The following commit has been merged in the master branch:
commit e00a186f38ff4394cb7151958c29d9265bf54dc7
Author: Andreas Tille <[email protected]>
Date: Tue Sep 1 22:34:58 2015 +0200
Add dependency data to keep up with package statistics
diff --git a/dependency_data/debian-med_2.2.json
b/dependency_data/debian-med_2.2.json
new file mode 100644
index 0000000..92b95fd
--- /dev/null
+++ b/dependency_data/debian-med_2.2.json
@@ -0,0 +1 @@
+{"oncology": {"ignore": [], "suggests": [], "depends": ["uw-prism", "planunc",
"dicompyler"], "recommends": [], "avoid": []}, "laboratory": {"ignore": [],
"suggests": [], "depends": ["opencfu", "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", "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", "kissplice",
"macs", "m
othur", "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-py
epl", "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", "catissuecore", "trapss
"], "suggests": ["emboss-explorer", "adun.app", "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",
"hyphygui", "hyphy-mpi | hyphy-pt", "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-core",
"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", "eigenso
ft", "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", "axe-demultiplexer",
"axparafit", "axpcoords", "barrnap", "bamtools", "bagpipe", "bigsdb", "bitseq",
"blasr", "blat", "bio-rainbow", "cassiopee", "cdbfasta", "cinema", "clearcut",
"clonalorigin", "cluster3", "crac", "crossbow", "cytoscape", "daligner",
"dazzle", "ea-utils", "ecell", "ecopcr", "edtsurf", "emmax",
"berkeley-express", "fasta3", "fasttree", "fastaq", "fastml2", "fastqc",
"unc-fish", "forester", "freecontact",
"freebayes", "fsa", "gatk", "genometools", "grabix", "grogui", "gwama",
"gubbins", "haploview", "hmmer2", "htqc", "idba", "iqtree", "iva", "jaligner",
"jbrowse", "kempbasu", "kissplice", "lagan", "ltrsift", "logomat-m", "kclust",
"khmer", "kmer", "mach-haplotyper", "macs", "macsyfinder", "mage2tab", "martj",
"progressivemauve", "mauve-aligner", "meme", "metastudent", "mhap",
"microbegps", "molekel", "mosaik-aligner", "mpsqed", "mrs", "mugsy",
"murasaki", "ncbi-seg", "ngila", "ngsqctoolkit", "nw-align", "oases",
"obitools", "r-other-apmswapp", "pal2nal", "paraclu", "parsinsert", "patman",
"patristic", "pbdagcon", "pcma", "perm", "phyloviz-core", "phyutility",
"plato", "plip", "prank", "predictprotein", "proalign", "prodigal", "prokka",
"pscan-tfbs", "psipred", "pycorrfit", "pyscanfcs", "python-reaper",
"python-pbalign", "python-kineticstools", "r8s", "r-bioc-rtracklayer",
"r-bioc-gviz", "r-bioc-biostrings", "r-bioc-annotate", "r-bioc-genefilter",
"r-bioc-ebseq", "r-bioc-limma", "r-b
ioc-edger", "r-cran-phangorn", "r-cran-metamix", "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", "repeatmasker-recon", "rosetta", "rsem",
"sap", "sga", "seqprep", "seqtk", "sequenceconverter.app", "situs", "smalt",
"smrtanalysis", "snpeff", "sortmerna", "spades", "ssaha", "staden", "stacks",
"strap", "strap-base", "subread", "suitename", "sumatra", "sumtrees", "swarm",
"tacg", "tantan", "toppred", "transdecoder", "treeview", "trinityrnaseq",
"uc-echo", "varscan", "vienna-rna", "vmd", "vsearch", "wgs-assembler", "wgsim",
"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", "gene
splicer", "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", "disulfind
er", "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": []},
"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", "mi
rth", "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", "liblimereg-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",
"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",
"libactiviz.net-cil", "libvistaio-dev", "libmia-2.2-dev", "libmiaviewit-dev",
"libmialm-dev", "python-mia | python3-mia", "libopenigtlin
k1-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-dicom0.5-dev", "libvtk-dicom-java", "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", "ctsi
m", "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", "tifffile", "mni-icbm152-nlin-2009",
"mni-colin27-nifti", "mipav", "jis
t", "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", "pro
align", "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-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", "python-screed", "python3-cutadapt |
python-cutadapt", "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", "li
bopenms-dev", "libgenometools0-dev", "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", "libdivsufsort-dev", "bioclipse", "libgff-perl",
"python-pysam", "python-pbcore", "python-pbh5tools", "python-cobra",
"libvcflib", "libtabixpp", "python3-ruffus | python-ruffus", "python3-hyphy |
python-hyphy", "python3-dendropy | python-dendropy", "python3-skbio |
python-skbio", "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": []}}
\ No newline at end of file
--
Debian Med metapackages
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