Author: tille
Date: Tue Apr 17 08:04:59 2012
New Revision: 3282
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3282
Log:
Rerun metapackage generation process since octave is now in testing
Modified:
projects/med/trunk/debian-med/debian-med-tasks.desc
projects/med/trunk/debian-med/debian/changelog
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=3282&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian-med-tasks.desc (original)
+++ projects/med/trunk/debian-med/debian-med-tasks.desc Tue Apr 17 08:04:59 2012
@@ -101,7 +101,6 @@
gassst
r-bioc-hilbertvis
r-other-mott-happy
- seq-gen
mira-assembler
alien-hunter
ncoils
@@ -167,6 +166,7 @@
libbiojava-java
libgenome-1.3-0-dev
libbio-mage-perl
+ libtfbs-perl
libgo-perl
r-cran-genetics
r-cran-haplo.stats
@@ -186,8 +186,10 @@
libjebl2-java
r-bioc-biobase
libffindex0-dev
- libics
- python-libtiff
+ librostlab3-dev
+ librostlab-doc
+ librostlab-blast0-dev
+ librostlab-blast-doc
Task: med-bio-ngs
Section: debian-med
@@ -358,6 +360,7 @@
mricron
voxbo
mrtrix
+ itksnap
mriconvert
sigviewer
tifffile
@@ -443,6 +446,7 @@
Packages: list
paw++
paw
+ octave
r-base
Task: med-practice
Modified: projects/med/trunk/debian-med/debian/changelog
URL:
http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/changelog?rev=3282&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog (original)
+++ projects/med/trunk/debian-med/debian/changelog Tue Apr 17 08:04:59 2012
@@ -1,4 +1,4 @@
-debian-med (1.11) UNRELEASED; urgency=low
+debian-med (1.11) unstable; urgency=low
* debian/control(.stub):
Standards-Version: 3.9.3 (no changes needed)
Modified: projects/med/trunk/debian-med/debian/control
URL:
http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/control?rev=3282&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control (original)
+++ projects/med/trunk/debian-med/debian/control Tue Apr 17 08:04:59 2012
@@ -60,8 +60,8 @@
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, ballview, bedtools, biomaj, blast2, bowtie, bowtie2,
boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign,
dialign-tx, disulfinder, dotur, embassy-domainatrix, embassy-domalign,
embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fastx-toolkit,
ffindex, figtree, filo, gamgi, garlic, gassst, gbrowse, gdpc, gff2aplot,
gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview,
jellyfish, jmol, kalign, last-align, librg-utils-perl, 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, profphd-net, profphd-utils, proftmb,
pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis,
r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml,
readseq, reprof, 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, bambus, beads, beast-mcmc, big-blast, bio-mauve, blimps-utils,
blixem, btk-core, cactus, caftools, cain, cap3, cdna-db, chado, cinema, circos,
clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust,
contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver,
dazzle, decipher, 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, 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, neobio, ngila, obo-edit, oligoarrayaux, omegamap, operondb,
pal2nal, paml, partigene, patman, pcma, pdb2pqr, pfaat, pftools, phagefinder,
phpphylotree, phy-spread, phylip, phylographer, phylowin, plato, prank,
proalign, profit, prot4est, pyrophosphate-tools, python-orange, python-rdkit,
python-reaper, qtlcart, r-ape, r-other-genabel,
r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder,
rdp-classifier, recombine, repeatfinder, repeatmasker, reputer, rmblast,
roche454ace2caf, rose, rosetta, sap, seaview, seqan-apps,
sequenceconverter.app, sift, smalt, snap, soapdenovo, spice, splitstree,
sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler,
tophat, trace2dbest, tracetuner, treebuilder3d, treeplot, treetime, treevolve,
trf, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd,
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, ballview, bedtools, biomaj, blast2, bowtie, bowtie2,
boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign,
dialign-tx, disulfinder, dotur, embassy-domainatrix, embassy-domalign,
embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fastx-toolkit,
ffindex, figtree, filo, gamgi, garlic, gassst, gbrowse, gdpc, gff2aplot,
gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview,
jellyfish, jmol, kalign, last-align, librg-utils-perl, 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, profphd-net, profphd-utils, proftmb,
pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis,
r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml,
readseq, reprof, rnahybrid, samtools, 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, bambus, beads, beast-mcmc, big-blast, bio-mauve, blimps-utils,
blixem, btk-core, cactus, caftools, cain, cap3, cdna-db, chado, cinema, circos,
clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust,
contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver,
dazzle, decipher, 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, 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, neobio, ngila, obo-edit, oligoarrayaux, omegamap, operondb,
pal2nal, paml, partigene, patman, pcma, pdb2pqr, pfaat, pftools, phagefinder,
phpphylotree, phy-spread, phylip, phylographer, phylowin, plato, prank,
proalign, profit, prot4est, pyrophosphate-tools, python-orange, python-rdkit,
python-reaper, qtlcart, r-ape, r-other-genabel,
r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder,
rdp-classifier, recombine, repeatfinder, repeatmasker, reputer, rmblast,
roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps,
sequenceconverter.app, sift, smalt, snap, soapdenovo, spice, splitstree,
sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler,
tophat, trace2dbest, tracetuner, treebuilder3d, treeplot, treetime, treevolve,
trf, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd,
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.
@@ -69,8 +69,8 @@
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,
libbiococoa-dev, libbiojava-java, libchado-perl, libffindex0-dev,
libgenome-1.3-0-dev, libgo-perl, libjebl2-java, libncbi6-dev, libpal-java,
librg-reprof-bundle-perl, libsrf-dev, libstaden-read-dev, libvibrant6-dev,
libzerg-perl, libzerg0-dev, mcl, python-biopython, python-cogent,
r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio, seqan-dev
-Suggests: bioclipse, biostrings, iranges, libajax6-dev, libbio-das-perl,
libgbfp-dev, libgff-perl, libmems-1.5-1, libnucleus6-dev, libqsearch-dev,
librg-blast-parser-perl, librostlab-blast-doc, librostlab-blast0-dev,
librostlab-doc, librostlab3-dev, libsbml5-dev, libtfbs-perl, octave-bioinfo,
pysam, python-mmtk, r-cran-rocr
+Recommends: bioperl, bioperl-run, biosquid, libace-perl, libbio-graphics-perl,
libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl,
libbiococoa-dev, libbiojava-java, libchado-perl, libffindex0-dev,
libgenome-1.3-0-dev, libgo-perl, libjebl2-java, libncbi6-dev, libpal-java,
librg-reprof-bundle-perl, librostlab-blast-doc, librostlab-blast0-dev,
librostlab-doc, librostlab3-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl,
libvibrant6-dev, libzerg-perl, libzerg0-dev, mcl, python-biopython,
python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio,
seqan-dev
+Suggests: bioclipse, biostrings, iranges, libajax6-dev, libbio-das-perl,
libgbfp-dev, libgff-perl, libmems-1.5-1, libnucleus6-dev, libqsearch-dev,
librg-blast-parser-perl, libsbml5-dev, octave-bioinfo, pysam, python-mmtk,
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.
@@ -120,8 +120,8 @@
Package: med-imaging
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: aeskulap, amide, biosig-tools, caret, ctn, ctsim, dcmtk,
dicom3tools, dicomnifti, dicomscope, ginkgocadx, gofigure2, gwyddion, imagej,
imagevis3d, libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix,
nifti-bin, odin, openmeeg-tools, openslide-tools, pixelmed-java, plastimatch,
python-dipy, python-mvpa, python-nifti, python-nipy, python-nipype,
python-nitime, sigviewer, sofa-apps, tifffile, via-bin, volview, voxbo, xmedcon
-Suggests: afni, ants, bioimagesuite, bioimagexd, blox, brainvisa, cdmedicpacs,
cellprofiler, cmtk, connectomeviewer, conquest-dicom-server, dcm4che, dcm4chee,
devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab,
elastix, fiji, freesurfer, fsl, fslview, gimias, hid, 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, omero, opendicom.net, openelectrophy, opensourcepacs, openwalnut,
piano, pngquant, pymeg, pysurfer, pyxid, slicer, stabilitycalc, stir, tempo,
visit, vmtk, xnat
+Recommends: aeskulap, amide, biosig-tools, caret, ctn, ctsim, dcmtk,
dicom3tools, dicomnifti, dicomscope, ginkgocadx, gofigure2, gwyddion, imagej,
imagevis3d, itksnap, libgdcm-tools, medcon, minc-tools, mriconvert, mricron,
mrtrix, nifti-bin, odin, openmeeg-tools, openslide-tools, pixelmed-java,
plastimatch, python-dipy, python-mvpa, python-nifti, python-nipy,
python-nipype, python-nitime, sigviewer, sofa-apps, tifffile, via-bin, volview,
voxbo, xmedcon
+Suggests: afni, ants, bioimagesuite, bioimagexd, blox, brainvisa, cdmedicpacs,
cellprofiler, cmtk, connectomeviewer, conquest-dicom-server, dcm4che, dcm4chee,
devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab,
elastix, fiji, freesurfer, fsl, fslview, gimias, hid, imagemagick, imview,
insightapplications, invesalius, isis, 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, omero,
opendicom.net, openelectrophy, opensourcepacs, openwalnut, piano, pngquant,
pymeg, pysurfer, pyxid, slicer, stabilitycalc, stir, tempo, visit, vmtk, xnat
Description: Debian Med imaging packages
This metapackage will install Debian packages which might be useful in
medical image processing.
@@ -172,8 +172,8 @@
Package: med-physics
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: paw, paw++, r-base
-Suggests: biosig, gate, octave, openvibe, paw-demos
+Recommends: octave, paw, paw++, r-base
+Suggests: biosig, gate, openvibe, paw-demos
Description: Debian Med packages for medical physicists
This metapackage contains dependencies for a
collection of software and documentation which is useful for
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