Author: tille
Date: Fri Jul 3 06:17:40 2015
New Revision: 4200
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=4200
Log:
Add dependency data created with blends-dev 0.7
Added:
projects/med/trunk/debian-med/dependency_data/debian-med_2.1.json
Added: projects/med/trunk/debian-med/dependency_data/debian-med_2.1.json
URL:
http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/dependency_data/debian-med_2.1.json?rev=4200&op=file
==============================================================================
--- projects/med/trunk/debian-med/dependency_data/debian-med_2.1.json (added)
+++ projects/med/trunk/debian-med/dependency_data/debian-med_2.1.json Fri Jul
3 06:17:40 2015
@@ -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"], "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", "ga
sic", "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"],
"recommends": [], "avoid": []}, "psychology": {"ignore": [], "suggests":
["science-psyc
hophysics", "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", "melting-gui", "biomaj-watcher", "cain",
"metastudent-data", "metastudent-data-2", "metastudent-data-3",
"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-gli
mmer", "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", "rna-star",
"topp", "openms", "scythe", "sickle", "acacia", "aegean", "arden", "biceps",
"emperor", "fitgcp", "gasic", "giira", "ipig", "aevol", "amos-assembler",
"hawkeye", "anfo", "apollo", "aragorn", "axparafit", "axpcoords", "barrnap",
"bamtools", "bagpipe", "bigsdb", "bitseq", "blat", "cassiopee", "cdbfasta",
"cinema", "clearcut", "clonalorigin", "cluster3", "crac", "crossbow",
"cytoscape", "dazzle", "ecell", "ecopcr", "edtsurf", "emmax", "express",
"fasta3", "fasttree", "fastaq", "fastml2", "fastqc", "unc-fish", "forester",
"freecontact", "freebayes", "fsa", "gatk", "genometools", "grabix", "grogui",
"gwama", "gubbins", "haploview", "hmmer2", "htqc", "hyphy", "idba", "iva",
"jaligner", "jbrowse", "kempbasu", "kissplice", "lagan", "ltrsift",
"logomat-m", "kclust", "khmer", "kmer", "mach-haplotyper", "macs",
"macsyfinder", "mage2tab", "martj", "progressivemauve", "mauve-aligner",
"meme", "metastudent", "microbegps
", "molekel", "mosaik-aligner", "mpsqed", "mrs", "mugsy", "murasaki",
"ncbi-seg", "ngila", "ngsqctoolkit", "nw-align", "oases", "obitools",
"r-other-apmswapp", "pal2nal", "paraclu", "parsinsert", "patman", "patristic",
"pcma", "perm", "phyloviz-core", "phyutility", "plato", "plip", "prank",
"predictprotein", "proalign", "prodigal", "prokka", "pscan-tfbs", "psipred",
"pycorrfit", "pyscanfcs", "python-reaper", "r8s", "r-bioc-rtracklayer",
"r-bioc-gviz", "r-bioc-biostrings", "r-bioc-ebseq", "r-cran-phangorn",
"r-cran-seqinr", "r-cran-vegan", "relion-gui", "relion-bin | relion-bin-mpi",
"r-other-valdar-bagphenotype.library", "rdp-alignment", "rdp-readseq",
"rdp-classifier", "rosetta", "rsem", "sap", "sga", "seqprep", "seqtk",
"sequenceconverter.app", "situs", "smalt", "smrtanalysis", "snpeff", "spades",
"ssaha", "staden", "stacks", "strap", "strap-base", "subread", "swarm", "tacg",
"toppred", "transdecoder", "treeview", "trinityrnaseq", "uc-echo", "varscan",
"vienna-rna", "vmd", "vsearc
h", "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", "twain", "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", "profi
t", "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",
"tryton-modules-health", "world-vista", "ipath", "patientos", "openmrs",
"hkma-cms", "oscar-mcmaster", "openeyes"], "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": []}, "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", "limereg-dev", "python-liba
vg", "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",
"libopensurgsim-dev", "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-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", "libcamitk3-dev",
"libpapyrus3-dev", "python-mne", "python-vmtk", "libvmtk-dev
", "libvigraimpex-dev", "python-vigra", "libvtk-dicom0.4-dev", "libedf-dev",
"python-imageio", "libismrmrd-dev"], "recommends": [], "avoid": []}, "imaging":
{"ignore": [], "suggests": ["imagemagick", "pngquant", "imview", "trimage",
"conquest-dbase", "conquest-mysql", "conquest-postgres", "conquest-sqlite",
"paraview", "orthanc-webviewer", "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",
"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", "vol
view", "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",
"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"], "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", "jmodeltest", "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-b
ioc-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", "python-screed", "ruby-bio", "libbiojava-java",
"libbiojava3-java", "libbiojava4-java", "libgenome-1.3-dev",
"libmuscle-3.7-dev", "libmems-1.6-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", "librdp-alignment-java",
"librdp-readseq-java", "librdp-taxonomy-tree-java", "python-biom-format",
"python-rdkit", "libgenome-perl", "libgenome-model-tools-music-perl", "pyfai",
"libhts-dev", "python-htseq", "python-csb | python3-csb", "python-miso",
"python-freecontact", "libkmer-dev", "libsnp-sites1-dev", "libssm-dev",
"librelion-dev", "librdp-taxonomy-tree-java", "bioclipse", "libgff-perl",
"python-pysam",
"python-pbcore", "python-pbh5tools", "python-cobra", "libvcflib",
"libtabixpp", "python-ruffus", "python-dendropy", "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", "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": []}}
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