[Blends-commit] [Git][blends-team/med][master] 4 commits: Drop mgltools-pmv which is constantly broken for several years
Andreas Tille
gitlab at salsa.debian.org
Fri Dec 6 17:50:15 GMT 2019
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
d1aaa341 by Andreas Tille at 2019-12-06T17:09:18Z
Drop mgltools-pmv which is constantly broken for several years
- - - - -
db3c9e30 by Andreas Tille at 2019-12-06T17:22:35Z
Re-render dependencies
- - - - -
20942675 by Andreas Tille at 2019-12-06T17:24:05Z
Render changelog entry and dependency data
- - - - -
8da479d6 by Andreas Tille at 2019-12-06T17:27:25Z
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + dependency_data/debian-med_3.5.1.json
- tasks/bio
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,30 @@
-debian-med (3.5.1) UNRELEASED; urgency=medium
+debian-med (3.5.1) unstable; urgency=medium
* Drop fastx-toolkit and libgtextutils since unmaintained and
libgtextutils has issued with gcc9
+ * Drop mgltools-pmv which is constantly broken for several years
- -- Andreas Tille <tille at debian.org> Mon, 02 Dec 2019 09:54:51 +0100
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-bio
+ added:
+ Recommends: r-bioc-geoquery, r-cran-wgcna
+ removed:
+ Recommends: mgltools-pmv, r-other-wgcna, fastx-toolkit
+ -med-bio-dev
+ added:
+ Suggests: r-bioc-geoquery
+ removed:
+ Suggests: libgtextutils-dev
+ -med-bio-ngs
+ removed:
+ Recommends: fastx-toolkit
+ -med-cloud
+ removed:
+ Recommends: fastx-toolkit
+
+ -- Andreas Tille <tille at debian.org> Fri, 06 Dec 2019 18:24:39 +0100
debian-med (3.5) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -211,7 +211,6 @@ Recommends: abacas,
fastqc,
fastqtl,
fasttree,
- fastx-toolkit,
ffindex,
figtree,
fitgcp,
@@ -543,7 +542,6 @@ Recommends: abacas,
theseus,
tigr-glimmer,
tm-align,
- tnseq-transit,
toil,
topp,
toppred,
@@ -690,7 +688,6 @@ Suggests: acacia,
metastudent-data-2,
metastudent-data-3,
mgltools-cadd,
- mgltools-pmv,
mgltools-vision,
migrate,
mindthegap,
@@ -784,6 +781,7 @@ Suggests: acacia,
r-bioc-annotationhub,
r-bioc-aroma.light,
r-bioc-ensembldb,
+ r-bioc-geoquery,
r-bioc-go.db,
r-bioc-metagenomeseq,
r-bioc-mofa,
@@ -803,8 +801,8 @@ Suggests: acacia,
r-cran-sctransform,
r-cran-seurat,
r-cran-tsne,
+ r-cran-wgcna,
r-other-apmswapp,
- r-other-wgcna,
raccoon,
ragout,
raxml-ng,
@@ -851,6 +849,7 @@ Suggests: acacia,
tide,
tigr-glimmer-mg,
tn-seqexplorer,
+ tnseq-transit,
treebuilder3d,
treetime,
trim-galore,
@@ -896,6 +895,7 @@ Recommends: bio-tradis,
libbio-coordinate-perl,
libbio-das-lite-perl,
libbio-eutilities-perl,
+ libbio-graphics-perl,
libbio-mage-perl,
libbio-mage-utils-perl,
libbio-primerdesigner-perl,
@@ -1020,7 +1020,6 @@ Recommends: bio-tradis,
python3-rdkit,
python3-ruffus,
python3-screed,
- python3-skbio,
python3-sqt,
python3-treetime,
r-bioc-biobase,
@@ -1060,7 +1059,6 @@ Suggests: biobambam2,
galaxy-lib,
libbam-dev,
libbigwig-dev,
- libbio-graphics-perl,
libbiod-dev,
libdisorder-dev,
libfast-perl,
@@ -1068,7 +1066,6 @@ Suggests: biobambam2,
libfreecontact-doc,
libgclib,
libgoby-java,
- libgtextutils-dev,
libmaus2-dev,
libmilib-java,
libmodhmm-dev,
@@ -1110,6 +1107,7 @@ Suggests: biobambam2,
python3-pyflow,
python3-roadrunner,
python3-seqcluster,
+ python3-skbio,
r-bioc-affy,
r-bioc-affyio,
r-bioc-altcdfenvs,
@@ -1137,6 +1135,7 @@ Suggests: biobambam2,
r-bioc-genomicalignments,
r-bioc-genomicfeatures,
r-bioc-genomicranges,
+ r-bioc-geoquery,
r-bioc-go.db,
r-bioc-graph,
r-bioc-gviz,
@@ -1244,7 +1243,6 @@ Recommends: abyss,
fastlink,
fastqc,
fasttree,
- fastx-toolkit,
fitgcp,
flexbar,
freecontact,
@@ -1605,7 +1603,6 @@ Recommends: cimg-dev,
libbart-dev,
libcifti-dev,
libedf-dev,
- libgdcm2-dev,
libgdf-dev,
libgiftiio-dev,
libinsighttoolkit4-dev,
@@ -1646,6 +1643,7 @@ Suggests: emokit,
libcv-dev,
libeegdev-dev,
libfreeimage-dev,
+ libgdcm2-dev,
libics-dev,
liblimereg-dev,
libmni-perllib-perl,
=====================================
dependency_data/debian-med_3.5.1.json
=====================================
@@ -0,0 +1 @@
+{"cms": {"depends": [], "suggests": ["zope-zms", "hid"], "recommends": ["xnat"], "ignore": [], "avoid": []}, "bio": {"depends": [], "suggests": ["dascrubber", "emboss-explorer", "adun.app", "cain", "skewer", "science-workflow", "getdata", "giira", "metastudent-data", "metastudent-data-2", "metastudent-data-3", "mrs", "python3-alignlib", "python3-loompy", "python3-py2bit", "r-bioc-tximport", "r-cran-corrplot", "r-cran-dynamictreecut", "r-cran-forecast", "r-cran-gprofiler", "r-cran-fitdistrplus", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-ensembldb", "r-bioc-go.db", "r-bioc-qusage", "r-cran-qqman", "r-cran-rentrez", "r-cran-boolnet", "r-cran-pheatmap", "r-bioc-savr", "r-cran-sctransform", "r-bioc-tximport", "strelka", "python3-pyflow", "maude"], "recommends": ["altree", "beast-mcmc", "beast2-mcmc", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle", "probalign", "treeviewx", "figtree", "hyphy-mpi | hyphy-pt", "spread-phy", "omegamap", "sweed", "phylip", "fastlink", "loki", "plink", "plink1.9", "r-cran-qtl", "r-cran-genabel", "gemma", "bolt-lmm", "amap-align", "boxshade", "gff2aplot", "muscle", "sim4", "sibsim4", "tabix", "wise", "maqview", "blasr", "daligner", "mhap", "bwa", "mummer", "e-mem", "ncbi-blast+-legacy", "plast", "ncbi-blast+", "mafft", "sra-toolkit", "t-coffee", "kalign", "ghmm", "hmmer", "gramalign", "exonerate", "elph", "dialign", "dialign-tx", "poa", "probcons", "proda", "seaview", "sigma-align", "wham-align", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "arb", "clustalx", "clustalo", "clustalw", "mothur", "bowtie", "bowtie2", "transtermhp", "last-align", "maq", "ssake", "velvet | velvet-long", "qiime", "scoary", "umap", "infernal", "rnahybrid", "adun-core", "avogadro", "garlic", "gamgi", "gdpc", "ghemical", "jmol", "pymol", "r-cran-bio3d", "msxpertsuite", "gromacs", "rasmol", "viewmol", "qutemol", "modeller", "plasmidomics", "gff2ps", "ncbi-epcr", "ncbi-tools-bin", "ncbi-tools-x11", "perlprimer", "readseq", "tigr-glimmer", "melting", "mipe", "primer3", "artemis", "gbrowse", "python3-biomaj3-daemon", "glam2", "raster3d", "phyml", "autodock", "autogrid", "autodock-vina", "autodocktools", "mgltools-vision", "mgltools-cadd", "mustang", "probabel", "theseus", "staden-io-lib-utils", "samtools", "bedtools", "datamash", "gassst", "hinge", "r-bioc-hilbertvis", "r-other-mott-happy.hbrem", "seq-gen", "snp-sites", "mira-assembler", "alien-hunter", "seqan-apps", "ncoils", "gentle", "gmap", "igv", "picard-tools", "acedb-other", "blixem", "dotter", "belvu", "paml", "velvetoptimiser", "ensembl", "mrbayes", "pdb2pqr", "squizz", "clonalframe", "clonalframeml", "dssp", "jellyfish", "jellyfish1", "ballview", "pynast", "pizzly", "raxml", "seqcluster", "mlv-smile", "cd-hit", "cufflinks", "eigensoft", "grinder", "jalview", "reprof", "tm-align", "norsnet", "norsp", "predictnls", "prime-phylo", "proftmb", "profbval", "profisis", "hhsuite", "ffindex", "flexbar", "blimps-utils", "sift", "neobio", "ray", "ugene", "logol", "soapdenovo", "soapdenovo2", "soapsnp", "soapaligner", "microbiomeutil", "chimeraslayer", "nast-ier", "wigeon", "minia", "trimmomatic", "trim-galore", "saint", "rtax", "rate4site", "rna-star", "sailfish", "topp", "openms", "scythe", "sickle", "smalr", "kmc", "king-probe", "ncl-tools", "tvc", "libvcflib-tools", "bppsuite", "bppphyview", "acacia", "adapterremoval", "aegean", "andi", "arden", "artfastqgenerator", "art-nextgen-simulation-tools", "assemblytics", "augustus", "baitfisher", "bandage", "beagle", "bedops", "biceps", "cnvkit", "csb", "diamond-aligner", "emperor", "euler2", "euler-sr", "fitgcp", "gasic", "ipig", "aevol", "alter-sequence-alignment", "amos-assembler", "hawkeye", "anfo", "apollo", "aragorn", "ariba", "atac", "atropos", "axe-demultiplexer", "axparafit", "axpcoords", "bali-phy", "barrnap", "bamtools", "bagpipe", "bax2bam", "bcbio", "bcftools", "bigsdb", "bio-eagle", "bio-tradis", "biobambam2", "biosyntax", "bismark", "bitseq", "blat", "blobology", "bio-rainbow", "braker", "card-rgi", "cassiopee", "ccs", "cdbfasta", "centrifuge", "cellprofiler", "chromhmm", "cgview", "brig", "cct", "cinema", "circlator", "clearcut", "clonalorigin", "cluster3", "chromimpute", "codonw", "condetri", "contrafold", "crac", "crossbow", "crux-toolkit", "cutadapt", "cytoscape", "dawg", "dazzdb", "dazzle", "deepbinner", "delly", "deepnano", "dendroscope", "dindel", "dwgsim", "ea-utils", "ecell", "ecopcr", "edtsurf", "emmax", "examl", "raxml-ng", "exabayes", "berkeley-express", "falcon", "fasta3", "fasttree", "fastahack", "fastaq", "fastml", "fastp", "fastqc", "fastqtl", "ffp", "filtlong", "unc-fish", "fml-asm", "forester", "freecontact", "freebayes", "fsa", "fsm-lite", "garli", "gatb-core", "gatk", "genometester", "genometools", "gffread", "grabix", "graphlan", "gwama", "gubbins", "haploview", "harvest-tools", "hilive", "hisat2", "hmmer2", "htqc", "idba", "idefix", "igdiscover", "indelible", "iqtree", "iva", "jaligner", "jbrowse", "jmodeltest", "kaptive", "kleborate", "kempbasu", "kineticstools", "kissplice", "kma", "kmerresistance", "kraken", "kraken2", "lagan", "lambda-align", "lambda-align2", "leaff", "ltrsift", "lofreq", "kallisto", "khmer", "kmer", "radiant", "lefse", "mach-haplotyper", "macs", "macsyfinder", "maffilter", "mage2tab", "tab2mage", "malt", "manta", "mapdamage", "martj", "mash", "progressivemauve", "mauve-aligner", "meme", "meryl", "metabit", "metaphlan2", "metastudent", "microbegps", "mindthegap", "miniasm", "minimac4", "minimap", "minimap2", "mirtop", "molekel", "mosaik-aligner", "mosdepth", "mmseqs2", "mpsqed", "mptp", "mugsy", "multiqc", "murasaki | murasaki-mpi", "mview", "nanocall", "nanook", "nanopolish", "ncbi-entrez-direct", "ncbi-seg", "nextsv", "ngila", "ngsqctoolkit", "nw-align", "oases", "obitools", "oncofuse", "optimir", "optitype", "paipline", "pal2nal", "paleomix", "paraclu", "parsinsert", "parsnp", "partitionfinder", "patman", "patristic", "pbalign", "pbbarcode", "pbdagcon", 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"r-bioc-geoquery", "r-bioc-ebseq", "r-bioc-impute", "r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-phyloseq", "r-bioc-mofa", "r-bioc-multiassayexperiment", "r-bioc-limma", "r-bioc-bitseq", "r-bioc-pcamethods", "r-cran-samr", "r-cran-rotl", "r-cran-adegenet", "r-cran-adephylo", "r-cran-ape", "r-cran-distory", "r-cran-drinsight", "r-cran-kaos", "r-cran-metamix", "r-cran-phangorn", "r-cran-phytools", "r-cran-pscbs", "r-cran-seurat", "r-cran-seqinr", "r-bioc-tfbstools", "r-bioc-cner", "r-cran-treescape", "r-cran-tsne", "r-cran-vegan", "r-cran-webgestaltr", "r-other-apmswapp", "r-other-hms-dbmi-spp", "r-cran-wgcna", "relion-bin+gui | relion-bin+mpi+gui", "relion-bin | relion-bin+mpi", "rdp-alignment", "rdp-readseq", "rdp-classifier", "reapr", "repeatmasker-recon", "repeatmasker", "resfinder", "roadtrips", "roary", "roguenarok", "rsat", "rsem", "sambamba", "samblaster", "salmon", "sap", "scrm", "sga", "seer", "segemehl", "seq-seq-pan", "seqmagick", "seqprep", "seqsero", "seqtk", "sequenceconverter.app", "sibelia", "sina", "sistr", "situs", "sim4db", "skesa", "smalt", "smithwaterman", "ssw-align", "smrtanalysis", "snpeff", "snpomatic", "solvate", "sortmerna", "snap-aligner", "sniffles", "sourmash", "spaced", "spades", "spaln", "sparta", "sprai", "srst2", "ssaha", "sspace", "staden", "stacks", "strap", "strap-base", "stringtie", "subread", "suitename", "sumatra", "sumaclust", "sumtrees", "surankco", "swarm", "tacg", "tantan", "toppred", "transdecoder", "tnseq-transit", "tn-seqexplorer", "toil", "tracetuner", "transrate-tools", "treeview", "trinityrnaseq", "uc-echo", "umis", "unanimity", "unicycler", "varna", "varmatch", "varscan", "vcfanno", "vdjtools", "vg", "vienna-rna", "virulencefinder", "vmd", "vsearch", "yaha", "canu", "zalign", "zodiac-zeden", "discosnp", "mapsembler2", "dnaclust", "r-cran-tcr", "r-cran-tigger", "r-cran-alakazam", "r-cran-shazam", "igor", "r-cran-sdmtools", "python3-presto", "changeo", "ncbi-igblast", "pigx-rnaseq", "pigx-scrnaseq", "copycat", "btk-core", "asap", "cactus", "contralign", "concavity", "conservation-code", "galaxy", "genographer", "phylographer", "phylowin", "phpphylotree", "twain", "rose", "glimmerhmm", "genezilla", "exalt", "jigsaw", "genesplicer", "mummergpu", "amoscmp", "minimus", "bambus", "gmv", "pyrophosphate-tools", "figaro", "mirbase", "uniprime", "genetrack", "operondb", "trnascan-se", "cdna-db", "coot", "caftools", "roche454ace2caf", "big-blast", "estferret", "lamarc", "lucy", "maxd", "mesquite", "migrate", "msatfinder", "oligoarrayaux", "partigene", "pfaat", "prot4est", "qtlcart", "rbs-finder", "splitstree", "taverna", "taxinspector", "tetra", "trace2dbest", "estscan", "profit", "obo-edit", "phagefinder", "compclust", "treebuilder3d", "excavator", "treetime", "abacas", "profnet-bval", "profnet-chop", "profnet-con", "profnet-isis", "profnet-md", "profnet-norsnet", "profnet-prof", "profnet-snapfun", "profphd-net", "profphd-utils", "profphd", "abyss", "ampliconnoise", "disulfinder", "circos", "runcircos-gui", "populations", "raccoon", "racon", "spoa", "rampler", "librg-utils-perl", "snap", "pyvcf", "vcftools", "beads", "x-tandem-pipeline", "forge", "metarep", "arachne", "maker2", "rmblast", "e-hive", "cmap", "gbrowse-syn", "tripal", "genemark", "annovar", "python3-orange", "tigr-glimmer-mg"], "ignore": ["mozilla-biofox", "riso", "catissuecore", "trapss"], "avoid": []}, "research": {"depends": [], "suggests": [], "recommends": ["r-cran-rpact", "openclinica"], "ignore": [], "avoid": []}, "data": {"depends": [], "suggests": ["sleepyhead", "oscar"], "recommends": ["freediams", "freemedforms-freedata", "python3-hl7", "drugref.org"], "ignore": [], "avoid": []}, "epi": {"depends": [], "suggests": ["r-cran-msm", "r-cran-cmprsk", "shiny-server", "repast"], "recommends": ["epigrass", "r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi", "r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "r-cran-seroincidence", "ushahidi", "r-cran-lexrankr", "r-cran-sf", "r-cran-sjplot", "python3-treetime", "netepi-analysis", "netepi-collection", "epifire"], "ignore": [], "avoid": []}, "bio-ngs": {"depends": [], "suggests": [], "recommends": ["bedtools", "bwa", "bowtie", "blasr", "daligner", "mhap", "last-align", "wham-align", "maq", "picard-tools", "r-bioc-hilbertvis", "rna-star", "samtools", "sra-toolkit", "ssake", "tabix", "bcftools", "vcftools", "velvet", "libvcflib-tools", "mothur", "qiime", "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", "dindel", "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", "pbh5tools", "pbjelly", "pbhoney", "pirs", "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", "dindel", "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": []}, "his": {"depends": [], "suggests": [], "recommends": ["care2x", "fis-gtm", "vista-foia", "ewd-920", "orthanc-wsi", "tryton-modules-health", "openmaxims", "world-vista", "ipath", "patientos", "openmrs", "hkma-cms", "oscar-mcmaster", "openeyes"], "ignore": [], "avoid": []}, "pharmacy": {"depends": [], "suggests": [], "recommends": ["chemtool", "raccoon", "r-cran-dosefinding", "r-cran-rpact"], "ignore": [], "avoid": []}, "practice": {"depends": [], "suggests": ["libctapimkt1", "openpms", "resmedicinae", "sqlclinic", "openrep"], "recommends": ["gnumed-client", "gnumed-server", "libchipcard-tools", "ginkgocadx", "freediams", "freemedforms-emr", "r-cran-medadherence", "entangle", "sleepyhead", "oscar", "orthanc", "orthanc-wsi", "medintux", "mirth", "tinyheb", "mirrormed", "elexis", "freeb", "freemed", "elementalclinic", "openemr", "clearhealth", "proteus", "thera-pi", "freeshim", "remitt", "qrisk2"], "ignore": ["clearhealth"], "avoid": []}, "laboratory": {"depends": [], "suggests": [], "recommends": ["opencfu", "orthanc-wsi", "openelis", "openfreezer", "catissuesuite"], "ignore": [], "avoid": []}, "cloud": {"depends": [], "suggests": ["python-cogent"], "recommends": ["altree", "clearcut", "fastdnaml", "fasttree", "parsinsert", "phyml", "phyutility", "prime-phylo", "mrbayes", "tree-puzzle | tree-ppuzzle", "alien-hunter", "bagpipe", "fastlink", "loki", "gasic", "genometools", "plink", "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", "neobio", "poa", "prank", "probcons", "proda", "pynast", "sibsim4", "sigma-align", "sim4", "snap", "squizz", "t-coffee", "wise", "zalign", "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", "aevol", "python3-biomaj3-cli", "bioperl", "bioperl-run", "cain", "clonalframe", "circos", "datamash", "prodigal", "python3-biopython", "qiime", "r-cran-pvclust", "r-cran-vegan"], "ignore": [], "avoid": []}, "imaging": {"depends": [], "suggests": ["imagemagick", "pngquant", "imview", "trimage", "python-nipy", "python-nipype", "python-nitime", "conquest-dbase", "conquest-mysql", "conquest-postgres", "conquest-sqlite", "paraview", "orthanc-webviewer", "orthanc-dicomweb", "orthanc-imagej", "orthanc-postgresql", "orthanc-mysql", "visit", "mrisim", "connectomeviewer", "eeglab", "elastix", "python-pyxid", "python-dipy", "dtitk", "openwalnut-qt4", "miview", "cmtk", "freesurfer", "isis", "pymeg", "stabilitycalc", "hid", "incf-nidash-oneclick-clients", "science-workflow"], "recommends": ["amide", "ctsim", "ctn", "dicomnifti", "imagej", "minc-tools", "medcon", "python3-nibabel", "python3-dicom", "xmedcon", "dcmtk", "nifti-bin", "aeskulap", "fsl", "fslview", "via-bin", "gwyddion", "sofa-apps", "python3-mvpa2", "caret", "libgdcm-tools", "slicer", "lipsia", "dicom3tools", "imagevis3d", "odin", "dicomscope", "pixelmed-apps", "vmtk", "ginkgocadx", "openslide-tools", "conquest-common", "camitk-imp", "crea", "orthanc", "teem-apps", "bioimagesuite", "drjekyll", "libdcm4che-java", "dcm4chee", "piano", "mesa-test-tools", "devide", "dicom4j", "opendicom.net", "afni", "blox", "ecg2png", "kradview", "opensourcepacs", "mni-autoreg", "mni-n3", "brainvisa", "maris", "micromanager", "fiji", "cdmedicpacs", "stir", "openelectrophy", "invesalius", "mricron", "voxbo", "mrtrix", "mrtrix3", "ants", "itksnap", "mriconvert", "mia-tools", "mialmpick", "mia-viewit", "ismrmrd-tools", "sigviewer", "tifffile", "mni-icbm152-nlin-2009", "mni-colin27-nifti", "mipav", "jist", "openmeeg-tools", "jemris", "insightapplications", "tempo", "dti-query", "plastimatch", "medisnap", "gimias", "mayam", "xnat", "biosig-tools", "python3-surfer", "dicoogle", "cellprofiler", "bioimagexd", "omero", "king", "vtk-dicom-tools", "gdf-tools", "fw4spl", "bart", "bart-view", "dcm2niix", "orthanc-wsi", "odil"], "ignore": [], "avoid": []}, "typesetting": {"depends": [], "suggests": ["kbibtex", "biber", "bibus", "jabref-plugin-oo", "r-cran-qqman"], "recommends": ["texlive-science", "texlive-latex-extra", "king"], "ignore": [], "avoid": []}, "bio-phylogeny": {"depends": [], "suggests": ["python3-treetime"], "recommends": ["altree", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle", "probalign", "treeviewx", "phylip", "muscle", "t-coffee", "kalign", "hmmer", "exonerate", "dialign", "dialign-tx", "poa", "probcons", "proda", "seaview", "sigma-align", "gmap", "clustalx", "clustalw", "mustang", "phyml", "beast-mcmc", "tm-align", "mrbayes", "figtree", "populations", "proalign", "prottest", "treeview", "phylowin", "gbioseq", "phpphylotree", "jstreeview", "treetime", "jmodeltest", "forester", "patristic", "spread-phy", "iqtree"], "ignore": [], "avoid": []}, "physics": {"depends": [], "suggests": ["paw-demos", "libbiosig-dev", "python3-biosig", "octave-biosig", "openvibe", "python3-multipletau"], "recommends": ["paw++", "paw", "octave", "r-base", "biosig-tools", "gdf-tools", "gate"], "ignore": [], "avoid": []}, "dental": {"depends": [], "suggests": [], "recommends": ["openmolar", "imagetooth", "entangle"], "ignore": [], "avoid": []}, "psychology": {"depends": [], "suggests": ["science-psychophysics", "python-pyepl"], "recommends": ["praat", "r-cran-foreign", "psignifit", "r-cran-psy", "psychopy", "r-cran-psych", "r-cran-psychometric", "r-cran-psychotree", "r-cran-psyphy"], "ignore": [], "avoid": []}, "rehabilitation": {"depends": [], "suggests": ["aghermann"], "recommends": ["sitplus"], "ignore": [], "avoid": []}, "oncology": {"depends": [], "suggests": [], "recommends": ["uw-prism", "orthanc-wsi", "planunc", "dicompyler"], "ignore": [], "avoid": []}, "bio-dev": {"depends": [], "suggests": ["python3-biopython-sql", "python-biopython-doc", "python-cogent", "python3-pycosat", "libfreecontact-doc", "python-corepywrap", "r-bioc-affy", "r-bioc-affyio", "r-bioc-altcdfenvs", "r-bioc-annotate", "r-bioc-annotationdbi", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-biocgenerics", "r-bioc-biomart", "r-bioc-biomformat", "r-bioc-biostrings", "r-bioc-biovizbase", "r-bioc-bitseq", "r-bioc-bsgenome", "r-bioc-cner", "r-bioc-cummerbund", "r-bioc-dada2", "r-bioc-deseq2", "r-bioc-dnacopy", "r-bioc-ebseq", "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-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-pcamethods", "r-bioc-phyloseq", "r-bioc-preprocesscore", "r-bioc-qusage", "r-bioc-rbgl", "r-bioc-rsamtools", "r-bioc-rentrez", "r-bioc-rtracklayer", "r-bioc-savr", "r-bioc-shortread", "r-bioc-snpstats", "r-bioc-tfbstools", "r-bioc-tximport", "r-bioc-variantannotation", "r-bioc-xvector", "r-cran-dt", "r-cran-dynamictreecut", "r-cran-future.apply", "r-cran-future.batchtools", "r-cran-ica", "r-cran-kaos", "r-cran-metap", "r-cran-natserv", "r-cran-pcapp", "r-cran-proc", "r-cran-rann", "r-cran-rocr", "r-cran-rsvd", "ruby-rgfa", "librostlab-doc", "librostlab-blast-doc", "libswarm2-dev", "python-pbcore", "python-pbh5tools", "python-pbcommand", "python-kineticstools", "libbam-dev", "libfast-perl", "libpbcopper-dev", "libdisorder-dev", "python3-pyflow", "libmilib-java", "vdjtools", "python3-alignlib", "python3-ctdopts", "ctdconverter", "libmodhmm-dev", "libsvmloc-dev", "libmaus2-dev"], "recommends": ["bioperl", "bioperl-run", "libncbi6-dev", "mcl", "biosquid", "cwltool", "snakemake", "libvibrant6-dev", "python3-biopython", "python3-screed", "python3-cutadapt", "python3-dnaio", "ruby-bio", "libbiojava-java", "libbiojava4-java", "libgenome-dev", "libmuscle-dev", "libmems-dev", "libhtsjdk-java", "libai-fann-perl", "libbio-mage-perl", "libnhgri-blastall-perl", "libtfbs-perl", "libfreecontact-dev", "libfreecontact-perl", "libgo-perl", "libbio-graphics-perl", "libbio-coordinate-perl", "libbio-primerdesigner-perl", "libace-perl", "libbiococoa-dev", "libstaden-read-dev", "libsrf-dev", "libzerg0-dev", "libzerg-perl", "librg-reprof-bundle-perl", "librcsb-core-wrapper0-dev", "libsbml5-dev", "sbmltoolbox", "seqan-dev", "libseqan2-dev", "libseqan3-dev", "libbio-mage-utils-perl", "libchado-perl", "libpal-java", "libbioparser-dev", "libspoa-dev", "libedlib-dev", "libthread-pool-dev", "libjebl2-java", "r-cran-adegenet", "r-cran-adephylo", "r-cran-boolnet", "r-cran-corrplot", "r-cran-distory", "r-cran-drinsight", "r-cran-forecast", "r-cran-fitdistrplus", "r-cran-genetics", "r-cran-gprofiler", "r-cran-haplo.stats", "r-cran-metamix", "r-cran-phangorn", "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-cran-pheatmap", "r-other-hms-dbmi-spp", "r-other-apmswapp", "r-bioc-biobase", "libffindex0-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", "bioclipse", "libgff-dev", "python3-pysam", "python3-cobra", "libtabixpp-dev", "python3-ruffus", "python3-hyphy", "python3-dendropy", "python3-skbio", "python3-pbconsensuscore", "python3-consensuscore2", "libconsensuscore-dev", "python3-pyvcf", "python3-pyfaidx", "python3-sqt", "libqes-dev", "libfast5-dev", "python3-fast5", "libpbseq-dev", "libpbdata-dev", "libpbihdf-dev", "libblasr-dev", "libminimap-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", "mgltools-networkeditor", "mgltools-vision", "mgltools-pybabel", "libssw-dev", "libssw-java", "libfml-dev", "libgkarrays-dev", "libjloda-java", "libvcflib-dev", "libswiss-perl", "python3-pybedtools", "python3-gffutils", "python3-bx", "toil", "galaxy-lib", "libbio-eutilities-perl", "libseqlib-dev", "libroadrunner-dev", "python3-roadrunner", "python3-biotools", "bio-tradis", "python3-biomaj3", "libbiod-dev", "python3-ete3", "python3-gfapy", "libgoby-java", "python3-seqcluster", "python3-cyvcf2", "libgatbcore-dev", "python3-airr", "python3-presto", "python3-bcbio", "libpll-dev", "libstatgen-dev", "python3-pyani", "python3-screed", "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", "biobambam2", "libcdk-java"], "ignore": ["golang-github-biogo-hts-dev"], "avoid": []}, "statistics": {"depends": [], "suggests": ["science-statistics"], "recommends": ["r-bioc-limma", "r-bioc-qvalue", "r-cran-randomforest", "r-cran-beeswarm", "r-cran-pvclust", "rstudio", "r-bioc-multtest", "r-cran-ade4", "r-cran-rwave", "r-cran-snowfall", "r-cran-wavethresh", "r-cran-waveslim"], "ignore": [], "avoid": []}, "tools": {"depends": [], "suggests": ["cycle", "mencal", "entangle", "goldencheetah", "sleepyhead", "oscar"], "recommends": ["pcalendar", "pondus", "mssstest", "wgerman-medical", "hunspell-de-med", "quitcount", "workrave", "edfbrowser", "hunspell-en-med", "cronometer", "python3-fitbit", "r-cran-fitcoach", "r-cran-fitbitscraper", "galileo", "nut-nutrition", "nutsqlite", "pesco"], "ignore": [], "avoid": []}, "imaging-dev": {"depends": [], "suggests": ["libvtk6-dev", "libnifti-doc", "libfreeimage-dev", "libics-dev", "liblimereg-dev", "python-nipy", "python-nipype", "python-nitime", "emokit", "python-pyxnat", "python-dipy", "python-cfflib", "libeegdev-dev", "libxdffileio-dev", "tifffile", "python-vmtk", "python-vigra", "libcamp-dev"], "recommends": ["ctn-dev", "cimg-dev", "libminc-dev", "libmdc2-dev", "libvtk7-dev", "libnifti-dev", "libinsighttoolkit4-dev", "libvolpack1-dev", "libgdcm2-dev", "python3-gdcm", "libopensurgsim-dev", "libmaxflow-dev", "python3-mvpa2", "libvia-dev", "odin", "libcv-dev", "libteem-dev", "gmic", "libgiftiio-dev", "libvistaio-dev", "libmia-2.4-dev", "libmiaviewit-dev", "libmialm-dev", "python3-mia", "libopenigtlink-dev", "r-cran-rniftilib", "libmni-perllib-perl", "python3-dicom", "libopenmeeg-dev", "python3-nibabel", "libgdf-dev", "octave-gdf", "libbiosig-dev", "python3-biosig", "libctk-dev", "libopenslide-dev", "python3-openslide", "libopenslide-java", "libbio-formats-java", "octave-dicom", "libcamitk-dev", "libpapyrus3-dev", "python3-mne", "libvmtk-dev", "libvigraimpex-dev", "libvtk-dicom-dev", "libedf-dev", "python3-imageio", "libismrmrd-dev", "libodil-dev", "libbart-dev", "octave-bart", "libcifti-dev", "libxdf-dev", "libsimpleitk1-dev", "python3-simpleitk"], "ignore": [], "avoid": []}}
\ No newline at end of file
=====================================
tasks/bio
=====================================
@@ -211,7 +211,7 @@ Recommends: autogrid
Recommends: autodock-vina
-Recommends: autodocktools, mgltools-pmv, mgltools-vision, mgltools-cadd
+Recommends: autodocktools, mgltools-vision, mgltools-cadd
Recommends: mustang
View it on GitLab: https://salsa.debian.org/blends-team/med/compare/eeb4d0058afe95ad3ac7b94cfaaf73737e3746ac...8da479d6c5272d0fe6a9841cd88f6d7ecd68397d
--
View it on GitLab: https://salsa.debian.org/blends-team/med/compare/eeb4d0058afe95ad3ac7b94cfaaf73737e3746ac...8da479d6c5272d0fe6a9841cd88f6d7ecd68397d
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