The following commit has been merged in the master branch:
commit 0d98b07277c34382b70139ea2e4e991a9b812723
Author: Andreas Tille <[email protected]>
Date: Tue Jan 24 10:01:53 2017 +0100
Prepare new version
diff --git a/debian/changelog b/debian/changelog
index 1f9e866..befc303 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,42 @@
+debian-med (3.0) UNRELEASED; urgency=medium
+
+ * Bump version for Stretch release
+
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-tools
+ added:
+ Depends: r-cran-fitcoach, pesco
+ -med-typesetting
+ added:
+ Suggests: r-cran-qqman
+ -med-bio
+ added:
+ Depends: euler2, nextsv, r-bioc-metagenomeseq, diamond-aligner,
+ bedops, ccs, euler-sr, r-bioc-mergeomics, baitfisher,
+ libvcflib-tools, r-bioc-phyloseq, r-cran-rotl, tvc
+ Suggests: r-cran-qqman, r-bioc-savr, r-cran-rentrez
+ removed:
+ Depends: fermi-lite
+ -med-imaging
+ added:
+ Depends: bart-view, dcm2niix
+ -med-bio-dev
+ added:
+ Depends: python3-gffutils, libjloda-java, libbio-eutilities-perl,
+ libvcflib-dev, python3-pybedtools, python3-fast5 |
python-fast5,
+ python3-misopy | python-misopy, libbio-coordinate-perl,
+ python3-skbio, python3-bx | python-bx, libswiss-perl,
+ python3-bd2k | python-bd2k
+ Suggests: r-bioc-biomformat, r-bioc-rbgl, ruby-rgfa, r-cran-rentrez,
+ libpbcopper-dev
+ removed:
+ Depends: libbiojava3-java, libvcflib, python3-skbio | python-skbio,
+ python-miso, unanimity
+
+ -- Andreas Tille <[email protected]> Tue, 24 Jan 2017 09:54:03 +0100
+
debian-med (2.4) unstable; urgency=medium
* rebuild using blends-dev 0.6.96
diff --git a/dependency_data/debian-med_3.0.json
b/dependency_data/debian-med_3.0.json
new file mode 100644
index 0000000..fed3201
--- /dev/null
+++ b/dependency_data/debian-med_3.0.json
@@ -0,0 +1 @@
+{"oncology": {"ignore": [], "suggests": [], "depends": ["uw-prism", "planunc",
"dicompyler"], "recommends": [], "avoid": []}, "laboratory": {"ignore": [],
"suggests": [], "depends": ["opencfu", "openelis", "openfreezer",
"catissuesuite"], "recommends": [], "avoid": []}, "pharmacy": {"ignore": [],
"suggests": [], "depends": ["chemtool", "raccoon", "r-cran-dosefinding"],
"recommends": [], "avoid": []}, "tools": {"ignore": [], "suggests": ["cycle",
"mencal", "entangle", "goldencheetah", "sleepyhead"], "depends": ["pcalendar",
"pondus", "mssstest", "wgerman-medical", "hunspell-de-med", "quitcount",
"workrave", "edfbrowser", "hunspell-en-med", "python-clips", "cronometer",
"python-fitbit", "r-cran-fitcoach", "r-cran-fitbitscraper", "galileo",
"nut-nutrition", "nutsqlite", "pesco"], "recommends": [], "avoid": []},
"cloud": {"ignore": [], "suggests": [], "depends": ["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-valdar-bagphenotype.library", "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",
"fastx-toolkit", "flexbar", "picard-tools", "samtools", "tabix", "vcftools",
"anfo", "cufflinks", "bowtie", "bowtie2", "bwa", "last-align", "maq", "perm",
"tophat", "smalt", "soapdenovo", "soapdenovo2", "abyss", "mapsembler2", "idba",
"minia", "mira-assembler", "ssake", "ve
lvet", "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", "python-cogent", "readseq", "tigr-glimmer", "seqan-apps",
"staden-io-lib-utils", "aevol", "biomaj", "bioperl", "bioperl-run", "cain",
"clonalframe", "circos", "datamash", "filo", "prodigal", "python-biopython",
"python3-biopython", "qiime", "r-bioc-edger", "r-cran-pvclust",
"r-cran-vegan"], "recommends": [], "avoid": []}, "statistics": {"ignore": [],
"suggests": ["science-statistics"], "depends": ["r-bioc-edger", "r-bioc-limma",
"r-bioc-qvalue", "r-cran-randomforest", "r-cran-beeswarm", "r-cran-pvclust",
"rstudio", "r-bioc-mult
test", "r-cran-ade4"], "recommends": [], "avoid": []}, "psychology":
{"ignore": [], "suggests": ["science-psychophysics", "python-visionegg"],
"depends": ["python-pyepl", "praat", "r-cran-foreign", "psignifit",
"python-pypsignifit", "r-cran-psy", "psychopy", "miscpsycho", "psych",
"psychometric", "psychotree", "psyphy"], "recommends": [], "avoid": []},
"research": {"ignore": [], "suggests": [], "depends": ["openclinica"],
"recommends": [], "avoid": []}, "typesetting": {"ignore": [], "suggests":
["kbibtex", "biber", "bibus", "referencer", "jabref-plugin-oo",
"r-cran-qqman"], "depends": ["texlive-science", "texlive-latex-extra", "king"],
"recommends": [], "avoid": []}, "dental": {"ignore": [], "suggests": [],
"depends": ["openmolar", "imagetooth", "entangle"], "recommends": [], "avoid":
[]}, "bio": {"ignore": ["mozilla-biofox", "riso", "catissuecore", "trapss"],
"suggests": ["emboss-explorer", "adun.app", "melting-gui", "biomaj",
"biomaj-watcher", "cain", "science-workflow", "metastud
ent-data", "metastudent-data-2", "metastudent-data-3", "mrs",
"r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-ensembldb",
"r-bioc-go.db", "r-bioc-savr", "r-cran-qqman", "r-cran-rentrez",
"r-cran-boolnet", "r-cran-pheatmap", "mobyle", "mobyle-programs",
"mobyle-tutorials", "maude"], "depends": ["altree", "beast-mcmc",
"beast2-mcmc", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle",
"probalign", "treeviewx", "figtree", "hyphygui", "hyphy-mpi | hyphy-pt",
"spread-phy", "phylip", "fastlink", "loki", "plink", "plink1.9", "r-cran-qtl",
"r-cran-genabel", "amap-align", "boxshade", "fastx-toolkit", "gff2aplot",
"muscle", "sim4", "sibsim4", "tabix", "tophat", "wise", "maqview", "blasr",
"daligner", "dascrubber", "mhap", "bwa", "mummer", "blast2", "plast",
"ncbi-blast+", "mafft", "sra-toolkit", "t-coffee", "kalign", "hmmer",
"exonerate", "dialign", "dialign-tx", "poa", "probcons", "proda", "seaview",
"sigma-align", "emboss", "embassy-domalign", "embassy-domainatrix",
"embassy-domsearc
h", "embassy-phylip", "arb", "clustalx", "clustalo", "clustalw", "mothur",
"bowtie", "bowtie2", "transtermhp", "last-align", "maq", "ssake", "velvet |
velvet-long", "qiime", "infernal", "rnahybrid", "adun-core", "garlic", "gamgi",
"gdpc", "ghemical", "jmol", "pymol", "r-cran-bio3d", "massxpert", "gromacs",
"rasmol", "modeller", "plasmidomics", "gff2ps", "ncbi-epcr", "ncbi-tools-bin",
"ncbi-tools-x11", "perlprimer", "readseq", "tigr-glimmer", "melting", "mipe",
"primer3", "artemis", "gbrowse", "glam2", "raster3d", "phyml", "autodock",
"autogrid", "autodock-vina", "autodocktools", "mgltools-pmv",
"mgltools-vision", "mgltools-cadd", "mustang", "probabel", "theseus",
"staden-io-lib-utils", "samtools", "bedtools", "filo", "gassst",
"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-dotter", "acedb-other-belvu",
"acedb-other", "python-cogent", "paml", "velv
etoptimiser", "ensembl", "mrbayes", "pdb2pqr", "squizz", "clonalframe",
"dssp", "jellyfish", "ballview", "pynast", "raxml", "mlv-smile", "cd-hit",
"cufflinks", "r-bioc-cummerbund", "eigensoft", "grinder", "jalview", "reprof",
"tm-align", "norsnet", "norsp", "predictnls", "prime-phylo", "proftmb",
"profbval", "profisis", "hhsuite", "ffindex", "flexbar", "blimps-utils",
"sift", "neobio", "ray", "ugene", "logol-bin", "soapdenovo", "soapdenovo2",
"microbiomeutil", "chimeraslayer", "nast-ier", "wigeon", "minia",
"trimmomatic", "saint", "rtax", "rate4site", "rna-star", "topp", "openms",
"scythe", "sickle", "kmc", "king-probe", "ncl-tools", "tvc", "libvcflib-tools",
"acacia", "adapterremoval", "aegean", "andi", "arden", "artfastqgenerator",
"art-nextgen-simulation-tools", "augustus", "baitfisher", "beagle", "bedops",
"biceps", "diamond-aligner", "emperor", "euler2", "euler-sr", "fitgcp",
"gasic", "giira", "ipig", "aevol", "alter-sequence-alignment",
"amos-assembler", "hawkeye", "anfo", "ap
ollo", "aragorn", "ariba", "atac", "axe-demultiplexer", "axparafit",
"axpcoords", "barrnap", "bamtools", "bagpipe", "bcftools", "bigsdb",
"bio-eagle", "bitseq", "blat", "blobology", "bio-rainbow", "cassiopee", "ccs",
"cdbfasta", "cgview", "brig", "cinema", "circlator", "clearcut",
"clonalorigin", "cluster3", "codonw", "condetri", "contrafold", "crac",
"crossbow", "crux-toolkit", "cutadapt", "cytoscape", "dawg", "dazzdb",
"dazzle", "deepnano", "dindel", "dwgsim", "ea-utils", "ecell", "ecopcr",
"edtsurf", "emmax", "berkeley-express", "falcon", "fasta3", "fasttree",
"fastahack", "fastaq", "fastml", "fastqc", "fastqtl", "ffp", "unc-fish",
"fml-asm", "forester", "freecontact", "freebayes", "fsa", "fsm-lite", "garli",
"gatk", "genometools", "grabix", "graphlan", "grogui", "gwama", "gubbins",
"haploview", "harvest-tools", "hilive", "hisat2", "hmmer2", "htqc", "idba",
"indelible", "iqtree", "iva", "jaligner", "jbrowse", "jmodeltest", "kempbasu",
"kineticstools", "kissplice", "kraken", "laga
n", "lambda-align", "leaff", "ltrsift", "lofreq", "logomat-m", "kclust",
"khmer", "kmer", "kronatools", "lefse", "mach-haplotyper", "macs",
"macsyfinder", "maffilter", "mage2tab", "malt", "manta", "mapdamage", "martj",
"mash", "progressivemauve", "mauve-aligner", "meme", "meryl", "metabit",
"metaphlan2", "metastudent", "microbegps", "miniasm", "minimap", "molekel",
"mosaik-aligner", "mpsqed", "mugsy", "murasaki", "nanocall", "nanopolish",
"ncbi-entrez-direct", "ncbi-seg", "nextsv", "ngila", "ngsqctoolkit",
"nw-align", "oases", "obitools", "r-other-apmswapp", "pal2nal", "paraclu",
"parsinsert", "parsnp", "partitionfinder", "patman", "patristic", "pbalign",
"pbbarcode", "pbdagcon", "pbsuite", "pbgenomicconsensus", "pbjelly", "pbhoney",
"pbh5tools", "pbsim", "pcma", "perm", "phast", "phipack", "phybin",
"phylophlan", "phyloviz-core", "phyutility", "piler", "pipasic", "inspect",
"tide", "physamp", "pirs", "placnet", "plato", "plip", "poretools", "prank",
"predictprotein", "proalign", "p
rodigal", "prokka", "proteinortho", "prottest", "pscan-tfbs", "psipred",
"pssh2", "pycorrfit", "pyscanfcs", "python-reaper", "qtltools", "qualimap",
"rambo-k", "rapmap", "r-bioc-rtracklayer", "r-bioc-gviz", "r-bioc-biostrings",
"r-bioc-annotate", "r-bioc-genefilter", "r-bioc-deseq2", "r-bioc-dnacopy",
"r-bioc-geneplotter", "r-bioc-mergeomics", "r-bioc-metagenomeseq",
"r-bioc-phyloseq", "r-bioc-ebseq", "r-bioc-limma", "r-bioc-edger",
"r-cran-rotl", "r-cran-adegenet", "r-cran-adephylo", "r-cran-distory",
"r-cran-metamix", "r-cran-phangorn", "r-cran-pscbs", "r-cran-seqinr",
"r-cran-vegan", "relion-bin+gui | relion-bin+mpi+gui", "relion-bin |
relion-bin+mpi", "r-other-valdar-bagphenotype.library", "rdp-alignment",
"rdp-readseq", "rdp-classifier", "reapr", "repeatmasker-recon", "repeatmasker",
"roadtrips", "roary", "rosetta", "rsat", "rsem", "salmon", "sap", "scrm",
"sga", "seer", "segemehl", "seqprep", "seqtk", "sequenceconverter.app",
"situs", "sim4db", "smalt", "smithwaterman", "ssw-a
lign", "smrtanalysis", "snpeff", "snpomatic", "sortmerna", "snap-aligner",
"sniffles", "spaced", "spades", "sparta", "sprai", "srst2", "ssaha", "sspace",
"staden", "stacks", "strap", "strap-base", "subread", "suitename", "sumatra",
"sumaclust", "sumtrees", "surankco", "swarm", "tacg", "tantan", "toppred",
"transdecoder", "transrate-tools", "treeview", "trinityrnaseq", "uc-echo",
"varna", "varmatch", "varscan", "vienna-rna", "vmd", "vsearch", "canu",
"zalign", "zodiac-zeden", "discosnp", "mapsembler2", "dnaclust", "copycat",
"btk-core", "asap", "cactus", "contralign", "concavity", "conservation-code",
"galaxy", "genographer", "pftools", "phylographer", "phylowin", "gbioseq",
"phpphylotree", "tracetuner", "twain", "rose", "glimmerhmm", "genezilla",
"exalt", "jigsaw", "genesplicer", "mummergpu", "amoscmp", "minimus", "bambus",
"gmv", "pyrophosphate-tools", "figaro", "mirbase", "elph", "uniprime",
"genetrack", "operondb", "trnascan-se", "cdna-db", "das-proserver", "spice",
"decipher", "
est-db", "finex", "hexamer", "coot", "r-cran-ape", "r-cran-treescape",
"caftools", "roche454ace2caf", "big-blast", "blixem", "cap3", "coalesce",
"estferret", "estscan", "fasta", "fluctuate", "lamarc", "lucy", "maxd",
"mesquite", "migrate", "msatfinder", "mview", "oligoarrayaux", "omegamap",
"partigene", "pfaat", "prot4est", "qtlcart", "rbs-finder", "recombine",
"splitstree", "taverna", "taxinspector", "tetra", "trace2dbest", "profit",
"obo-edit", "jstreeview", "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", "populations", "raccoon",
"librg-utils-perl", "snap", "vcftools", "hilbertvisgui", "beads",
"x-tandem-pipeline", "forge", "metarep", "arachne", "maker2", "rmblast",
"e-hive", "cmap", "gbrowse-syn", "tripal", "genemark", "python
-orange", "tigr-glimmer-mg"], "recommends": [], "avoid": []}, "his":
{"ignore": [], "suggests": [], "depends": ["care2x", "fis-gtm", "vista-foia",
"ewd-920", "tryton-modules-health", "openmaxims", "world-vista", "ipath",
"patientos", "openmrs", "hkma-cms", "oscar-mcmaster", "openeyes"],
"recommends": [], "avoid": []}, "bio-ngs": {"ignore": [], "suggests": [],
"depends": ["bedtools", "bwa", "bowtie", "blasr", "daligner", "mhap",
"fastx-toolkit", "filo", "last-align", "maq", "picard-tools", "r-bioc-edger",
"r-bioc-hilbertvis", "rna-star", "samtools", "sra-toolkit", "ssake", "tabix",
"tophat", "bcftools", "vcftools", "velvet", "sprai", "mothur", "qiime",
"cufflinks", "mira-assembler", "kissplice", "dindel", "mosaik-aligner",
"forge", "uc-echo", "annovar"], "recommends": [], "avoid": []}, "practice":
{"ignore": ["clearhealth"], "suggests": ["libctapimkt1", "openpms",
"resmedicinae", "sqlclinic", "openrep"], "depends": ["gnumed-client",
"gnumed-server", "libchipcard-tools", "ginkgocadx",
"freediams", "freemedforms-emr", "r-cran-medadherence", "entangle",
"sleepyhead", "orthanc", "medintux", "mirth", "tinyheb", "mirrormed", "elexis",
"freeb", "freemed", "elementalclinic", "openemr", "clearhealth", "proteus",
"thera-pi", "freeshim", "remitt", "qrisk2"], "recommends": [], "avoid": []},
"imaging-dev": {"ignore": [], "suggests": ["libvtkedge-dev", "igstk-examples",
"libnifti-doc", "libfreeimage-dev", "libics-dev", "liblimereg-dev",
"python-libavg", "emokit", "libeegdev-dev", "libxdffileio-dev",
"python-tifffile", "libcamp0.7-dev"], "depends": ["ctn-dev", "cimg-dev",
"libminc-dev", "libmdc2-dev", "libvtk6-dev", "libnifti-dev", "libigstk4-dev",
"libinsighttoolkit4-dev", "libvolpack1-dev", "python-gdcm",
"libopensurgsim-dev", "libmaxflow-dev", "python-mvpa2", "python-nipy",
"python-nipype", "python-nitime", "python-casmoothing", "libvia-dev", "odin",
"libcv-dev", "libvxl1-dev", "libteem-dev", "gmic", "libgiftiio-dev",
"libvistaio-dev", "libmia-2.4-dev", "libmiaviewit-dev",
"libmialm-dev", "python-mia | python3-mia", "libopenigtlink-dev",
"r-cran-rniftilib", "libmni-perllib-perl", "python-dicom", "libopenmeeg-dev",
"python-nibabel", "libgdf-dev", "octave-gdf", "python-pyxnat", "python-dipy",
"libbiosig-dev", "libctk-dev", "python-cfflib", "libopenslide-dev",
"python-openslide", "libopenslide-java", "libbio-formats-java", "octave-dicom",
"libcamitk-dev", "libpapyrus3-dev", "python-mne", "python-vmtk", "libvmtk-dev",
"libvigraimpex-dev", "python-vigra", "libvtk-dicom-dev", "libvtk-dicom-java",
"libedf-dev", "python-imageio", "libismrmrd-dev", "libodil0-dev",
"libbart-dev", "octave-bart", "libcifti-dev"], "recommends": [], "avoid": []},
"imaging": {"ignore": [], "suggests": ["imagemagick", "pngquant", "imview",
"trimage", "conquest-dbase", "conquest-mysql", "conquest-postgres",
"conquest-sqlite", "paraview", "orthanc-webviewer", "orthanc-dicomweb",
"orthanc-imagej", "orthanc-postgresql", "visit", "mrisim", "connectomeviewer",
"eeglab", "elastix", "python
-pyxid", "dtitk", "openwalnut-qt4", "miview", "cmtk", "freesurfer", "xnat",
"isis", "pymeg", "stabilitycalc", "hid", "incf-nidash-oneclick-clients",
"science-workflow"], "depends": ["amide", "ctsim", "ctn", "dicomnifti",
"imagej", "minc-tools", "medcon", "python-nibabel", "python-dicom", "xmedcon",
"dcmtk", "nifti-bin", "aeskulap", "fsl", "fslview", "via-bin", "gwyddion",
"sofa-apps", "python-mvpa2", "python-nipy", "python-nipype", "caret",
"libgdcm-tools", "slicer", "lipsia", "dicom3tools", "imagevis3d", "odin",
"dicomscope", "pixelmed-apps", "vmtk", "gofigure2", "ginkgocadx",
"openslide-tools", "volview", "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", "ants", "itksnap", "mriconvert", "mia-tools",
"mialmpick", "mia-viewit", "ismrmrd-tools", "sigviewer", "python-tifffile",
"mni-icbm152-nlin-2009", "mni-colin27-nifti", "mipav", "jist",
"openmeeg-tools", "jemris", "insightapplications", "tempo", "dti-query",
"plastimatch", "medisnap", "gimias", "mayam", "biosig-tools", "python-surfer",
"dicoogle", "cellprofiler", "bioimagexd", "omero", "king", "vtk-dicom-tools",
"gdf-tools", "fw4spl", "bart", "bart-view", "dcm2niix"], "recommends":
["python-nitime", "python-dipy"], "avoid": []}, "data": {"ignore": [],
"suggests": ["sleepyhead"], "depends": ["freediams", "freemedforms-freedata",
"python-hl7", "drugref.org"], "recommends": [], "avoid": []}, "cms": {"ignore":
[], "suggests": ["zope-zms", "xnat", "hid"], "depends": [], "recommends": [],
"avoid": []}, "bio-phylogeny": {"ignore": [], "suggests": [], "depends":
["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"], "recommends": [], "avoid": []},
"bio-dev": {"ignore": [], "suggests": ["python3-biopython-sql |
python-biopython-sql", "python-biopython-doc", "libfreecontact-doc",
"r-cran-rocr", "r-bioc-affy", "r-bioc-affyio", "r-bioc-altcdfenvs",
"r-bioc-annotationdbi", "r-bioc-biocgenerics", "r-bioc-biomart",
"r-bioc-biomformat", "r-bioc-biovizbase", "r-bioc-bsgenome",
"r-bioc-genomeinfodb", "r-bioc-genomicalignments", "r-bioc-genomicfeatures",
"r-bioc-genomicranges", "r-bioc-graph", "r-bioc-hypergraph", "r-bioc-iranges",
"r-bioc-makecdfenv", "r-bioc-preprocesscore", "r-bioc-rbgl", "r-bioc-rsamtools
", "r-bioc-shortread", "r-bioc-snpstats", "r-bioc-variantannotation",
"r-bioc-xvector", "r-cran-rentrez", "ruby-rgfa", "librostlab-doc",
"librostlab-blast-doc", "libswarm2-dev", "libgtextutils-dev", "libbam-dev",
"libpbcopper-dev", "libdisorder-dev"], "depends": ["bioperl", "bioperl-run",
"libncbi6-dev", "mcl", "biosquid", "libvibrant6-dev", "python3-biopython |
python-biopython", "python-cogent", "python-screed", "python3-cutadapt |
python-cutadapt", "ruby-bio", "libbiojava-java", "libbiojava4-java",
"libgenome-1.3-dev", "libmuscle-3.7-dev", "libmems-1.6-dev", "libhtsjdk-java",
"libai-fann-perl", "libbio-mage-perl", "libnhgri-blastall-perl",
"libtfbs-perl", "libfreecontact-dev", "libfreecontact-perl", "libgo-perl",
"r-cran-genetics", "r-cran-haplo.stats", "r-cran-phylobase", "r-cran-rncl",
"r-cran-rnexml", "octave-bioinfo", "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", "python-corepywrap",
"librcsb-core-wrapper0-dev", "libsbml5-dev", "sbmltoolbox", "seqan-dev",
"libbio-mage-utils-perl", "libchado-perl", "libpal-java", "libjebl2-java",
"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", "libbio-das-lite-perl", "python-mmtk", "libopenms-dev",
"libgenometools0-dev", "librdp-taxonomy-tree-java", "python-biom-format",
"python-rdkit", "libgenome-perl", "libgenome-model-tools-music-perl", "pyfai",
"libhts-dev", "python-htseq", "python3-intervaltree-bio |
python-intervaltree-bio", "python3-csb | python-csb", "python3-misopy |
python-misopy", "python-freecontact", "python3-pymummer", "libkmer-dev",
"libsnp-sites1-dev", "libssm-dev", "librelion-dev", "libdivsufsort-dev",
"bioclipse", "libgff-dev", "libgff-perl", "python-pysam", "python-pb
core", "python-pbh5tools", "python-cobra", "libtabixpp-dev", "python3-ruffus |
python-ruffus", "python3-hyphy | python-hyphy", "python3-dendropy |
python-dendropy", "python3-skbio", "python3-pbconsensuscore |
python-pbconsensuscore", "python3-consensuscore2 | python-consensuscore2",
"libconsensuscore-dev", "python-pbcommand", "python3-pyvcf | python-pyvcf",
"python3-pyfaidx | python-pyfaidx", "python-kineticstools", "python3-pyfasta |
python-pyfasta", "libqes-dev", "libfast5-dev", "python3-fast5 | python-fast5",
"libpbseq-dev", "libpbdata-dev", "libpbihdf-dev", "libblasr-dev",
"libminimap-dev", "libncl-dev", "libngs-sdk-dev", "libngs-java", "python3-ngs |
python-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 | python-bx",
"python3-bd2k | python-bd2k", "libbio-eutilities-perl"], "recommends": [],
"avoid": []}, "epi": {"ignore": [], "suggests": ["r-cran-msm", "r-cran-cmprsk",
"repast"], "depends": ["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", "netepi-analysis",
"netepi-collection"], "recommends": [], "avoid": []}, "physics": {"ignore": [],
"suggests": ["paw-demos", "libbiosig-dev", "python-biosig", "octave-biosig",
"openvibe", "python-multipletau"], "depends": ["paw++", "paw", "octave",
"r-base", "biosig-tools", "gdf-tools", "gate"], "recommends": [], "avoid": []},
"rehabilitation": {"ignore": [], "suggests": ["aghermann"], "depends":
["sitplus"], "recommends": [], "avoid":
[]}}
\ No newline at end of file
--
Debian Med metapackages
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