Author: tille
Date: Sun Mar 29 14:59:02 2015
New Revision: 4161
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=4161
Log:
Add dependency data for version 2.0
Added:
projects/med/trunk/debian-med/dependency_data/debian-med_2.0.json
Added: projects/med/trunk/debian-med/dependency_data/debian-med_2.0.json
URL:
http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/dependency_data/debian-med_2.0.json?rev=4161&op=file
==============================================================================
--- projects/med/trunk/debian-med/dependency_data/debian-med_2.0.json (added)
+++ projects/med/trunk/debian-med/dependency_data/debian-med_2.0.json Sun Mar
29 14:59:02 2015
@@ -0,0 +1 @@
+{"oncology": {"ignore": [], "suggests": [], "depends": ["uw-prism", "planunc",
"dicompyler"], "recommends": [], "avoid": []}, "laboratory": {"ignore": [],
"suggests": [], "depends": ["openelis", "openfreezer", "catissuesuite"],
"recommends": [], "avoid": []}, "research": {"ignore": [], "suggests": [],
"depends": ["openclinica"], "recommends": [], "avoid": []}, "tools": {"ignore":
[], "suggests": ["cycle", "mencal", "entangle", "goldencheetah"], "depends":
["pcalendar", "pondus", "mssstest", "wgerman-medical", "hunspell-de-med",
"quitcount", "workrave", "edfbrowser", "hunspell-en-med", "python-clips",
"cronometer", "python3-fitbitscraper", "python-fitbit", "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", "kissplic
e", "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"],
"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": []},
"pharmacy": {"ignore": [], "suggests": [], "depends": ["chemtool", "raccoon",
"r-cran-dosefinding"], "recommends": [], "avoid": []}, "typesetting":
{"ignore": [], "suggests": ["kbibtex", "biber", "bibus", "referencer",
"jabref-plugin-oo"], "depends": ["texlive-science", "texlive-latex-extra",
"king"], "recommends": [], "avoid": []}, "bio-ngs": {"ignore": [], "suggests":
[], "depends": ["bedtools", "bwa", "bowtie", "fastx-toolkit", "filo",
"last-align", "maq", "picard-tools", "r-bioc-edger", "r-bioc-hilbertvis",
"samtools", "sra-toolkit", "ssake", "tabix", "tophat", "vcftools", "velvet",
"mothur", "qiime", "cufflinks", "mira-assembler", "kissplice",
"mosaik-aligner", "forge", "uc-echo", "annovar"], "recommends": [], "avoid":
[]}, "bio": {"ignore": ["mozilla-biofox", "riso", "catissue
core", "trapss"], "suggests": ["emboss-explorer", "melting-gui",
"biomaj-watcher", "cain", "r-cran-boolnet", "mobyle", "mobyle-programs",
"mobyle-tutorials", "maude"], "depends": ["altree", "beast-mcmc", "fastdnaml",
"njplot", "tree-puzzle | tree-ppuzzle", "probalign", "treeviewx", "figtree",
"spread-phy", "phylip", "fastlink", "loki", "plink", "r-cran-qtl",
"r-cran-genabel", "amap-align", "boxshade", "fastx-toolkit", "gff2aplot",
"muscle", "sim4", "sibsim4", "tabix", "tophat", "wise", "maqview", "bwa",
"mummer", "blast2", "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 | clustalw-mpi", "mothur", "bowtie",
"bowtie2", "transtermhp", "last-align", "maq", "ssake", "velvet", "qiime",
"infernal", "rnahybrid", "adun.app", "garlic", "gamgi", "gdpc
", "ghemical", "jmol", "pymol", "r-other-bio3d", "massxpert", "gromacs",
"rasmol", "modeller", "plasmidomics", "gff2ps", "ncbi-epcr", "ncbi-tools-bin",
"ncbi-tools-x11", "perlprimer", "readseq", "tigr-glimmer", "melting", "mipe",
"primer3", "gbrowse", "biomaj", "glam2", "raster3d", "phyml", "autodock",
"autogrid", "autodock-vina", "autodocktools", "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", "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", "topp", "openms",
"acacia", "arden", "biceps", "emperor", "fitgcp", "gasic", "giira", "ipig",
"aevol", "amos-assembler", "hawkeye", "anfo", "apollo", "aragorn", "axparafit",
"axpcoords", "bamtools", "bagpipe", "bigsdb", "bitseq", "blat", "cassiopee",
"cdbfasta", "cinema", "clearcut", "clonalorigin", "cluster3", "crac",
"crossbow", "cytoscape", "dazzle", "ecell", "edtsurf", "emmax", "fasttree",
"fastaq", "fastqc", "unc-fish", "forester", "freecontact", "freebayes", "fsa",
"genometools", "grabix", "grogui", "haploview", "hmmer2", "idba", "jbrowse",
"kempbasu", "kissplice", "lagan", "ltrsift", "logomat-m", "kclust",
"mach-haplotyper", "macs", "mage2tab", "martj", "mauvealigner", "meme",
"metastudent", "molekel", "mosaik-
aligner", "mpsqed", "mrs", "mugsy", "murasaki", "ncbi-seg", "ngila",
"ngsqctoolkit", "nw-align", "oases", "pal2nal", "paraclu", "parsinsert",
"patman", "patristic", "pcma", "perm", "phyloviz-core", "phyutility", "plato",
"prank", "predictprotein", "proalign", "prodigal", "pscan-tfbs", "psipred",
"pycorrfit", "pyscanfcs", "python-reaper", "r-bioc-rtracklayer", "r-bioc-gviz",
"r-bioc-biostrings", "r-cran-vegan", "relion-gui", "relion-bin |
relion-bin-mpi", "r-other-valdar-bagphenotype.library", "rdp-classifier",
"rosetta", "sap", "sga", "seqtk", "sequenceconverter.app", "situs", "smalt",
"snpeff", "spades", "ssaha", "staden", "strap", "strap-base", "tacg",
"treeview", "uc-echo", "varscan", "vienna-rna", "vmd", "wgs-assembler",
"zalign", "zodiac-zeden", "discosnp", "mapsembler2", "dnaclust", "copycat",
"btk-core", "asap", "cactus", "contralign", "concavity", "conservation-code",
"galaxy", "genographer", "pftools", "phylographer", "phylowin", "gbioseq",
"phpphylotree", "tracetuner", "tw
ain", "rose", "glimmerhmm", "genezilla", "exalt", "jigsaw", "genesplicer",
"mummergpu", "amoscmp", "minimus", "bambus", "gmv", "pyrophosphate-tools",
"figaro", "mirbase", "elph", "uniprime", "genetrack", "operondb",
"trnascan-se", "artemis", "act", "cdna-db", "das-proserver", "spice",
"decipher", "est-db", "finex", "hexamer", "coot", "r-cran-ape", "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", "codonw", "compclust", "treebuilder3d",
"excavator", "tigr-assembler", "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", "repeatmasker", "rmblast", "augustus", "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", "gnuhealth",
"world-vista", "ipath", "patientos", "openmrs", "hkma-cms", "oscar-mcmaster",
"openeyes"], "recommends": [], "avoid": []}, "dental": {"ignore": [],
"suggests": [], "depends": ["openmolar", "imagetooth", "entangle"],
"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", "clinica", "entangle", "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", "insighttoolkit3-examples",
"libnifti-doc", "libvtk5.4", "libics-dev", "python-libavg", "emokit",
"libeegdev-dev", "libxdffileio-dev", "python-tifffile"], "depends": ["ctn-dev",
"cimg-dev", "libminc-dev", "libmdc2-dev", "libvtk5-dev", "libnifti-dev",
"libigstk4-dev", "libinsighttoolkit3-dev | libinsighttoolkit4-dev",
"libvolpack1-dev", "python-gdcm", "python-mvpa2", "python-nipy",
"python-nipype", "python-nitime", "python-casmoothing", "libvia-dev", "odin",
"libcv-dev", "libvxl1-dev", "libteem-dev", "gmic", "libgiftiio-dev",
"libactiviz.net-cil", "libvistaio-dev", "libmia-2.2-dev", "libmiaviewit-dev",
"libmialm-dev", "python-mia | python3-mia", "libopenigtlink1-de
v", "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", "libcamitk3-dev", "libpapyrus3-dev",
"python-mne", "python-vmtk", "libvmtk-dev", "libvigraimpex-dev",
"python-vigra", "libvtk-dicom0.4-dev", "libedf-dev"], "recommends": [],
"avoid": []}, "imaging": {"ignore": [], "suggests": ["imagemagick", "pngquant",
"imview", "trimage", "conquest-dbase", "conquest-mysql", "conquest-postgres",
"conquest-sqlite", "paraview", "visit", "mrisim", "connectomeviewer", "eeglab",
"elastix", "python-pyxid", "dtitk", "openwalnut-qt4", "miview", "cmtk",
"freesurfer", "xnat", "isis", "pymeg", "stabilitycalc", "hid",
"incf-nidash-oneclick-clients"], "depends": ["amide", "ctsim", "ctn",
"dicomnifti", "imagej", "minc-tools", "medcon", "python-nibabel", "pytho
n-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", "sigviewer",
"tifffile", "mni-icbm152-nlin-2009", "mni-colin27-nifti", "mipav", "jist",
"openmeeg-tools", "jemris", "insightapplications", "tempo", "dti-query",
"plastimatch", "medisna
p", "gimias", "mayam", "biosig-tools", "python-surfer", "dicoogle",
"cellprofiler", "bioimagexd", "omero", "king", "vtk-dicom-tools", "gdf-tools"],
"recommends": ["python-nitime", "python-dipy"], "avoid": []}, "data":
{"ignore": [], "suggests": [], "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 |
clustalw-mpi", "mustang", "phyml", "beast-mcmc", "tm-align", "mrbayes",
"figtree", "populations", "proalign", "prottest", "treeview", "phylowin",
"gbioseq", "phpphylotree", "jstreeview", "treetime", "jm
odeltest", "forester", "patristic", "spread-phy"], "recommends": [], "avoid":
[]}, "bio-dev": {"ignore": [], "suggests": ["python-biopython-sql |
python3-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"], "depends": ["bioperl", "bioperl-run", "libncbi6-dev",
"mcl", "biosquid", "libvibrant6-dev", "python-biopython | python3-biopython",
"python-cogent", "ruby-bio", "libbiojava-java", "libbiojava3-java",
"libgenome-1.3-dev",
"libai-fann-perl", "libbio-mage-perl", "libnhgri-blastall-perl",
"libtfbs-perl", "libfreecontact0-dev", "libfreecontact-perl", "libgo-perl",
"r-cran-genetics", "r-cran-haplo.stats", "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", "libbio-das-perl",
"python-mmtk", "libopenms-dev", "libgenometools0-dev", "python-biom-format",
"python-rdkit", "libgenome-perl", "libgenome-model-tools-music-perl", "pyfai",
"libhts-dev", "python-htseq", "python-csb | python3-csb", "python-freecontact
", "libsnp-sites1-dev", "libssm-dev", "librelion-dev", "bioclipse",
"libgff-perl", "libmems-1.5-1", "python-pysam", "libgbfp-dev",
"octace-bioinfo"], "recommends": [], "avoid": []}, "epi": {"ignore": [],
"suggests": ["r-cran-msm", "repast"], "depends": ["epigrass",
"r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi",
"r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "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": []}}
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