The following commit has been merged in the master branch:
commit b6636cb0b421e4c4af5b758f21efe8884162d4cc
Author: Andreas Tille <[email protected]>
Date: Mon Sep 12 14:41:44 2016 +0200
Run blends-dev 0.7 make dist to get json data and enhanced d/changelog
diff --git a/debian/changelog b/debian/changelog
index d4cf845..e90772b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,65 @@ debian-med (2.3) unstable; urgency=medium
* med-bio: Add mgltools-pmv, mgltools-vision, mgltools-cadd
Closes: #732069
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-tools
+ added:
+ Depends: galileo, r-cran-fitbitscraper
+ Suggests: sleepyhead
+ -med-statistics
+ added:
+ Depends: r-cran-ade4, rstudio, r-bioc-multtest
+ -med-bio-ngs
+ added:
+ Depends: sprai, rna-star, daligner, mhap, dindel, blasr, bcftools
+ -med-bio
+ added:
+ Depends: pbbarcode, spaced, varmatch, cgview, phipack, ffp,
snap-aligner, plast, kineticstools, brig, harvest-tools, transrate-tools,
meryl, metabit, parsnp, beagle, maffilter, pbhoney, jmodeltest, mgltools-cadd,
roadtrips, roary, sim4db, alter-sequence-alignment, graphlan,
ncbi-entrez-direct, falconkit, partitionfinder, art-nextgen-simulation-tools,
sspace, phybin, fastahack, phylophlan, crux-toolkit, varna, dindel,
smithwaterman, r-bioc-geneplotter, dawg, lefse, r-bioc-deseq2, fsm-lite,
nanopolish, physamp, minimap, kmc, snpomatic, proteinortho, phast, prottest,
qualimap, sprai, fml-asm, circlator, inspect, pipasic, hilive, mgltools-pmv,
fastqtl, piler, r-cran-adephylo, r-cran-pscbs, hisat2, ssw-align, garli, pssh2,
plink1.9, r-cran-adegenet, velvet | velvet-long, condetri, fastml, mapdamage,
rsat, r-cran-distory, segemehl, andi, ncl-tools, sumaclust, sniffles, pbalign,
scrm, miniasm, poretools, sparta, pbh5tools, r-cran-bio3d, kronatools,
beast2-mcmc, clustalw, dwgsim, pir
s, reapr, r-cran-treescape, leaff, seer, surankco, tide, placnet, canu,
rambo-k, lofreq, artfastqgenerator, lambda-align, rapmap, metaphlan2,
r-bioc-dnacopy, mgltools-vision, indelible, salmon, dazzdb, srst2, king-probe,
cutadapt, pbgenomicconsensus, ariba, pbsuite, adapterremoval, kraken, pbjelly,
mash, fermi-lite, pbsim, bcftools
+ Suggests: science-workflow, r-bioc-aroma.light, r-cran-pheatmap, mrs,
r-bioc-annotationhub, r-bioc-ensembldb, r-bioc-go.db
+ removed:
+ Depends: python-kineticstools, r-other-bio3d, velvet, tigr-assembler,
clustalw | clustalw-mpi, python-pbalign, wgsim, wgs-assembler, mrs, act, r8s,
fastml2
+ -med-his
+ added:
+ Depends: openmaxims
+ -med-practice
+ added:
+ Depends: sleepyhead, orthanc
+ removed:
+ Depends: clinica
+ -med-imaging-dev
+ added:
+ Depends: libinsighttoolkit4-dev, octave-bart, libvtk-dicom-dev,
libbart-dev, libodil0-dev, libmia-2.4-dev, libcamitk4-dev, libopenigtlink-dev,
libvtk6-dev
+ Suggests: libcamp0.7-dev, libfreeimage-dev
+ removed:
+ Depends: libopenigtlink1-dev, libactiviz.net-cil, libvtk5-dev,
libinsighttoolkit3-dev | libinsighttoolkit4-dev, libvtk-dicom0.5-dev,
libmia-2.2-dev, libcamitk3-dev
+ Suggests: libvtk5.4, insighttoolkit3-examples
+ -med-imaging
+ added:
+ Depends: fw4spl, python-tifffile, bart
+ Suggests: science-workflow, orthanc-postgresql, orthanc-imagej,
orthanc-dicomweb
+ removed:
+ Depends: tifffile
+ -med-data
+ added:
+ Suggests: sleepyhead
+ -med-bio-phylogeny
+ added:
+ Depends: iqtree, clustalw
+ removed:
+ Depends: clustalw | clustalw-mpi
+ -med-bio-dev
+ added:
+ Depends: python3-pyvcf | python-pyvcf, libsmithwaterman-dev,
mgltools-vision, libbpp-phyl-omics-dev, python3-csb | python-csb, libqcpp-dev,
libbio-das-lite-perl, libhtsjdk-java, libqes-dev, python3-biopython |
python-biopython, python-kineticstools, libfreecontact-dev, libssw-dev,
libminimap-dev, r-cran-rnexml, libssw-java, r-cran-rncl, python3-pymummer,
python3-ngs | python-ngs, libpbdata-dev, libbpp-raa-dev,
python3-pbconsensuscore | python-pbconsensuscore, libblasr-dev, libbpp-qt-dev,
python3-intervaltree-bio | python-intervaltree-bio, libncl-dev, libngs-java,
python3-pyfaidx | python-pyfaidx, libbpp-seq-dev, libfast5-dev,
r-cran-phylobase, python-pbcommand, libncbi-vdb-dev, libbpp-core-dev,
libpbbam-dev, libconsensuscore-dev, libpbihdf-dev, libtabixpp-dev,
python3-pyfasta | python-pyfasta, libbpp-phyl-dev, libfml-dev,
python3-consensuscore2 | python-consensuscore2, mgltools-networkeditor,
libpbseq-dev, libgff-dev, libngs-sdk-dev, octave-bioinfo, libbpp-popgen-dev,
mgltool
s-pybabel, libfastahack-dev, ruby-crb-blast, libbpp-seq-omics-dev
+ Suggests: python3-biopython-sql | python-biopython-sql,
libdisorder-dev, libbam-dev
+ removed:
+ Depends: libgbfp-dev, python-biopython | python3-biopython, libtabixpp,
libfreecontact0-dev, python-csb | python3-csb, libbio-das-perl
+ Suggests: python-biopython-sql | python3-biopython-sql
+ -med-epi
+ added:
+ Suggests: r-cran-cmprsk
+
-- Andreas Tille <[email protected]> Mon, 12 Sep 2016 10:03:11 +0200
debian-med (2.2) unstable; urgency=medium
diff --git a/dependency_data/debian-med_2.3.json
b/dependency_data/debian-med_2.3.json
new file mode 100644
index 0000000..7e62406
--- /dev/null
+++ b/dependency_data/debian-med_2.3.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-fitbitscraper", "galileo", "nut-nutrition"],
"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", "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", "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-multtest",
"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"], "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-watcher", "cain", "science-workflow", "metastudent-data",
"metastudent-data-2", "metastudent-data-3", "mrs", "r-bi
oc-annotationhub", "r-bioc-aroma.light", "r-bioc-ensembldb", "r-bioc-go.db",
"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", "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-domsearch",
"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",
"biomaj", "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", "velvetoptimiser", "ensembl", "mrbayes", "pdb2pqr",
"squizz", "clonalframe", "dssp", "jellyfish", "ballview", "pynast", "raxm
l", "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",
"acacia", "adapterremoval", "aegean", "andi", "arden", "artfastqgenerator",
"art-nextgen-simulation-tools", "augustus", "beagle", "biceps", "emperor",
"fermi-lite", "fitgcp", "gasic", "giira", "ipig", "aevol",
"alter-sequence-alignment", "amos-assembler", "hawkeye", "anfo", "apollo",
"aragorn", "ariba", "axe-demultiplexer", "axparafit", "axpcoords", "barrnap",
"bamtools", "bagpipe", "bcftools", "bigsdb", "bitseq", "blat", "bio-rainbow",
"cassiopee", "cdbfasta", "cgview",
"brig", "cinema", "circlator", "clearcut", "clonalorigin", "cluster3",
"codonw", "condetri", "crac", "crossbow", "crux-toolkit", "cutadapt",
"cytoscape", "dawg", "dazzdb", "dazzle", "dindel", "dwgsim", "ea-utils",
"ecell", "ecopcr", "edtsurf", "emmax", "berkeley-express", "falconkit",
"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", "lagan",
"lambda-align", "leaff", "ltrsift", "lofreq", "logomat-m", "kclust", "khmer",
"kmer", "kronatools", "lefse", "mach-haplotyper", "macs", "macsyfinder",
"maffilter", "mage2tab", "mapdamage", "martj", "mash", "progressivemauve",
"mauve-aligner", "meme", "meryl
", "metabit", "metaphlan2", "metastudent", "microbegps", "miniasm", "minimap",
"molekel", "mosaik-aligner", "mpsqed", "mugsy", "murasaki", "nanopolish",
"ncbi-entrez-direct", "ncbi-seg", "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",
"prodigal", "prokka", "proteinortho", "prottest", "pscan-tfbs", "psipred",
"pssh2", "pycorrfit", "pyscanfcs", "python-reaper", "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-g
eneplotter", "r-bioc-ebseq", "r-bioc-limma", "r-bioc-edger",
"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-align", "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", "t
axinspector", "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", "libcamitk4-dev", "l
ibpapyrus3-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"], "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", "p
ython-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", "omer
o", "king", "vtk-dicom-tools", "gdf-tools", "fw4spl", "bart"], "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-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-rsamtools", "r-bioc-shortread",
"r-bioc-snpstats", "r-bioc-variantannotation", "r-bioc-xvector",
"librostlab-doc", "librostlab-blast-doc", "libswarm2-dev", "libgtextutils-dev",
"libbam-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", "libbiojava3-java", "libbiojav
a4-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-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-csb | python-csb", "python-miso",
"python-freecontact", "python3-pymummer", "libkmer-dev", "libsnp-sites1-dev",
"libssm-dev", "librelion-dev", "libdivsufsort-dev", "bioclipse", "libgff-dev",
"libgff-perl", "python-pysam", "python-pbcore", "python-pbh5tools",
"python-cobra", "libvcflib", "libtabixpp-dev", "python3-ruffus |
python-ruffus", "python3-hyphy | python-hyphy", "python3-dendropy |
python-dendropy", "python3-skbio | python-skbio", "python3-pbconsensuscore |
python-pbconsensuscore", "python3-consensuscore2 | python-consensuscore2",
"libconsensuscore-dev", "python-pbcommand", "python3-pyvcf | python-pyvcf",
"python3-pyfaidx | python-pyfaidx", "python3-intervaltree-bio |
python-intervaltree-bio", "python-kineticstools", "python3-pyfasta |
python-pyfasta", "libqes-dev", "libfast5-dev", "libpbseq-dev", "libpbdata-d
ev", "libpbihdf-dev", "libblasr-dev", "libbio-das-lite-perl",
"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"], "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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