[Blends-commit] r3084 - in /projects/med/trunk/debian-med: config/control debian-med-tasks.desc debian/changelog debian/control
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Fri Dec 16 12:35:37 UTC 2011
Author: tille
Date: Fri Dec 16 12:35:37 2011
New Revision: 3084
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3084
Log:
Commit status after updating dependencies
Modified:
projects/med/trunk/debian-med/config/control
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/config/control
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/config/control?rev=3084&op=diff
==============================================================================
--- projects/med/trunk/debian-med/config/control (original)
+++ projects/med/trunk/debian-med/config/control Fri Dec 16 12:35:37 2011
@@ -18,6 +18,7 @@
* med-bio-dev developing applications in biological research
* med-cloud command line biol. applications for cloud computing
* med-data drug databases
+ * med-dental helping tools for dentists
* med-epi epidemiology
* med-imaging image processing
* med-imaging-dev developing applications for image processing
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=3084&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian-med-tasks.desc (original)
+++ projects/med/trunk/debian-med/debian-med-tasks.desc Fri Dec 16 12:35:37 2011
@@ -109,9 +109,11 @@
mrbayes
squizz
clonalframe
+ jellyfish
raxml
mlv-smile
tm-align
+ jalview
ncbi-blast+
abacas
profnet-bval
@@ -127,7 +129,6 @@
disulfinder
populations
vcftools
- jellyfish
Task: med-bio-dev
Section: debian-med
@@ -146,11 +147,10 @@
libvibrant6-dev
python-biopython
python-cogent
- libbio-ruby
+ ruby-bio
libbiojava-java
libgenome-1.3-0-dev
libbio-mage-perl
- libtfbs-perl
libgo-perl
r-cran-genetics
r-cran-haplo.stats
@@ -209,6 +209,7 @@
mrbayes
figtree
populations
+ spread
Task: med-cloud
Section: debian-med
@@ -238,6 +239,17 @@
Packages: list
freediams
python-hl7
+
+Task: med-dental
+Section: debian-med
+Description: Debian Med packages related to dental practice
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for dentists to manage their practice.
+Relevance: 10
+Key:
+ med-dental
+Packages: list
+ imagetooth
Task: med-epi
Section: debian-med
@@ -251,6 +263,7 @@
Key:
med-epi
Packages: list
+ epigrass
r-cran-epibasix
r-cran-epitools
r-cran-epi
@@ -305,6 +318,7 @@
dicom3tools
dicomscope
pixelmed-java
+ gofigure2
ginkgocadx
openslide-tools
mricron
@@ -313,7 +327,9 @@
mriconvert
connectomeviewer
sigviewer
+ tifffile
openmeeg-tools
+ plastimatch
biosig-tools
python-nitime
python-dipy
@@ -343,6 +359,7 @@
python-nitime
libvia-dev
libcv-dev
+ libvxl1-dev
libteem1-dev
gmic
libgiftiio-dev
@@ -352,6 +369,7 @@
libgdf-dev
python-dipy
libbiosig-dev
+ libactiviz.net5.6-cil
python-cfflib
libopenslide-dev
@@ -359,7 +377,7 @@
Section: debian-med
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
- ontology.
+ oncology.
Relevance: 10
Key:
med-oncology
Modified: projects/med/trunk/debian-med/debian/changelog
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/changelog?rev=3084&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog (original)
+++ projects/med/trunk/debian-med/debian/changelog Fri Dec 16 12:35:37 2011
@@ -1,9 +1,11 @@
-debian-med (1.10) UNRELEASED; urgency=low
+debian-med (1.10) unstable; urgency=low
* tasks/oncology: Fix typo
Closes: #647987
-
- -- Andreas Tille <tille at debian.org> Fri, 28 Oct 2011 15:48:39 +0200
+ * tasks/dental: Fullfilled dependency imagetooth results in new
+ metapackage med-dental
+
+ -- Andreas Tille <tille at debian.org> Fri, 16 Dec 2011 13:25:18 +0100
debian-med (1.9) unstable; urgency=low
Modified: projects/med/trunk/debian-med/debian/control
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/control?rev=3084&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control (original)
+++ projects/med/trunk/debian-med/debian/control Fri Dec 16 12:35:37 2011
@@ -39,6 +39,7 @@
* med-bio-dev developing applications in biological research
* med-cloud command line biol. applications for cloud computing
* med-data drug databases
+ * med-dental helping tools for dentists
* med-epi epidemiology
* med-imaging image processing
* med-imaging-dev developing applications for image processing
@@ -59,8 +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, 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
+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, jalview, 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, clustalo, 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, phylip, phylographer, phylowin, plato, prank, proalign, profit, prot4est, pyrophosphate-tools, python-orange, python-pynast, python-rdkit, python-reaper, qiime, 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, 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, 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.
@@ -68,8 +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, 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
+Recommends: bioperl, bioperl-run, biosquid, libace-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbiococoa-dev, libbiojava-java, libgenome-1.3-0-dev, libgo-perl, libjebl2-java, libncbi6-dev, libsrf-dev, libstaden-read-dev, libvibrant6-dev, mcl, python-biopython, python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio, 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, libtfbs-perl, 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.
@@ -95,11 +96,20 @@
which can be installed using this metapackage. It is supported by the
GNUmed Electronic Medical Record package.
+Package: med-dental
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: imagetooth
+Suggests: openmolar
+Description: Debian Med packages related to dental practice
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for dentists to manage their practice.
+
Package: med-epi
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-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
+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
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 +120,8 @@
Package: med-imaging
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-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
+Recommends: aeskulap, amide, biosig-tools, caret, connectomeviewer, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, ginkgocadx, gofigure2, gwyddion, imagej, libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix, nifti-bin, 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, voxbo, xmedcon
+Suggests: afni, ants, bioimagesuite, bioimagexd, blox, brainvisa, cdmedicpacs, cellprofiler, cmtk, conquest-dicom-server, dcm4che, dcm4chee, devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, imagemagick, imagevis3d, 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, omero, opendicom.net, openelectrophy, opensourcepacs, openwalnut, piano, 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.
@@ -134,8 +144,8 @@
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, 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
+Recommends: cimg-dev, ctn-dev, gmic, libactiviz.net5.6-cil, 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, libvxl1-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, libbio-formats-java, libctkcore0-dev, libmni-perllib-perl, libnifti-doc, libopenslide-java, libvista2-dev, libvtk5.4, 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.
@@ -147,7 +157,7 @@
Suggests: planunc, uw-prism
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
- ontology.
+ oncology.
Package: med-pharmacy
Architecture: all
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