[Blends-commit] r3000 - in /projects/med/trunk/debian-med: debian-med-tasks.desc debian/control
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Thu Oct 27 08:58:19 UTC 2011
Author: tille
Date: Thu Oct 27 08:58:18 2011
New Revision: 3000
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3000
Log:
Updated metapackages to current status of pool (now we include also ginkgocadx in med-imaging)
Modified:
projects/med/trunk/debian-med/debian-med-tasks.desc
projects/med/trunk/debian-med/debian/control
Modified: projects/med/trunk/debian-med/debian-med-tasks.desc
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian-med-tasks.desc?rev=3000&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian-med-tasks.desc (original)
+++ projects/med/trunk/debian-med/debian-med-tasks.desc Thu Oct 27 08:58:18 2011
@@ -51,6 +51,7 @@
clustalw
mothur
bowtie
+ dotur
transtermhp
last-align
maq
@@ -93,9 +94,11 @@
staden-io-lib-utils
samtools
bedtools
+ filo
r-bioc-hilbertvis
r-other-mott-happy
seq-gen
+ mira-assembler
alien-hunter
ncoils
picard-tools
@@ -109,11 +112,22 @@
raxml
mlv-smile
tm-align
- populations
- dotur
ncbi-blast+
abacas
+ profnet-bval
+ profnet-chop
+ profnet-con
+ profnet-isis
+ profnet-md
+ profnet-norsnet
+ profnet-prof
+ profnet-snapfun
+ profphd-net
ampliconnoise
+ disulfinder
+ populations
+ vcftools
+ jellyfish
Task: med-bio-dev
Section: debian-med
@@ -149,6 +163,7 @@
seqan-dev
libbio-mage-utils-perl
libjebl2-java
+ r-bioc-biobase
Task: med-bio-ngs
Section: debian-med
@@ -158,6 +173,7 @@
Relevance: 10
Packages: list
mothur
+ mira-assembler
Task: med-bio-phylogeny
Section: debian-med
@@ -190,9 +206,9 @@
mustang
phyml
tm-align
- populations
mrbayes
figtree
+ populations
Task: med-cloud
Section: debian-med
@@ -221,6 +237,7 @@
med-data
Packages: list
freediams
+ python-hl7
Task: med-epi
Section: debian-med
@@ -234,7 +251,6 @@
Key:
med-epi
Packages: list
- epigrass
r-cran-epibasix
r-cran-epitools
r-cran-epi
@@ -282,17 +298,20 @@
gwyddion
sofa-apps
python-mvpa
+ python-nipy
python-nipype
caret
libgdcm-tools
dicom3tools
dicomscope
pixelmed-java
+ ginkgocadx
+ openslide-tools
mricron
voxbo
mrtrix
- ants
mriconvert
+ connectomeviewer
sigviewer
openmeeg-tools
biosig-tools
@@ -313,16 +332,17 @@
libminc-dev
libmdc2-dev
libnifti-dev
+ libigstk4-dev
libinsighttoolkit3-dev
libvolpack1-dev
libgdcm2-dev
python-gdcm
python-mvpa
+ python-nipy
python-nipype
python-nitime
libvia-dev
libcv-dev
- libvxl1-dev
libteem1-dev
gmic
libgiftiio-dev
@@ -333,6 +353,18 @@
python-dipy
libbiosig-dev
python-cfflib
+ libopenslide-dev
+
+Task: med-oncology
+Section: debian-med
+Description: Debian Med packages for oncology
+ This metapackage will install tools that are useful for radiation
+ ontology.
+Relevance: 10
+Key:
+ med-oncology
+Packages: list
+ dicompyler
Task: med-pharmacy
Section: debian-med
@@ -374,7 +406,7 @@
gnumed-client
gnumed-server
libchipcard-tools
- aeskulap
+ ginkgocadx
freediams
r-cran-medadherence
@@ -394,6 +426,17 @@
r-cran-psy
psychopy
+Task: med-rehabilitation
+Section: debian-med
+Description: Debian Med packages for rehabilitation technologies
+ This metapackage will install tools that are useful for
+ rehabilitation and therapy.
+Relevance: 10
+Key:
+ med-rehabilitation
+Packages: list
+ sitplus
+
Task: med-statistics
Section: debian-med
Description: Debian Med statistics
@@ -418,13 +461,13 @@
Key:
med-tools
Packages: list
- mencal
- cycle
+ pcalendar
pondus
wgerman-medical
hunspell-de-med
quitcount
workrave
+ edfbrowser
Task: med-typesetting
Section: debian-med
Modified: projects/med/trunk/debian-med/debian/control
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/control?rev=3000&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control (original)
+++ projects/med/trunk/debian-med/debian/control Thu Oct 27 08:58:18 2011
@@ -59,8 +59,8 @@
Package: med-bio
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, bedtools, biomaj, blast2, bowtie, boxshade, bwa, clonalframe, clustalw, clustalx, dialign, dialign-tx, dotur, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fastx-toolkit, figtree, gamgi, garlic, gbrowse, gdpc, gff2aplot, gff2ps, ghemical, glam2, gromacs, hmmer, infernal, jmol, kalign, last-align, loki, mafft, maq, maqview, massxpert, melting, mipe, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, pymol, python-cogent, r-bioc-hilbertvis, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, rnahybrid, samtools, seq-gen, sibsim4, sigma-align, sim4, squizz, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, velvet, wise
-Suggests: abyss, act, agdbnet, amos-assembler, amoscmp, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, ballview, bambus, beads, beast-mcmc, big-blast, bio-mauve, blast+, blixem, btk-core, cactus, caftools, cap3, cd-hit, cdna-db, chado, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, denoiser, disulfinder, e-hive, ecell, elph, embassy-phylip, emboss-explorer, emboss-kaptain, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fasttree, figaro, filo, finex, fluctuate, forester, forge, galaxy, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, gentle, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, igv, jalview, jbrowse, jigsaw, jstreeview, jtreeview, kempbasu, lagan, lamarc, logomat-m, lucy, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, molekel, molphy, mozilla-biofox, msatfinder, mugsy, mummergpu, murasaki, mview, ngila, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phylip, phylographer, phylowin, prank, proalign, profit, profnet-bval, prot4est, pyrophosphate-tools, python-orange, python-pynast, python-reaper, qiime, qtlcart, r-ape, r-other-genabel, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdkit, rdp-classifier, recombine, repeatfinder, repeatmasker, reputer, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seqan-apps, sequenceconverter.app, smalt, snap, soapdenovo, spice, splitstree, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, trace2dbest, tracetuner, treebuilder3d, treeplot, treetime, treevolve, trf, tripal, trnascan-se, twain, uniprime, vcftools, vienna-rna, wgs-assembler, x-tandem-pipeline, zodiac
+Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, bedtools, biomaj, blast2, bowtie, boxshade, bwa, clonalframe, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fastx-toolkit, figtree, filo, gamgi, garlic, gbrowse, gdpc, gff2aplot, gff2ps, ghemical, glam2, gromacs, hmmer, infernal, jellyfish, jmol, kalign, last-align, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd-net, pymol, python-cogent, r-bioc-hilbertvis, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, rnahybrid, samtools, seq-gen, sibsim4, sigma-align, sim4, squizz, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise
+Suggests: abyss, act, agdbnet, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, ballview, bambus, beads, beast-mcmc, big-blast, bio-mauve, blixem, btk-core, cactus, caftools, cain, cap3, cd-hit, cdna-db, chado, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, denoiser, e-hive, ecell, eigensoft, elph, embassy-phylip, emboss-explorer, emboss-kaptain, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fasttree, figaro, finex, fluctuate, forester, forge, galaxy, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, gentle, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, igv, jalview, jbrowse, jigsaw, jstreeview, jtreeview, kempbasu, lagan, lamarc, logomat-m, lucy, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, molphy, mozilla-biofox, msatfinder, mugsy, mummergpu, murasaki, mview, ngila, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phylip, phylographer, phylowin, plato, prank, proalign, profit, prot4est, pyrophosphate-tools, python-orange, python-pynast, python-reaper, qiime, qtlcart, r-ape, r-other-genabel, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdkit, rdp-classifier, recombine, repeatfinder, repeatmasker, reputer, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seqan-apps, sequenceconverter.app, smalt, snap, soapdenovo, spice, splitstree, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, trace2dbest, tracetuner, treebuilder3d, treeplot, treetime, treevolve, trf, tripal, trnascan-se, twain, uniprime, vienna-rna, wgs-assembler, x-tandem-pipeline, zodiac
Description: Debian Med micro-biology packages
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences.
@@ -68,8 +68,8 @@
Package: med-bio-dev
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: bioperl, bioperl-run, biosquid, libace-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbio-ruby, libbiococoa-dev, libbiojava-java, libgenome-1.3-0-dev, libgo-perl, libjebl2-java, libncbi6-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, mcl, python-biopython, python-cogent, r-cran-genetics, r-cran-haplo.stats, seqan-dev
-Suggests: bioclipse, bioconductor, biostrings, iranges, libajax5-dev, libajax6-dev, libbio-das-perl, libchado-perl, libgff-perl, libmems-1.5-1, libnucleus5-dev, libnucleus6-dev, libqsearch-dev, libsbml1, octave-bioinfo, pysam, r-cran-rocr
+Recommends: bioperl, bioperl-run, biosquid, libace-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbio-ruby, libbiococoa-dev, libbiojava-java, libgenome-1.3-0-dev, libgo-perl, libjebl2-java, libncbi6-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, mcl, python-biopython, python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, seqan-dev
+Suggests: bioclipse, biostrings, iranges, libajax5-dev, libajax6-dev, libbio-das-perl, libchado-perl, libgbfp-dev, libgff-perl, libmems-1.5-1, libnucleus5-dev, libnucleus6-dev, libqsearch-dev, libsbml1, octave-bioinfo, pysam, r-cran-rocr
Description: Debian Med packages for development of micro-biology applications
This metapackage will install Debian packages which might be helpful
for development of applications for micro-biological research.
@@ -88,8 +88,8 @@
Package: med-data
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: freediams
-Suggests: drugref.org, python-hl7
+Recommends: freediams, python-hl7
+Suggests: drugref.org
Description: Debian Med drug databases
There is at least one free medical drug database packaged for Debian
which can be installed using this metapackage. It is supported by the
@@ -98,8 +98,8 @@
Package: med-epi
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: epigrass, r-cran-diagnosismed, r-cran-epi, r-cran-epibasix, r-cran-epicalc, r-cran-epir, r-cran-epitools
-Suggests: netepi-analysis, netepi-collection, r-cran-msm, r-cran-surveillance, repast, swarm
+Recommends: r-cran-diagnosismed, r-cran-epi, r-cran-epibasix, r-cran-epicalc, r-cran-epir, r-cran-epitools
+Suggests: epigrass, netepi-analysis, netepi-collection, r-cran-msm, r-cran-surveillance, repast, swarm
Description: Debian Med epidemiology related packages
This metapackage will install tools that are useful in epidemiological
research. Several packages making use of the GNU R data language for
@@ -110,8 +110,8 @@
Package: med-imaging
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: aeskulap, amide, ants, biosig-tools, caret, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, gwyddion, imagej, libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix, nifti-bin, openmeeg-tools, pixelmed-java, python-dipy, python-mvpa, python-nifti, python-nipype, python-nitime, sigviewer, sofa-apps, via-bin, voxbo, xmedcon
-Suggests: afni, bioimagesuite, blox, brainvisa, cdmedicpacs, cmtk, connectomeviewer, conquest-dicom-server, dcm4che, dcm4chee, devide, dicom4j, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, ginkgocadx, gofigure2, imagemagick, imview, insightapplications, invesalius, isis, itksnap, jemris, jist, kradview, libvista2, lipsia, loci-bio-formats, maris, mayam, medisnap, mesa-test-tools, micromanager, mipav, miview, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mrisim, odin, opendicom.net, openelectrophy, opensourcepacs, openwalnut, piano, plastimatch, pngquant, python-nipy, pyxid, slicer, stir, tempo, visit, vmtk, xnat
+Recommends: aeskulap, amide, biosig-tools, caret, connectomeviewer, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, ginkgocadx, gwyddion, imagej, libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix, nifti-bin, openmeeg-tools, openslide-tools, pixelmed-java, python-dipy, python-mvpa, python-nifti, python-nipy, python-nipype, python-nitime, sigviewer, sofa-apps, via-bin, voxbo, xmedcon
+Suggests: afni, ants, bioimagesuite, blox, brainvisa, cdmedicpacs, cmtk, conquest-dicom-server, dcm4che, dcm4chee, devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, gofigure2, imagemagick, imview, insightapplications, invesalius, isis, itksnap, jemris, jist, kradview, libvista2, lipsia, maris, mayam, medisnap, mesa-test-tools, micromanager, mipav, miview, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mrisim, odin, opendicom.net, openelectrophy, opensourcepacs, openwalnut, piano, plastimatch, pngquant, pymeg, pysurfer, pyxid, slicer, stabilitycalc, stir, tempo, visit, vmtk, volview, xnat
Description: Debian Med imaging packages
This metapackage will install Debian packages which might be useful in
medical image processing.
@@ -134,11 +134,20 @@
Package: med-imaging-dev
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: cimg-dev, ctn-dev, gmic, libbiosig-dev, libcv-dev, libgdcm2-dev, libgdf-dev, libgiftiio-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti-dev, libopenmeeg-dev, libteem1-dev, libvia-dev, libvolpack1-dev, libvxl1-dev, python-cfflib, python-dicom, python-dipy, python-gdcm, python-mvpa, python-nibabel, python-nipype, python-nitime
-Suggests: emokit, igstk-examples, insighttoolkit3-examples, libactiviz.net5.6-cil, libctkcore0-dev, libigstk4-dev, libmni-perllib-perl, libnifti-doc, libvista2-dev, libvtk5.4, odin, python-libavg, python-nipy, pyxnat
+Recommends: cimg-dev, ctn-dev, gmic, libbiosig-dev, libcv-dev, libgdcm2-dev, libgdf-dev, libgiftiio-dev, libigstk4-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti-dev, libopenmeeg-dev, libopenslide-dev, libteem1-dev, libvia-dev, libvolpack1-dev, python-cfflib, python-dicom, python-dipy, python-gdcm, python-mvpa, python-nibabel, python-nipy, python-nipype, python-nitime
+Suggests: emokit, igstk-examples, insighttoolkit3-examples, libactiviz.net5.6-cil, libbio-formats-java, libctkcore0-dev, libmni-perllib-perl, libnifti-doc, libopenslide-java, libvista2-dev, libvtk5.4, libvxl1-dev, odin, python-libavg, python-openslide, pyxnat
Description: Debian Med packages for medical image development
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing.
+
+Package: med-oncology
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: dicompyler
+Suggests: planunc, uw-prism
+Description: Debian Med packages for oncology
+ This metapackage will install tools that are useful for radiation
+ ontology.
Package: med-pharmacy
Architecture: all
@@ -164,7 +173,7 @@
Package: med-practice
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: aeskulap, freediams, gnumed-client, gnumed-server, libchipcard-tools, r-cran-medadherence
+Recommends: freediams, ginkgocadx, gnumed-client, gnumed-server, libchipcard-tools, r-cran-medadherence
Suggests: clearhealth, elementalclinic, elexis, freeb, freeicd, freemed, freemedforms, freeshim, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, qrisk2, remitt, resmedicinae, sqlclinic, thera-pi, tinyheb
Description: Debian Med packages for practice management
This metapackage contains dependencies for a collection of software
@@ -179,6 +188,14 @@
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
+Package: med-rehabilitation
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: sitplus
+Description: Debian Med packages for rehabilitation technologies
+ This metapackage will install tools that are useful for
+ rehabilitation and therapy.
+
Package: med-statistics
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
@@ -191,8 +208,8 @@
Package: med-tools
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: cycle, hunspell-de-med, mencal, pondus, quitcount, wgerman-medical, workrave
-Suggests: cl-pubmed, hunspell-en-med, linuxorg-pcal, mssstest, python-clips
+Recommends: edfbrowser, hunspell-de-med, pcalendar, pondus, quitcount, wgerman-medical, workrave
+Suggests: cl-pubmed, cycle, hunspell-en-med, mencal, mssstest, python-clips
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
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