at debian.org>  Wed, 08 Feb 2023 11:04:38 +0100
 
 debian-med (3.7.3) unstable; urgency=medium
 


=====================================
dependency_data/debian-med_3.8.json
=====================================
@@ -0,0 +1 @@
+{"bio-dev": {"depends": [], "suggests": ["conda-package-handling", "python3-conda-package-streaming", "cwlformat", "python3-biopython-sql", "python-biopython-doc", "python3-joypy", "python3-ncls", "python3-pycosat", "libtfbs-perl", "libfreecontact-dev", "libfreecontact-perl", "libfreecontact-doc", "qiime", "q2-alignment", "q2-composition", "q2-cutadapt", "q2-dada2", "q2-deblur", "q2-demux", "q2-diversity", "q2-emperor", "q2-feature-classifier", "q2-feature-table", "q2-fragment-insertion", "q2-gneiss", "q2-longitudinal", "q2-metadata", "q2-phylogeny", "q2-quality-control", "q2-quality-filter", "q2-sample-classifier", "q2-shogun", "q2-taxa", "q2-types", "q2-vsearch", "q2cli", "q2cwl", "q2lint", "q2templates", "r-bioc-affxparser", "r-bioc-affy", "r-bioc-affyio", "r-bioc-altcdfenvs", "r-bioc-annotate", "r-bioc-annotationdbi", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-arrayexpress", "r-bioc-biocgenerics", "r-bioc-biocneighbors", "r-bioc-biomart", "r-bioc-biomformat", "r-bioc-biostrings", "r-bioc-biovizbase", "r-bioc-bitseq", "r-bioc-bridgedbr", "r-bioc-bsgenome", "r-bioc-cager", "r-bioc-cner", "r-bioc-complexheatmap", "r-bioc-cummerbund", "r-bioc-ctc", "r-bioc-dada2", "r-bioc-deseq", "r-bioc-deseq2", "r-bioc-dnacopy", "r-bioc-ebseq", "r-bioc-enrichedheatmap", "r-bioc-ensembldb", "r-bioc-genefilter", "r-bioc-geneplotter", "r-bioc-genomeinfodb", "r-bioc-genomicalignments", "r-bioc-genomicfeatures", "r-bioc-genomicranges", "r-bioc-geoquery", "r-bioc-go.db", "r-bioc-graph", "r-bioc-gseabase", "r-bioc-gsva", "r-bioc-gviz", "r-bioc-hypergraph", "r-bioc-impute", "r-bioc-iranges", "r-bioc-limma", "r-bioc-makecdfenv", "r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-mofa", "r-bioc-multiassayexperiment", "r-bioc-nanostringqcpro", "r-bioc-oligo", "r-bioc-oligoclasses", "r-bioc-org.hs.eg.db", "r-bioc-pcamethods", "r-bioc-phyloseq", "r-bioc-preprocesscore", "r-bioc-purecn", "r-bioc-qusage", "r-bioc-rbgl", "r-bioc-rsamtools", "r-bioc-rentrez", "r-bioc-rtracklayer", "r-bioc-s4vectors", "r-bioc-savr", "r-bioc-shortread", "r-bioc-snpstats", "r-bioc-structuralvariantannotation", "r-bioc-titancna", "r-bioc-tfbstools", "r-bioc-tximport", "r-bioc-variantannotation", "r-bioc-xvector", "r-cran-adegenet", "r-cran-adephylo", "r-cran-amap", "r-cran-biwt", "r-cran-dt", "r-cran-dynamictreecut", "r-cran-fastcluster", "r-cran-future.apply", "r-cran-future.batchtools", "r-cran-ica", "r-cran-itertools", "r-cran-kaos", "r-cran-metap", "r-cran-minerva", "r-cran-natserv", "r-cran-nmf", "r-cran-optimalcutpoints", "r-cran-parmigene", "r-cran-pcapp", "r-cran-proc", "r-cran-rann", "r-cran-rcpphnsw", "r-cran-robustrankaggreg", "r-cran-rocr", "r-cran-rook", "r-cran-rsvd", "r-cran-shazam", "r-cran-sitmo", "r-cran-venndiagram", "ruby-rgfa", "librostlab-doc", "librostlab-blast-doc", "libswarm2-dev", "python3-networkx", "libbam-dev", "libfast-perl", "libpbcopper-dev", "libminimap-dev", "libdisorder-dev", "cthreadpool-dev", "python3-pyflow", "libmilib-java", "vdjtools", "python3-alignlib", "python3-ctdopts", "ctdconverter", "libmodhmm-dev", "libsvmloc-dev", "python3-bel-resources", "libmaus2-dev", "libbbhash-dev", "python3-intake", "libconcurrentqueue-dev", "libxxsds-dynamic-dev", "libatomicqueue-dev", "libargs-dev", "libsuma-dev", "capsule-nextflow", "libcapsule-maven-nextflow-java", "libgatk-bwamem-java", "libgatk-bwamem-jni", "libgatk-fermilite-java", "libgatk-fermilite-jni", "libgenomicsdb-java", "libgenomicsdb-dev", "libgatk-native-bindings-java", "libicb-utils-java", "libbiosoup-dev", "libvbz-hdf-plugin-dev", "python3-bioblend", "libterraces-dev", "libbtllib-dev", "libsavvy-dev", "python3-cgelib"], "recommends": ["bioperl", "bioperl-run", "libncbi6-dev", "mcl", "biosquid", "cwltool", "snakemake", "python3-wdlparse", "libvibrant6-dev", "python3-biopython", "python3-cogent3", "python3-screed", "python3-cutadapt", "python3-dnaio", "python3-tinyalign", "ruby-bio", "libbiojava-java", "libbiojava4-java", "libbiojava6-java", "libgenome-dev", "libmuscle-dev", "libmems-dev", "libhtsjdk-java", "libai-fann-perl", "libbio-mage-perl", "libnhgri-blastall-perl", "libhdf5-dev", "libgo-perl", "libbio-graphics-perl", "libbio-coordinate-perl", "libbio-primerdesigner-perl", "libbio-alignio-stockholm-perl", "libbio-cluster-perl", "libbio-db-biofetch-perl", "libbio-db-embl-perl", "libbio-db-hts-perl", "libbio-db-ncbihelper-perl", "libbio-db-seqfeature-perl", "libbio-featureio-perl", "libbio-tools-run-remoteblast-perl", "libbio-variation-perl", "libace-perl", "libbiococoa-dev", "libcifpp-dev", "libstaden-read-dev", "libsrf-dev", "libzerg0-dev", "libzerg-perl", "librg-reprof-bundle-perl", "python3-corepywrap", "librcsb-core-wrapper0-dev", "libsbml5-dev", "sbmltoolbox", "libseqan2-dev", "libseqan3-dev", "libbio-mage-utils-perl", "libchado-perl", "libpal-java", "libpdb-redo-dev", "libbioparser-dev", "libspoa-dev", "libedlib-dev", "libthread-pool-dev", "python3-pyspoa", "libjebl2-java", "r-cran-boolnet", "r-cran-corrplot", "r-cran-distory", "r-cran-drinsight", "r-cran-forecast", "r-cran-fitdistrplus", "r-cran-genetics", "r-cran-gprofiler2", "r-cran-haplo.stats", "r-cran-metamix", "r-cran-phangorn", "r-cran-pheatmap", "r-cran-phylobase", "r-cran-pscbs", "r-cran-qqman", "r-cran-rentrez", "r-cran-rncl", "r-cran-rnexml", "r-cran-rotl", "r-cran-samr", "r-cran-sctransform", "r-cran-seurat", "r-cran-seqinr", "r-cran-tsne", "r-cran-vegan", "r-cran-webgestaltr", "r-other-apmswapp", "r-bioc-biobase", "libffindex0-dev", "libpwiz-dev", "librostlab3-dev", "librostlab-blast0-dev", "librg-blast-parser-perl", "libsort-key-top-perl", "libhmsbeagle-dev", "libforester-java", "libbambamc-dev", "libbamtools-dev", "libpbbam-dev", "libbigwig-dev", "libbio-das-lite-perl", "libopenms-dev", "libgenometools0-dev", "librdp-taxonomy-tree-java", "python3-biom-format", "python3-rdkit", "libgenome-perl", "libgenome-model-tools-music-perl", "pyfai", "libhts-dev", "python3-htseq", "python3-intervaltree-bio", "python3-csb", "python3-misopy", "python3-freecontact", "python3-pymummer", "libkmer-dev", "libsnp-sites1-dev", "libssm-dev", "librelion-dev", "libdivsufsort-dev", "nim-hts-dev", "nim-kexpr-dev", "nim-lapper-dev", "bioclipse", "libgff-dev", "python3-pysam", "python3-pbcore", "python3-cobra", "python3-pybigwig", "python3-bcbio-gff", "libtabixpp-dev", "python3-ruffus", "python3-dendropy", "python3-skbio", "libparasail-dev", "python3-parasail", "python3-pbconsensuscore", "python3-consensuscore2", "libconsensuscore-dev", "python3-pbcommand", "python3-pyvcf", "python3-pyfaidx", "python3-shasta", "python3-sqt", "python3-kineticstools", "libqes-dev", "libfast5-dev", "python3-fast5", "ont-fast5-api", "libpbseq-dev", "libpbdata-dev", "libpbihdf-dev", "libblasr-dev", "libminimap2-dev", "libncl-dev", "libngs-sdk-dev", "libngs-java", "python3-ngs", "libncbi-vdb-dev", "libqcpp-dev", "libbpp-core-dev", "libbpp-phyl-dev", "libbpp-phyl-omics-dev", "libbpp-popgen-dev", "libbpp-qt-dev", "libbpp-raa-dev", "libbpp-seq-dev", "libbpp-seq-omics-dev", "octace-bioinfo", "ruby-crb-blast", "libsmithwaterman-dev", "libfastahack-dev", "libssw-dev", "libssw-java", "libfml-dev", "libgkarrays-dev", "libjloda-java", "libvcflib-dev", "libswiss-perl", "python3-pybedtools", "python3-gffutils", "python3-bx", "toil", "python3-galaxy-lib", "libbio-eutilities-perl", "libseqlib-dev", "libroadrunner-dev", "python3-roadrunner", "python3-biotools", "bio-tradis", "python3-biomaj3", "python3-ete3", "python3-gfapy", "goby-java", "python3-seqcluster", "python3-cyvcf2", "libgatbcore-dev", "python3-airr", "python3-presto", "python3-bcbio", "libpll-dev", "libstatgen-dev", "python3-pyani", "python3-treetime", "libbio-tools-run-alignment-tcoffee-perl", "libbio-asn1-entrezgene-perl", "libbio-chado-schema-perl", "libbio-samtools-perl", "libbio-scf-perl", "libbio-tools-phylo-paml-perl", "libbio-tools-run-alignment-clustalw-perl", "python3-pybel", "python3-mirtop", "libnexml-java", "python3-cgecore", "python3-deeptools", "python3-deeptoolsintervals", "python3-py2bit", "python3-loompy", "gffread", "libgclib-dev", "biobambam2", "libcdk-java", "libhtscodecs-dev", "python3-torch", "python3-pyabpoa", "python3-anndata", "python3-bx", "python3-cooler", "python3-pairix", "python3-pangolearn", "python3-pyranges", "python3-streamz", "libssu-dev", "python3-unifrac", "python3-nanoget", "python3-peptidebuilder", "libopenmm-dev", "libmmblib-dev", "python3-scanpy", "python3-propka", "python3-cigar", "python3-compclust", "libslow5-dev", "python3-slow5", "python3-gtfparse", "python3-pyfastx", "python3-bioframe"], "ignore": ["golang-github-biogo-hts-dev"], "avoid": []}, "oncology": {"depends": [], "suggests": ["python3-dicompylercore"], "recommends": ["uw-prism", "orthanc-wsi", "planunc", "simrisc"], "ignore": [], "avoid": []}, "bio-ngs": {"depends": [], "suggests": ["python3-anndata", "r-bioc-isoformswitchanalyzer", "r-bioc-mofa2", "graphmap2", "nanolyse", "nanoplot"], "recommends": ["bedtools", "bwa", "bowtie", "blasr", "daligner", "mhap", "last-align", "wham-align", "maq", "picard-tools", "r-bioc-edger", "r-bioc-hilbertvis", "r-bioc-rsubread", "rna-star", "samtools", "sra-toolkit", "ssake", "tabix", "bcftools", "vcftools", "velvet", "libvcflib-tools", "mothur", "qiime", "q2cli", "microbiomeutil", "r-bioc-metagenomeseq", "rtax", "sortmerna", "srst2", "stacks", "subread", "sumatra", "sumaclust", "vsearch", "wigeon", "anfo", "arden", "bowtie", "bowtie2", "artfastqgenerator", "art-nextgen-simulation-tools", "last-align", "maq", "ssake", "velvet | velvet-long", "bamtools", "bcbio", "bcftools", "berkeley-express", "bio-rainbow", "canu", "crac", "cufflinks", "cutadapt", "deepnano", "discosnp", "dnaclust", "dwgsim", "ea-utils", "fastaq", "fastp", "fastqc", "flexbar", "fml-asm", "fsm-lite", "grinder", "giira", "hinge", "hilive", "hisat2", "idba", "igdiscover", "igv", "iva", "khmer", "kissplice", "kraken", "kraken2", "macs", "mapdamage", "maqview", "mira-assembler", "mapsembler2", "nanopolish", "paleomix", "pbsuite", "pbjelly", "pbhoney", "pirs", "pizzly", "placnet", "poretools", "python3-gffutils", "python3-pybedtools", "python3-sqt", "qcumber", "quorum", "r-bioc-deseq2", "salmon", "sambamba", "samblaster", "scythe", "seqprep", "seqtk", "sga", "sickle", "smalt", "smrtanalysis", "snap-aligner", "sniffles", "snp-sites", "snpomatic", "soapdenovo", "soapdenovo2", "spades", "sprai", "sra-toolkit", "stringtie", "transrate-tools", "trimmomatic", "trinityrnaseq", "uc-echo", "velvetoptimiser", "kissplice", "scoary", "umap", "mosaik-aligner", "r-cran-tcr", "r-cran-tigger", "r-cran-alakazam", "r-cran-shazam", "igor", "python3-airr", "python3-presto", "changeo", "vdjtools", "forge", "uc-echo", "annovar"], "ignore": [], "avoid": []}, "typesetting": {"depends": [], "suggests": ["kbibtex", "biber", "bibus", "jabref-plugin-oo", "r-cran-qqman"], "recommends": ["texlive-science", "texlive-latex-extra", "king"], "ignore": [], "avoid": []}, "cloud": {"depends": [], "suggests": [], "recommends": ["altree", "clearcut", "fastdnaml", "fasttree", "parsinsert", "phyml", "phyutility", "prime-phylo", "mrbayes", "tree-puzzle | tree-ppuzzle", "alien-hunter", "bagpipe", "fastlink", "loki", "gasic", "genometools", "plink", "plink1.9", "plink2", "probabel", "r-cran-qtl", "r-other-mott-happy.hbrem", "amap-align", "blast2", "biosquid", "boxshade", "cassiopee", "cdbfasta", "cd-hit", "clustalo", "clustalw", "conservation-code", "dialign", "dialign-tx", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "exonerate", "gff2aplot", "gff2ps", "glam2", "gmap", "hmmer", "jellyfish", "kalign", "mafft", "mlv-smile", "mummer", "muscle", "muscle3", "neobio", "poa", "prank", "probcons", "proda", "sibsim4", "sigma-align", "sim4", "snap", "squizz", "t-coffee", "wise", "bamtools", "bedtools", "flexbar", "picard-tools", "samtools", "tabix", "vcftools", "anfo", "cufflinks", "bowtie", "bowtie2", "bwa", "last-align", "maq", "perm", "hisat2", "smalt", "soapdenovo", "soapdenovo2", "abyss", "mapsembler2", "idba", "minia", "mira-assembler", "ssake", "velvet", "ampliconnoise", "arden", "fastqc", "discosnp", "dnaclust", "fitgcp", "giira", "grinder", "kissplice", "macs", "mothur", "paraclu", "r-bioc-hilbertvis", "sra-toolkit", "aragorn", "infernal", "rnahybrid", "rtax", "autodock", "autodock-vina", "autogrid", "concavity", "dssp", "freecontact", "gromacs", "hhsuite", "mustang", "pdb2pqr", "raster3d", "theseus", "melting", "mipe", "ncbi-epcr", "primer3", "acedb-other", "disulfinder", "ncbi-tools-bin", "ncoils", "readseq", "tigr-glimmer", "seqan-apps", "staden-io-lib-utils", "python3-cogent3", "aevol", "python3-biomaj3-cli", "bioperl", "bioperl-run", "clonalframe", "circos", "datamash", "prodigal", "python3-biopython", "qiime", "r-bioc-edger", "r-cran-pvclust", "r-cran-vegan"], "ignore": [], "avoid": []}, "bio": {"depends": [], "suggests": ["conda-package-handling", "dascrubber", "emboss-explorer", "dnapi", "nano-snakemake", "catfishq", "q2-cutadapt", "q2-demux", "q2-feature-classifier", "q2-feature-table", "q2-metadata", "q2-quality-filter", "q2-types", "q2cli", "q2templates", "q2-taxa", "q2-alignment", "q2-emperor", "q2-composition", "q2-sample-classifier", "q2-vsearch", "q2-dada2", "q2-deblur", "q2-diversity", "q2-gneiss", "q2-longitudinal", "q2-phylogeny", "q2-quality-control", "q2-fragment-insertion", "tandem-genotypes", "python3-intake", "python3-ncls", "python3-pychopper", "python3-pyrle", "python3-pyranges", "python3-anndata", "adun.app", "illustrate", "science-workflow", "getdata", "epigrass", "hts-nim-tools", "idseq-bench", "libhdf5-dev", "libhnswlib-dev", "metastudent-data", "metastudent-data-2", "mrs", "nanocomp", "python3-alignlib", "python3-cgecore", "python3-cyvcf2", "python3-deeptools", "python3-deeptoolsintervals", "python3-htseq", "python3-loompy", "python3-nanomath", "python3-nanoget", "python3-pybel", "python3-pyfaidx", "python3-pyflow", "python3-py2bit", "python3-pysam", "python3-tinyalign", 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\ No newline at end of file



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