[Blends-commit] r4087 - in /projects/med/trunk/debian-med: debian-med-tasks.desc debian/changelog debian/control debian/control.stub
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Thu Oct 23 21:47:40 UTC 2014
Author: tille
Date: Thu Oct 23 21:47:40 2014
New Revision: 4087
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=4087
Log:
Run make dist for new verison 1.99 (will be 2.0 in Jessie)
Modified:
projects/med/trunk/debian-med/debian-med-tasks.desc
projects/med/trunk/debian-med/debian/changelog
projects/med/trunk/debian-med/debian/control
projects/med/trunk/debian-med/debian/control.stub
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=4087&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian-med-tasks.desc (original)
+++ projects/med/trunk/debian-med/debian-med-tasks.desc Thu Oct 23 21:47:40 2014
@@ -15,6 +15,7 @@
probalign
treeviewx
figtree
+ phylip
fastlink
loki
plink
@@ -28,6 +29,7 @@
sim4
sibsim4
tabix
+ tophat
wise
maqview
bwa
@@ -45,6 +47,7 @@
poa
probcons
proda
+ seaview
sigma-align
emboss
embassy-domalign
@@ -54,12 +57,14 @@
clustalo
clustalw
mothur
+ bowtie
bowtie2
transtermhp
last-align
maq
ssake
velvet
+ qiime
infernal
rnahybrid
adun.app
@@ -92,12 +97,15 @@
autogrid
autodock-vina
mustang
+ probabel
theseus
staden-io-lib-utils
samtools
bedtools
filo
r-bioc-hilbertvis
+ r-other-mott-happy.hbrem
+ snp-sites
mira-assembler
alien-hunter
seqan-apps
@@ -108,6 +116,7 @@
acedb-other-belvu
acedb-other
python-cogent
+ velvetoptimiser
mrbayes
pdb2pqr
squizz
@@ -151,6 +160,9 @@
topp
openms
arden
+ fitgcp
+ gasic
+ giira
ipig
aevol
anfo
@@ -172,12 +184,14 @@
metastudent
mrs
ncbi-seg
+ paraclu
parsinsert
perm
phyutility
prank
predictprotein
proalign
+ prodigal
pycorrfit
pyscanfcs
r-bioc-rtracklayer
@@ -235,9 +249,11 @@
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
@@ -254,6 +270,8 @@
librg-reprof-bundle-perl
python-corepywrap
librcsb-core-wrapper0-dev
+ libsbml5-dev
+ sbmltoolbox
seqan-dev
libbio-mage-utils-perl
libchado-perl
@@ -276,9 +294,12 @@
libgenome-perl
libgenome-model-tools-music-perl
pyfai
+ libhts-dev
python-htseq
python-csb
python-freecontact
+ libsnp-sites1-dev
+ libssm-dev
python-pysam
Task: med-bio-ngs
@@ -289,6 +310,7 @@
Relevance: 10
Packages: list
mothur
+ qiime
mira-assembler
kissplice
uc-echo
@@ -308,6 +330,7 @@
tree-puzzle
probalign
treeviewx
+ phylip
muscle
t-coffee
kalign
@@ -318,6 +341,7 @@
poa
probcons
proda
+ seaview
sigma-align
clustalx
clustalw
@@ -340,9 +364,6 @@
Key:
med-cloud
Packages: list
- clustalw
- autodock
- raster3d
python-cogent
Task: med-cms
@@ -395,6 +416,7 @@
epigrass
r-cran-epibasix
r-cran-epitools
+ r-cran-surveillance
r-cran-epi
r-cran-diagnosismed
r-cran-epicalc
@@ -440,32 +462,39 @@
med-imaging
Packages: list
amide
+ ctsim
ctn
dicomnifti
imagej
minc-tools
medcon
python-nibabel
+ python-dicom
xmedcon
dcmtk
nifti-bin
aeskulap
fslview
gwyddion
+ sofa-apps
python-mvpa2
caret
libgdcm-tools
dicom3tools
imagevis3d
+ odin
dicomscope
pixelmed-apps
gofigure2
ginkgocadx
openslide-tools
+ conquest-common
camitk-imp
orthanc
teem-apps
invesalius
+ mricron
+ voxbo
mrtrix
ants
itksnap
@@ -479,6 +508,7 @@
python-surfer
king
vtk-dicom-tools
+ gdf-tools
python-nitime
python-dipy
@@ -504,13 +534,15 @@
python-mvpa2
python-nitime
python-casmoothing
+ odin
libcv-dev
+ libvxl1-dev
libteem-dev
gmic
libgiftiio-dev
libactiviz.net-cil
libvistaio-dev
- libmia-2.0-dev
+ libmia-2.2-dev
libmiaviewit-dev
libmialm-dev
python-mia
@@ -518,6 +550,7 @@
python-dicom
python-nibabel
libgdf-dev
+ octave-gdf
python-pyxnat
python-dipy
libbiosig-dev
@@ -529,6 +562,7 @@
python-mne
libvigraimpex-dev
python-vigra
+ libedf-dev
Task: med-oncology
Section: debian-med
@@ -565,8 +599,12 @@
Key:
med-physics
Packages: list
+ paw++
+ paw
octave
r-base
+ biosig-tools
+ gdf-tools
Task: med-practice
Section: debian-med
@@ -603,6 +641,7 @@
psignifit
python-pypsignifit
r-cran-psy
+ psychopy
Task: med-rehabilitation
Section: debian-med
@@ -627,6 +666,7 @@
r-bioc-limma
r-bioc-qvalue
r-cran-randomforest
+ r-cran-beeswarm
r-cran-pvclust
Task: med-tools
@@ -648,7 +688,6 @@
hunspell-en-med
python-clips
cronometer
- python3-fitbitscraper
python-fitbit
nut-nutrition
Modified: projects/med/trunk/debian-med/debian/changelog
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/changelog?rev=4087&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog (original)
+++ projects/med/trunk/debian-med/debian/changelog Thu Oct 23 21:47:40 2014
@@ -1,4 +1,4 @@
-debian-med (1.13.3) UNRELEASED; urgency=low
+debian-med (1.99) unstable; urgency=low
* debian/control.stub:
- Build-Depends: blends-dev (>= 0.6.92) to get Section: metapackage entries
@@ -148,7 +148,7 @@
removed:
Depends: biosig
- -- Andreas Tille <tille at debian.org> Thu, 18 Apr 2013 07:42:55 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 23 Oct 2014 23:42:18 +0200
debian-med (1.13.2) 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=4087&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control (original)
+++ projects/med/trunk/debian-med/debian/control Thu Oct 23 21:47:40 2014
@@ -4,8 +4,8 @@
Uploaders: Andreas Tille <tille at debian.org>
Section: misc
Priority: extra
-Build-Depends-Indep: blends-dev (>= 0.6.16.3)
-Standards-Version: 3.9.5
+Build-Depends-Indep: blends-dev (>= 0.6.92)
+Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/blends/projects/med/trunk/debian-med/
Vcs-Svn: svn://anonscm.debian.org/blends/projects/med/trunk/debian-med/
@@ -54,7 +54,7 @@
Debian by simply installing the relevant metapackage
Package: med-bio
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: abacas,
@@ -78,6 +78,7 @@
bedtools,
biomaj,
blast2,
+ bowtie,
bowtie2,
boxshade,
bwa,
@@ -113,16 +114,19 @@
ffindex,
figtree,
filo,
+ fitgcp,
flexbar,
freecontact,
gamgi,
garlic,
+ gasic,
gbrowse,
gdpc,
genometools,
gentle,
gff2aplot,
gff2ps,
+ giira,
glam2,
grinder,
gromacs,
@@ -173,10 +177,12 @@
norsnet,
norsp,
openms,
+ paraclu,
parsinsert,
pdb2pqr,
perlprimer,
perm,
+ phylip,
phyml,
phyutility,
picard-tools,
@@ -190,9 +196,11 @@
prime-phylo,
primer3,
proalign,
+ probabel,
probalign,
probcons,
proda,
+ prodigal,
profbval,
profisis,
profnet-bval,
@@ -212,6 +220,7 @@
pynast,
pyscanfcs,
python-cogent,
+ qiime,
r-bioc-biostrings,
r-bioc-cummerbund,
r-bioc-gviz,
@@ -222,6 +231,7 @@
r-cran-qtl,
r-cran-vegan,
r-other-bio3d,
+ r-other-mott-happy.hbrem,
rasmol,
raster3d,
rate4site,
@@ -233,6 +243,7 @@
rtax,
saint,
samtools,
+ seaview,
seqan-apps,
seqtk,
sibsim4,
@@ -240,6 +251,7 @@
sim4,
smalt,
snap,
+ snp-sites,
soapdenovo,
soapdenovo2,
squizz,
@@ -252,6 +264,7 @@
theseus,
tigr-glimmer,
tm-align,
+ tophat,
topp,
transtermhp,
tree-puzzle | tree-ppuzzle,
@@ -260,6 +273,7 @@
uc-echo,
vcftools,
velvet,
+ velvetoptimiser,
wigeon,
wise,
zalign
@@ -289,7 +303,6 @@
blat,
blimps-utils,
blixem,
- bowtie,
btk-core,
cactus,
caftools,
@@ -328,18 +341,16 @@
estscan,
exalt,
excavator,
- fas,
fasta,
fastaq,
figaro,
finex,
- fitgcp,
fluctuate,
forester,
forge,
freebayes,
+ fsa,
galaxy,
- gasic,
gassst,
gbioseq,
gbrowse-syn,
@@ -349,7 +360,6 @@
genezilla,
genographer,
ghemical,
- giira,
glimmerhmm,
gmap,
gmv,
@@ -396,6 +406,7 @@
murasaki,
mview,
ngila,
+ ngsqctoolkit,
nw-align,
oases,
obo-edit,
@@ -412,7 +423,6 @@
pftools,
phagefinder,
phpphylotree,
- phylip,
phylographer,
phyloviz-core,
phylowin,
@@ -424,22 +434,22 @@
pyrophosphate-tools,
python-orange,
python-reaper,
- qiime,
qtlcart,
r-cran-boolnet,
- r-other-mott-happy,
r-other-valdar-bagphenotype.library,
raccoon,
rbs-finder,
rdp-classifier,
recombine,
+ relion-bin,
+ relion-bin-mpi,
+ relion-gui,
repeatmasker,
rmblast,
roche454ace2caf,
rose,
rosetta,
sap,
- seaview,
seq-gen,
sequenceconverter.app,
sga,
@@ -459,7 +469,6 @@
tetra,
tigr-assembler,
tigr-glimmer-mg,
- tophat,
trace2dbest,
tracetuner,
treebuilder3d,
@@ -482,7 +491,7 @@
structural biology and bioinformatics for use in life sciences.
Package: med-bio-dev
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: bioperl,
@@ -503,11 +512,13 @@
libffindex0-dev,
libfreecontact-perl,
libfreecontact0-dev,
+ libgenome-1.3-dev,
libgenome-model-tools-music-perl,
libgenome-perl,
libgenometools0-dev,
libgo-perl,
libhmsbeagle-dev,
+ libhts-dev,
libjebl2-java,
libncbi6-dev,
libnhgri-blastall-perl,
@@ -518,16 +529,20 @@
librg-reprof-bundle-perl,
librostlab-blast0-dev,
librostlab3-dev,
+ libsbml5-dev,
+ libsnp-sites1-dev,
libsort-key-top-perl,
libsrf-dev,
+ libssm-dev,
libstaden-read-dev,
+ libtfbs-perl,
libvibrant6-dev,
libzerg-perl,
libzerg0-dev,
mcl,
pyfai,
python-biom-format,
- python-biopython,
+ python-biopython | python3-biopython,
python-cogent,
python-corepywrap,
python-csb | python3-csb,
@@ -540,44 +555,34 @@
r-cran-genetics,
r-cran-haplo.stats,
ruby-bio,
+ sbmltoolbox,
seqan-dev
Suggests: bioclipse,
libbio-das-perl,
libforester-java,
libfreecontact-doc,
libgbfp-dev,
- libgenome-1.3-0-dev,
libgff-perl,
libgtextutils-dev,
libmems-1.5-1,
+ librelion-dev,
librostlab-blast-doc,
librostlab-doc,
- libsbml5-dev,
libswarm2-dev,
- libtfbs-perl,
octace-bioinfo,
python-biopython-doc,
- python-biopython-sql,
- python3-biopython,
- python3-biopython-sql,
+ python-biopython-sql | python3-biopython-sql,
r-bioc-affy,
- r-cran-rocr,
- sbmltoolbox
+ 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
-Section: metapackage
-Architecture: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: autodock,
- clustalw,
- python-cogent,
- raster3d
-Suggests: bagpipe,
- clustalw-mpi,
- r-other-valdar-bagphenotype.library
+Section: metapackages
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: python-cogent
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
@@ -585,7 +590,7 @@
in cloud computing clusters, where space can be limited.
Package: med-data
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: freediams,
@@ -598,7 +603,7 @@
the application.
Package: med-dental
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: entangle,
@@ -609,7 +614,7 @@
which might be helpful for dentists to manage their practice.
Package: med-epi
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: epigrass,
@@ -618,12 +623,13 @@
r-cran-epibasix,
r-cran-epicalc,
r-cran-epir,
- r-cran-epitools
+ r-cran-epitools,
+ r-cran-surveillance
Suggests: netepi-analysis,
netepi-collection,
r-cran-msm,
- r-cran-surveillance,
- repast
+ repast,
+ ushahidi
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
@@ -632,7 +638,7 @@
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
Package: med-his
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: fis-gtm
@@ -656,7 +662,7 @@
the packaging work.
Package: med-imaging
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: aeskulap,
@@ -665,12 +671,15 @@
biosig-tools,
camitk-imp,
caret,
+ conquest-common,
ctn,
+ ctsim,
dcmtk,
dicom3tools,
dicomnifti,
dicomscope,
fslview,
+ gdf-tools,
ginkgocadx,
gofigure2,
gwyddion,
@@ -686,19 +695,24 @@
mialmpick,
minc-tools,
mriconvert,
+ mricron,
mrtrix,
nifti-bin,
+ odin,
openslide-tools,
orthanc,
pixelmed-apps,
plastimatch,
+ python-dicom,
python-dipy,
python-mvpa2,
python-nibabel,
python-nitime,
python-surfer,
sigviewer,
+ sofa-apps,
teem-apps,
+ voxbo,
vtk-dicom-tools,
xmedcon
Suggests: afni,
@@ -710,9 +724,11 @@
cellprofiler,
cmtk,
connectomeviewer,
- conquest-dicom-server,
+ conquest-dbase,
+ conquest-mysql,
+ conquest-postgres,
+ conquest-sqlite,
crea,
- ctsim,
dcm4chee,
devide,
dicom4j,
@@ -749,9 +765,7 @@
mni-colin27-nifti,
mni-icbm152-nlin-2009,
mni-n3,
- mricron,
mrisim,
- odin,
omero,
opendicom.net,
openelectrophy,
@@ -766,7 +780,6 @@
python-nipype,
python-pyxid,
slicer,
- sofa-apps,
stabilitycalc,
stir,
tempo,
@@ -776,7 +789,6 @@
visit,
vmtk,
volview,
- voxbo,
xnat
Description: Debian Med imaging packages
This metapackage will install Debian packages which might be useful in
@@ -798,7 +810,7 @@
ftp://medical.nema.org/medical/dicom/2008/ .
Package: med-imaging-dev
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: cimg-dev,
@@ -808,12 +820,13 @@
libbiosig-dev,
libcamitk3-dev,
libcv-dev,
+ libedf-dev,
libgdcm2-dev,
libgdf-dev,
libgiftiio-dev,
libinsighttoolkit3-dev | libinsighttoolkit4-dev,
libmdc2-dev,
- libmia-2.0-dev,
+ libmia-2.2-dev,
libmialm-dev,
libmiaviewit-dev,
libminc-dev,
@@ -825,6 +838,9 @@
libvistaio-dev,
libvolpack1-dev,
libvtk5-dev,
+ libvxl1-dev,
+ octave-gdf,
+ odin,
python-casmoothing,
python-cfflib,
python-dicom,
@@ -857,10 +873,8 @@
libvtk-dicom0.4-dev,
libvtk5.4,
libvtkedge-dev,
- libvxl1-dev,
libxdffileio-dev,
octave-dicom,
- odin,
python-libavg,
python-nipy,
python-nipype,
@@ -871,7 +885,7 @@
for developing applications for medical image processing.
Package: med-oncology
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: dicompyler
@@ -882,7 +896,7 @@
oncology.
Package: med-pharmacy
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: chemtool,
@@ -894,17 +908,21 @@
pharmaceutical research.
Package: med-physics
-Section: metapackage
-Architecture: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: octave,
- r-base
-Suggests: biosig,
- gate,
- openvibe,
+Section: metapackages
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: biosig-tools,
+ gdf-tools,
+ octave,
paw,
paw++,
+ r-base
+Suggests: gate,
+ libbiosig-dev,
+ octave-biosig,
+ openvibe,
paw-demos,
+ python-biosig,
python-multipletau
Description: Debian Med packages for medical physicists
This metapackage contains dependencies for a
@@ -913,7 +931,7 @@
and related fields.
Package: med-practice
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: clinica,
@@ -950,11 +968,12 @@
which might be helpful for practitioners to manage their practice.
Package: med-psychology
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: praat,
psignifit,
+ psychopy,
python-pyepl,
python-pypsignifit,
r-cran-foreign,
@@ -962,7 +981,6 @@
Suggests: miscpsycho,
psych,
psychometric,
- psychopy,
psychotree,
psyphy,
python-visionegg,
@@ -972,7 +990,7 @@
which might be helpful for psychological research.
Package: med-rehabilitation
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends:
@@ -983,22 +1001,22 @@
rehabilitation and therapy.
Package: med-statistics
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: r-bioc-edger,
r-bioc-limma,
r-bioc-qvalue,
+ r-cran-beeswarm,
r-cran-pvclust,
r-cran-randomforest
-Suggests: r-cran-beeswarm,
- science-statistics
+Suggests: science-statistics
Description: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
Package: med-tools
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: cronometer,
@@ -1010,7 +1028,6 @@
pondus,
python-clips,
python-fitbit,
- python3-fitbitscraper,
quitcount,
wgerman-medical,
workrave
@@ -1018,13 +1035,14 @@
entangle,
goldencheetah,
mencal,
- mssstest
+ mssstest,
+ python3-fitbitscraper
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.
Package: med-typesetting
-Section: metapackage
+Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: king,
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=4087&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control.stub (original)
+++ projects/med/trunk/debian-med/debian/control.stub Thu Oct 23 21:47:40 2014
@@ -4,7 +4,7 @@
Section: misc
Priority: extra
Build-Depends-Indep: blends-dev (>= 0.6.92)
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/blends/projects/med/trunk/debian-med/
Vcs-Svn: svn://anonscm.debian.org/blends/projects/med/trunk/debian-med/
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