[Blends-commit] r2461 - in /projects/med/trunk/debian-med: config/control debian/changelog debian/control debian/control.stub tasks/cloud
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Thu Nov 18 08:26:07 UTC 2010
Author: tille
Date: Thu Nov 18 08:26:05 2010
New Revision: 2461
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2461
Log:
Upload of current Debian Med packages with target Squeeze to fix a bug in upgrade and reflect the recent status of package pool
Modified:
projects/med/trunk/debian-med/config/control
projects/med/trunk/debian-med/debian/changelog
projects/med/trunk/debian-med/debian/control
projects/med/trunk/debian-med/debian/control.stub
projects/med/trunk/debian-med/tasks/cloud
Modified: projects/med/trunk/debian-med/config/control
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/config/control?rev=2461&op=diff
==============================================================================
--- projects/med/trunk/debian-med/config/control (original)
+++ projects/med/trunk/debian-med/config/control Thu Nov 18 08:26:05 2010
@@ -1,6 +1,6 @@
Package: med-config
Architecture: all
-Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.12)
+Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.15)
Conflicts: med-common
Replaces: med-common
Provides: med-common
Modified: projects/med/trunk/debian-med/debian/changelog
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/changelog?rev=2461&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog (original)
+++ projects/med/trunk/debian-med/debian/changelog Thu Nov 18 08:26:05 2010
@@ -1,3 +1,17 @@
+debian-med (1.8) testing-proposed-updates; urgency=low
+
+ [Steffen Möller]
+ * Added task cloud: Cloud computing image for Debian Med
+
+ [Andreas Tille]
+ * config/control: Depends: blends-common (>= 0.6.15)
+ * debian/control.stub: Build-Depends-Indep: blends-dev (>= 0.6.15)
+ which provides postrm / preinst scripts for each metapackage to
+ enable handling failed-upgrade
+ Closes: ##603853
+
+ -- Andreas Tille <tille at debian.org> Thu, 18 Nov 2010 08:16:45 +0100
+
debian-med (1.7) unstable; urgency=low
* Rebuild against blends-dev >= 0.6.14 to prevent
Modified: projects/med/trunk/debian-med/debian/control
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/control?rev=2461&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control (original)
+++ projects/med/trunk/debian-med/debian/control Thu Nov 18 08:26:05 2010
@@ -5,7 +5,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends-Indep: blends-dev (>= 0.6.14)
+Build-Depends-Indep: blends-dev (>= 0.6.15)
Standards-Version: 3.9.1
Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/blends/projects/med/trunk/debian-med/
@@ -21,7 +21,7 @@
Package: med-config
Architecture: all
-Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.12)
+Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.15)
Conflicts: med-common
Replaces: med-common
Provides: med-common
@@ -57,8 +57,8 @@
Package: med-bio
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: adun.app, alien-hunter, altree, amap-align, autodock, ballview, blast2, boxshade, bwa, dialign, dialign-tx, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, gamgi, garlic, gdpc, gff2aplot, gff2ps, ghemical, glam2, gromacs, hmmer, infernal, kalign, last-align, loki, mafft, maq, massxpert, melting, mipe, mummer, muscle, mustang, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, primer3, probcons, proda, pymol, r-bioc-hilbertvis, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, readseq, rnahybrid, samtools, sibsim4, sigma-align, sim4, ssake, staden-io-lib-utils, t-coffee, theseus, tigr-glimmer, tree-puzzle | tree-ppuzzle, treeviewx, velvet, wise
-Suggests: acedb-other, acedb-other-belvu, acedb-other-dotter, act, agdbnet, amos-assembler, amoscmp, arb, artemis, asap, autodocktools, axparafit, axpcoords, bambus, beast-mcmc, big-blast, bio-mauve, blixem, bowtie, btk-core, cactus, caftools, cap3, cd-hit, cdna-db, clustalw, clustalw-mpi, clustalx, cluster3, coalesce, codonw, compclust, contralign, coot, copycat, crossbow, cytoscape, das-proserver, dazzle, decipher, denoiser, dotter, dotur, ecell, elph, embassy-phylip, emboss-explorer, emboss-kaptain, est-db, estferret, estscan, exalt, excavator, fasta, fastx-toolkit, figaro, finex, fluctuate, forester, galaxy, gbioseq, gbrowse, genesplicer, genetrack, genezilla, genographer, gentle, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, igv, jalview, jigsaw, jmol, jstreeview, jtreeview, kempbasu, lagan, lamarc, logomat-m, lucy, mage2tab, martj, mauvealigner, maxd, melting-gui, meme, mesquite, migrate, minimus, mira, mirbase, molekel, molphy, mothur, mozilla-biofox, mrbayes, msatfinder, mummergpu, murasaki, mview, ncbi-tools++, ngila, obo-edit, oligoarrayaux, omegamap, operondb, paml, partigene, patman, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phylip, phylographer, phylowin, populations, prank, proalign, profit, prot4est, pyrophosphate-tools, python-cogent, python-pynast, qiime, qtlcart, r-ape, r-other-genabel, r-other-valdar-bagphenotype.library, raster3d, raxml, rbs-finder, recombine, repeatfinder, reputer, roche454ace2caf, rose, rosetta, seaview, seq-gen, seqan-apps, sequenceconverter.app, smile, spice, splitstree, ssaha, tacg, taverna, taxinspector, tetra, tigr-assembler, tm-align, trace2dbest, tracetuner, transtermhp, treebuilder3d, treeplot, treetime, treevolve, trnascan-se, twain, uniprime, vienna-rna, wgs-assembler
+Recommends: adun.app, alien-hunter, altree, amap-align, autodock, ballview, blast2, boxshade, bwa, dialign, dialign-tx, emboss, exonerate, fastdnaml, fastlink, gamgi, garlic, gdpc, gff2aplot, gff2ps, ghemical, glam2, gromacs, hmmer, infernal, kalign, last-align, loki, mafft, maq, massxpert, melting, mipe, mummer, muscle, mustang, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, primer3, probcons, proda, pymol, r-bioc-hilbertvis, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, readseq, rnahybrid, samtools, sibsim4, sigma-align, sim4, ssake, staden-io-lib-utils, t-coffee, theseus, tigr-glimmer, tree-puzzle | tree-ppuzzle, treeviewx, velvet, wise
+Suggests: acedb-other, acedb-other-belvu, acedb-other-dotter, act, agdbnet, amos-assembler, amoscmp, arb, artemis, asap, autodocktools, axparafit, axpcoords, bagphenotype, bambus, beast-mcmc, big-blast, bio-mauve, blixem, bowtie, btk-core, cactus, caftools, cap3, cd-hit, cdna-db, clustalw, clustalw-mpi, clustalx, cluster3, coalesce, codonw, compclust, contralign, coot, copycat, crossbow, cytoscape, das-proserver, dazzle, decipher, denoiser, dotter, dotur, ecell, elph, embassy-domainatrix, embassy-domalign, embassy-domsearch, embassy-phylip, emboss-explorer, emboss-kaptain, est-db, estferret, estscan, exalt, excavator, fasta, fastx-toolkit, figaro, finex, fluctuate, forester, galaxy, gbioseq, gbrowse, genesplicer, genetrack, genezilla, genographer, gentle, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, igv, jalview, jigsaw, jmol, jstreeview, jtreeview, kempbasu, lagan, lamarc, logomat-m, lucy, mage2tab, martj, mauvealigner, maxd, melting-gui, meme, mesquite, migrate, minimus, mira, mirbase, molekel, molphy, mothur, mozilla-biofox, mrbayes, msatfinder, mummergpu, murasaki, mview, ncbi-tools++, ngila, obo-edit, oligoarrayaux, omegamap, operondb, paml, partigene, patman, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phylip, phylographer, phylowin, populations, prank, proalign, profit, prot4est, pyrophosphate-tools, python-cogent, python-pynast, qiime, qtlcart, r-ape, r-other-genabel, r-other-valdar-bagphenotype.library, raster3d, raxml, rbs-finder, recombine, repeatfinder, reputer, roche454ace2caf, rose, rosetta, seaview, seq-gen, seqan-apps, sequenceconverter.app, smile, spice, splitstree, ssaha, tacg, taverna, taxinspector, tetra, tigr-assembler, tm-align, trace2dbest, tracetuner, transtermhp, treebuilder3d, treeplot, treetime, treevolve, trnascan-se, twain, uniprime, vienna-rna, wgs-assembler
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.
@@ -67,10 +67,21 @@
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: bioperl, bioperl-run, biosquid, libace-perl, libajax6-dev, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbio-ruby, libbiojava-java, libgenome-1.3-0-dev, libgo-perl, libncbi6-dev, libnucleus6-dev, libqsearch-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, mcl, octave-bioinfo, python-biopython, r-cran-genetics, r-cran-haplo.stats, seqan-dev
-Suggests: bioclipse, bioconductor, libajax5-dev, libbio-das-perl, libbiococoa-dev, libgff-perl, libmems-1.5-1, libnucleus5-dev, libsbml1, limma, r-cran-rocr
+Suggests: bioclipse, bioconductor, libajax5-dev, libbio-das-perl, libbiococoa-dev, libgff-perl, libmems-1.5-1, libnucleus5-dev, libsbml1, limma, python-cogent, 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.
+
+Package: med-cloud
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: autodock
+Suggests: clustalw, clustalw-mpi, python-cogent, raster3d
+Description: Cloud computing image for Debian Med.
+ This metapackage will install Debian packages related to molecular biology,
+ structural biology and bioinformatics for use in life sciences, that do not
+ depend on graphical toolkits and therefore can fit on system images for use
+ in cloud computing clusters, where space can be limited.
Package: med-data
Architecture: all
@@ -99,7 +110,7 @@
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: aeskulap, amide, ants, caret, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, fslview, gwyddion, imagej, itksnap, libgdcm-tools, lipsia, medcon, minc-tools, mrtrix, nifti-bin, odin, openmeeg-tools, pixelmed-java, python-mvpa, python-nifti, python-nipy, python-nipype, slicer, sofa-apps, via-bin, voxbo, xmedcon
-Suggests: afni, bioimagesuite, blox, brainvisa, cdmedicpacs, connectomeviewer, conquest-dicom-server, dcm4che, devide, dicom4j, drjekyll, ecg2png, fiji, fsl, gofigure2, imagemagick, imview, invesalius, jemris, jist, kradview, libvista2, loci-bio-formats, maris, mesa-test-tools, micromanager, mipav, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mricron, mrisim, opendicom.net, openelectrophy, opensourcepacs, piano, pngquant, sigviewer, stir, visit, vmtk
+Suggests: afni, bioimagesuite, blox, brainvisa, cdmedicpacs, connectomeviewer, conquest-dicom-server, dcm4che, devide, dicom4j, drjekyll, dti-query, ecg2png, fiji, fsl, gofigure2, imagemagick, imview, insightapplications, invesalius, jemris, jist, kradview, libvista2, loci-bio-formats, maris, mesa-test-tools, micromanager, mipav, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mriconvert, mricron, mrisim, opendicom.net, openelectrophy, opensourcepacs, piano, pngquant, python-nitime, sigviewer, stir, tempo, visit, vmtk
Description: Cross-platform for visualizing, processing and analysing of bioimages
GoFigure2 is an open-source, cross-platform application for
visualizing, processing and analyzing of multidimensional microscopy
@@ -109,8 +120,8 @@
Package: med-imaging-dev
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: cimg-dev, ctn-dev, gmic, libcv-dev, libgdcm2-dev, libgiftiio-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libopenmeeg-dev, libteem1-dev, libvia-dev, libvolpack1-dev, libvxl1-dev, odin, python-dicom, python-gdcm, python-mvpa, python-nipy, python-nipype
-Suggests: igstk-examples, insighttoolkit3-examples, libbiosig4c++-dev, libigstk4-dev, libmni-perllib-perl, libnifti-dev, libnifti-doc, libvista2-dev, libvtk5.4, python-libavg
+Recommends: cimg-dev, ctn-dev, gmic, libcv-dev, libgdcm2-dev, libgiftiio-dev, libigstk4-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti-dev, libopenmeeg-dev, libteem1-dev, libvia-dev, libvolpack1-dev, libvxl1-dev, odin, python-dicom, python-gdcm, python-mvpa, python-nipy, python-nipype
+Suggests: igstk-examples, insighttoolkit3-examples, libbiosig-dev, libgdf-dev, libmni-perllib-perl, libnifti-doc, libvista2-dev, libvtk5.4, python-libavg, python-nibabel, python-nitime
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.
@@ -127,8 +138,8 @@
Package: med-physics
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: octave3.2, paw, paw++, r-base
-Suggests: biosig, gate, openvibe, paw-demos
+Recommends: octave3.2, r-base
+Suggests: biosig, gate, openvibe, paw, paw++, paw-demos
Description: Debian Med packages for medical physicists
This metapackage contains dependencies for a
collection of software and documentation which is useful for
@@ -139,7 +150,7 @@
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: aeskulap, freediams, gnumed-client, gnumed-server, libchipcard-tools, r-cran-medadherence
-Suggests: clearhealth, elementalclinic, elexis, freeb, freemed, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, resmedicinae, sqlclinic, tinyheb
+Suggests: clearhealth, elementalclinic, elexis, freeb, freemed, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, resmedicinae, sqlclinic, thera-pi, tinyheb
Description: Debian Med packages for practice management
This metapackage contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
Modified: projects/med/trunk/debian-med/debian/control.stub
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/control.stub?rev=2461&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control.stub (original)
+++ projects/med/trunk/debian-med/debian/control.stub Thu Nov 18 08:26:05 2010
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends-Indep: blends-dev (>= 0.6.14)
+Build-Depends-Indep: blends-dev (>= 0.6.15)
Standards-Version: 3.9.1
Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/blends/projects/med/trunk/debian-med/
Modified: projects/med/trunk/debian-med/tasks/cloud
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/cloud?rev=2461&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/cloud (original)
+++ projects/med/trunk/debian-med/tasks/cloud Thu Nov 18 08:26:05 2010
@@ -1,5 +1,5 @@
Task: Cloud
-Description: Cloud computing image for Debian Med.
+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
depend on graphical toolkits and therefore can fit on system images for use
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