[Blends-commit] r4159 - in /projects/med/branch/jessie: ./ debian-med/ debian-med/debian-med-tasks.desc debian-med/debian/changelog debian-med/debian/control debian-med/dependency_data/debian-med_2.0.json debian-med/tasks/cloud
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Sun Mar 29 14:53:58 UTC 2015
Author: tille
Date: Sun Mar 29 14:53:58 2015
New Revision: 4159
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=4159
Log:
Add version 2.0 as Jessie branch
Added:
projects/med/branch/jessie/
projects/med/branch/jessie/debian-med/
- copied from r4158, projects/med/tags/1.99/
projects/med/branch/jessie/debian-med/dependency_data/debian-med_2.0.json
Modified:
projects/med/branch/jessie/debian-med/debian-med-tasks.desc
projects/med/branch/jessie/debian-med/debian/changelog
projects/med/branch/jessie/debian-med/debian/control
projects/med/branch/jessie/debian-med/tasks/cloud
Modified: projects/med/branch/jessie/debian-med/debian-med-tasks.desc
URL: http://svn.debian.org/wsvn/blends/projects/med/branch/jessie/debian-med/debian-med-tasks.desc?rev=4159&op=diff
==============================================================================
--- projects/med/branch/jessie/debian-med/debian-med-tasks.desc (original)
+++ projects/med/branch/jessie/debian-med/debian-med-tasks.desc Sun Mar 29 14:53:58 2015
@@ -173,6 +173,7 @@
clearcut
edtsurf
fasttree
+ fastaq
fastqc
freecontact
genometools
@@ -198,6 +199,7 @@
r-bioc-gviz
r-bioc-biostrings
r-cran-vegan
+ relion-bin
seqtk
smalt
staden
@@ -300,6 +302,7 @@
python-freecontact
libsnp-sites1-dev
libssm-dev
+ librelion-dev
python-pysam
Task: med-bio-ngs
@@ -364,7 +367,86 @@
Key:
med-cloud
Packages: list
+ altree
+ clearcut
+ fastdnaml
+ fasttree
+ parsinsert
+ phyml
+ phyutility
+ alien-hunter
+ fastlink
+ loki
+ gasic
+ genometools
+ plink
+ amap-align
+ blast2
+ biosquid
+ boxshade
+ cassiopee
+ cdbfasta
+ cd-hit
+ bamtools
+ bedtools
+ fastx-toolkit
+ flexbar
+ picard-tools
+ samtools
+ anfo
+ bowtie
+ bowtie2
+ bwa
+ last-align
+ maq
+ perm
+ tophat
+ smalt
+ mapsembler2
+ idba
+ minia
+ mira-assembler
+ ssake
+ velvet
+ ampliconnoise
+ arden
+ fastqc
+ discosnp
+ dnaclust
+ fitgcp
+ giira
+ grinder
+ kissplice
+ macs
+ mothur
+ aragorn
+ infernal
+ rnahybrid
+ rtax
+ autodock
+ autodock-vina
+ autogrid
+ concavity
+ dssp
+ freecontact
+ melting
+ mipe
+ ncbi-epcr
+ primer3
+ acedb-other
+ disulfinder
+ ncbi-tools-bin
+ ncoils
python-cogent
+ aevol
+ biomaj
+ bioperl
+ bioperl-run
+ cain
+ clonalframe
+ circos
+ datamash
+ filo
Task: med-cms
Section: debian-med
@@ -641,7 +723,6 @@
psignifit
python-pypsignifit
r-cran-psy
- psychopy
Task: med-rehabilitation
Section: debian-med
Modified: projects/med/branch/jessie/debian-med/debian/changelog
URL: http://svn.debian.org/wsvn/blends/projects/med/branch/jessie/debian-med/debian/changelog?rev=4159&op=diff
==============================================================================
--- projects/med/branch/jessie/debian-med/debian/changelog (original)
+++ projects/med/branch/jessie/debian-med/debian/changelog Sun Mar 29 14:53:58 2015
@@ -1,3 +1,19 @@
+debian-med (2.0) unstable; urgency=medium
+
+ * Fixed syntax of med-cloud and rerender dependencies
+ * Versioned Build-Depends: blends-dev (>= 0.6.92.2) to ensure no packages
+ from non-free or unstable will be included by accident
+ * Since last metapackage creation (and before freeze) the following
+ packages made it into testing:
+ fastaq,
+ relion-bin + librelion-dev
+ These were adde to the list of Recommends
+ * After the freeze the package
+ psychopy
+ was removed from testing and thus it is removed from Recommends
+
+ -- Andreas Tille <tille at debian.org> Sun, 29 Mar 2015 13:47:07 +0200
+
debian-med (1.99) unstable; urgency=low
* debian/control.stub:
Modified: projects/med/branch/jessie/debian-med/debian/control
URL: http://svn.debian.org/wsvn/blends/projects/med/branch/jessie/debian-med/debian/control?rev=4159&op=diff
==============================================================================
--- projects/med/branch/jessie/debian-med/debian/control (original)
+++ projects/med/branch/jessie/debian-med/debian/control Sun Mar 29 14:53:58 2015
@@ -106,6 +106,7 @@
embassy-domsearch,
emboss,
exonerate,
+ fastaq,
fastdnaml,
fastlink,
fastqc,
@@ -238,6 +239,7 @@
raxml,
ray,
readseq,
+ relion-bin,
reprof,
rnahybrid,
rtax,
@@ -342,7 +344,6 @@
exalt,
excavator,
fasta,
- fastaq,
figaro,
finex,
fluctuate,
@@ -441,7 +442,6 @@
rbs-finder,
rdp-classifier,
recombine,
- relion-bin,
relion-bin-mpi,
relion-gui,
repeatmasker,
@@ -525,6 +525,7 @@
libopenms-dev,
libpal-java,
librcsb-core-wrapper0-dev,
+ librelion-dev,
librg-blast-parser-perl,
librg-reprof-bundle-perl,
librostlab-blast0-dev,
@@ -565,7 +566,6 @@
libgff-perl,
libgtextutils-dev,
libmems-1.5-1,
- librelion-dev,
librostlab-blast-doc,
librostlab-doc,
libswarm2-dev,
@@ -582,7 +582,89 @@
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: python-cogent
+Recommends: acedb-other,
+ aevol,
+ alien-hunter,
+ altree,
+ amap-align,
+ ampliconnoise,
+ anfo,
+ aragorn,
+ arden,
+ autodock,
+ autodock-vina,
+ autogrid,
+ bamtools,
+ bedtools,
+ biomaj,
+ bioperl,
+ bioperl-run,
+ biosquid,
+ blast2,
+ bowtie,
+ bowtie2,
+ boxshade,
+ bwa,
+ cain,
+ cassiopee,
+ cd-hit,
+ cdbfasta,
+ circos,
+ clearcut,
+ clonalframe,
+ concavity,
+ datamash,
+ discosnp,
+ disulfinder,
+ dnaclust,
+ dssp,
+ fastdnaml,
+ fastlink,
+ fastqc,
+ fasttree,
+ fastx-toolkit,
+ filo,
+ fitgcp,
+ flexbar,
+ freecontact,
+ gasic,
+ genometools,
+ giira,
+ grinder,
+ idba,
+ infernal,
+ kissplice,
+ last-align,
+ loki,
+ macs,
+ mapsembler2,
+ maq,
+ melting,
+ minia,
+ mipe,
+ mira-assembler,
+ mothur,
+ ncbi-epcr,
+ ncbi-tools-bin,
+ ncoils,
+ parsinsert,
+ perm,
+ phyml,
+ phyutility,
+ picard-tools,
+ plink,
+ primer3,
+ python-cogent,
+ rnahybrid,
+ rtax,
+ samtools,
+ smalt,
+ ssake,
+ tophat,
+ velvet
+Suggests: abyss,
+ bagpipe,
+ cufflinks
Description: Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences, that do not
@@ -973,7 +1055,6 @@
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: praat,
psignifit,
- psychopy,
python-pyepl,
python-pypsignifit,
r-cran-foreign,
@@ -981,6 +1062,7 @@
Suggests: miscpsycho,
psych,
psychometric,
+ psychopy,
psychotree,
psyphy,
python-visionegg,
Added: projects/med/branch/jessie/debian-med/dependency_data/debian-med_2.0.json
URL: http://svn.debian.org/wsvn/blends/projects/med/branch/jessie/debian-med/dependency_data/debian-med_2.0.json?rev=4159&op=file
==============================================================================
--- projects/med/branch/jessie/debian-med/dependency_data/debian-med_2.0.json (added)
+++ projects/med/branch/jessie/debian-med/dependency_data/debian-med_2.0.json Sun Mar 29 14:53:58 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", "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-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", "catissuecore", "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", "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", "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-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"], "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", "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", "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-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": []}}
Modified: projects/med/branch/jessie/debian-med/tasks/cloud
URL: http://svn.debian.org/wsvn/blends/projects/med/branch/jessie/debian-med/tasks/cloud?rev=4159&op=diff
==============================================================================
--- projects/med/branch/jessie/debian-med/tasks/cloud (original)
+++ projects/med/branch/jessie/debian-med/tasks/cloud Sun Mar 29 14:53:58 2015
@@ -6,19 +6,19 @@
in cloud computing clusters, where space can be limited.
X-Begin-Category: Phylogenetic analysis
-Depends:
+Depends: \
altree, clearcut, fastdnaml, fasttree, parsinsert, phyml, phyutility,
prime-phylo, mrbayes, tree-puzzle | tree-ppuzzle
X-End-Category: Phylogenetic analysis
X-Begin-Category: Genetics and genomics
-Depends:
+Depends: \
alien-hunter, bagpipe, fastlink, loki, gasic, genometools, plink,
probabel, r-cran-qtl, r-other-valdar-bagphenotype.library, r-other-mott-happy.hbrem
X-End-Category: Genetics
X-Begin-Category: Sequence alignments and related programs.
-Depends:
+Depends: \
amap-align, blast2, biosquid, boxshade, cassiopee, cdbfasta, cd-hit,
clustalo, clustalw, conservation-code, dialign, dialign-tx,
emboss, embassy-domalign, embassy-domainatrix, embassy-domsearch,
@@ -29,56 +29,54 @@
X-End-Category: Sequence alignments and related programs.
X-Begin-Category: High throughput sequencing
-Depends:
+Depends: \
bamtools, bedtools, fastx-toolkit, flexbar, picard-tools, samtools,
tabix, vcftools
Comment: Processing
-Depends:
+Depends: \
anfo, cufflinks, bowtie, bowtie2, bwa, last-align, maq, perm, tophat, smalt,
soapdenovo, soapdenovo2
Comment: Aligners
-Depends:
+Depends: \
abyss, mapsembler2, idba, minia, mira-assembler, ssake, velvet
Comment: Assembly
-Depends:
+Depends: \
ampliconnoise, arden, fastqc
Comment: Filtering and QC
-Depends:
+Depends: \
discosnp, dnaclust, fitgcp, giira, grinder, kissplice, macs, mothur,
paraclu, r-bioc-hilbertvis, sra-toolkit
Comment: Other
X-End-Category: High throughput sequencing
X-Begin-Category: Analysis of RNA sequences.
-Depends:
+Depends: \
aragorn, infernal, rnahybrid, rtax
X-End-Category: Analysis of RNA sequences.
X-Begin-Category: Molecular modelling and molecular dynamics
-Depends:
+Depends: \
autodock, autodock-vina, autogrid, concavity, dssp, freecontact,
gromacs, hhsuite, mustang, pdb2pqr, raster3d, theseus
Comment: non-free
X-End-Category: Molecular modelling and molecular dynamics
X-Begin-Category: Tools for the molecular biologist.
-Depends:
+Depends: \
melting, mipe, ncbi-epcr, primer3
Comment: Oligonucleotides and PCR
-Depends:
- acedb-other, disulfinder, ncbi-tools-bin, ncoils,
- readseq, tigr-glimmer, seqan-apps, staden-io-libs-utils
-Depends: python-cogent
-Comment: non-free
+Depends: \
+ acedb-other, disulfinder, ncbi-tools-bin, ncoils, python-cogent,
+ readseq, tigr-glimmer, seqan-apps, staden-io-lib-utils
X-End-Category: Tools for the molecular biologist.
X-Begin-Category: Others
-Depends:
+Depends: \
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
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