[Blends-commit] r4019 - 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
Tue Apr 15 15:44:28 UTC 2014
Author: tille
Date: Tue Apr 15 15:44:28 2014
New Revision: 4019
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=4019
Log:
Regenerate source with old blends-dev code since the new code has some flaws we need to fix first
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=4019&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian-med-tasks.desc (original)
+++ projects/med/trunk/debian-med/debian-med-tasks.desc Tue Apr 15 15:44:28 2014
@@ -4,184 +4,207 @@
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences.
Relevance: 10
-Key:
+Enhances: t-coffee
+Key:
med-bio
Packages: list
- abacas
- acedb-other
- acedb-other-belvu
- acedb-other-dotter
- adun.app
+ altree
+ fastdnaml
+ njplot
+ tree-puzzle
+ probalign
+ treeviewx
+ figtree
+ fastlink
+ loki
+ plink
+ r-cran-qtl
+ r-cran-genabel
+ amap-align
+ boxshade
+ fastx-toolkit
+ gff2aplot
+ muscle
+ sim4
+ sibsim4
+ tabix
+ wise
+ maqview
+ bwa
+ mummer
+ blast2
+ ncbi-blast+
+ mafft
+ sra-toolkit
+ t-coffee
+ kalign
+ hmmer
+ exonerate
+ dialign
+ dialign-tx
+ poa
+ probcons
+ proda
+ sigma-align
+ emboss
+ embassy-domalign
+ embassy-domainatrix
+ embassy-domsearch
+ clustalx
+ clustalo
+ clustalw
+ mothur
+ bowtie2
+ transtermhp
+ last-align
+ maq
+ ssake
+ velvet
+ infernal
+ rnahybrid
+ adun.app
+ garlic
+ gamgi
+ gdpc
+ jmol
+ pymol
+ r-other-bio3d
+ massxpert
+ gromacs
+ rasmol
+ plasmidomics
+ gff2ps
+ ncbi-epcr
+ ncbi-tools-bin
+ ncbi-tools-x11
+ perlprimer
+ readseq
+ tigr-glimmer
+ melting
+ mipe
+ primer3
+ gbrowse
+ biomaj
+ glam2
+ raster3d
+ phyml
+ autodock
+ autogrid
+ autodock-vina
+ mustang
+ theseus
+ staden-io-lib-utils
+ samtools
+ bedtools
+ filo
+ r-bioc-hilbertvis
+ mira-assembler
alien-hunter
- amap-align
- ampliconnoise
- aragorn
- autodock
- autodock-vina
- autogrid
- ballview
- bedtools
- biomaj
- blast2
- bowtie
- bowtie2
- boxshade
- bwa
- cd-hit
- cdbfasta
- chimeraslayer
- clonalframe
- clustalo
- clustalw
- clustalx
- concavity
- conservation-code
- dialign
- dialign-tx
- disulfinder
- dotur
- dssp
- edtsurf
- embassy-domainatrix
- embassy-domalign
- embassy-domsearch
- emboss
- exonerate
- fastdnaml
- fastlink
- fastqc
- fasttree
- fastx-toolkit
- ffindex
- figtree
- filo
- flexbar
- freecontact
- gamgi
- garlic
- gbrowse
- gdpc
- genometools
- gentle
- gff2aplot
- gff2ps
- ghemical
- glam2
+ seqan-apps
+ ncoils
+ gentle
+ picard-tools
+ acedb-other-dotter
+ acedb-other-belvu
+ acedb-other
+ python-cogent
+ mrbayes
+ pdb2pqr
+ squizz
+ clonalframe
+ dssp
+ jellyfish
+ pynast
+ raxml
+ mlv-smile
+ cd-hit
+ r-bioc-cummerbund
grinder
- gromacs
- hhsuite
- hmmer
- hmmer2
- infernal
jalview
- jellyfish
- jmol
- kalign
- kissplice
- last-align
- librg-utils-perl
- logol-bin
- loki
- ltrsift
- macs
- mafft
- maq
- maqview
- massxpert
- melting
- metastudent
- microbiomeutil
- mipe
- mira-assembler
- mlv-smile
- mrbayes
- mrs
- mummer
- muscle
- mustang
- nast-ier
- ncbi-blast+
- ncbi-epcr
- ncbi-seg
- ncbi-tools-bin
- ncbi-tools-x11
- ncoils
- neobio
- njplot
+ reprof
+ tm-align
norsnet
norsp
- perlprimer
- phyml
- picard-tools
- plasmidomics
- plink
- poa
- populations
predictnls
- predictprotein
- primer3
- proalign
- probalign
- probcons
- proda
+ prime-phylo
+ proftmb
profbval
profisis
- profnet-bval
- profnet-chop
- profnet-con
- profnet-isis
- profnet-md
- profnet-norsnet
- profnet-prof
- profnet-snapfun
+ hhsuite
+ ffindex
+ flexbar
+ neobio
+ ray
+ logol-bin
+ soapdenovo
+ soapdenovo2
+ microbiomeutil
+ chimeraslayer
+ nast-ier
+ wigeon
+ minia
+ trimmomatic
+ saint
+ rtax
+ rate4site
+ topp
+ openms
+ arden
+ ipig
+ aevol
+ anfo
+ aragorn
+ cdbfasta
+ clearcut
+ edtsurf
+ fasttree
+ fastqc
+ freecontact
+ genometools
+ hmmer2
+ idba
+ kissplice
+ ltrsift
+ macs
+ metastudent
+ mrs
+ ncbi-seg
+ parsinsert
+ prank
+ predictprotein
+ proalign
+ pycorrfit
+ r-bioc-rtracklayer
+ r-bioc-gviz
+ r-bioc-biostrings
+ r-cran-vegan
+ seqtk
+ uc-echo
+ zalign
+ discosnp
+ mapsembler2
+ dnaclust
+ concavity
+ conservation-code
+ abacas
+ profnet-bval
+ profnet-chop
+ profnet-con
+ profnet-isis
+ profnet-md
+ profnet-norsnet
+ profnet-prof
+ profnet-snapfun
+ profphd-net
+ profphd-utils
profphd
- profphd-net
- profphd-utils
- proftmb
- pymol
- pynast
- python-cogent
- qiime
- r-bioc-biostrings
- r-bioc-cummerbund
- r-bioc-hilbertvis
- r-cran-genabel
- r-cran-qtl
- r-cran-vegan
- r-other-bio3d
- r-other-mott-happy
- rasmol
- raster3d
- raxml
- ray
- readseq
- reprof
- rnahybrid
- samtools
- sibsim4
- sigma-align
- sim4
- soapdenovo
- squizz
- sra-toolkit
- ssake
- staden-io-lib-utils
- t-coffee
- tabix
- theseus
- tigr-glimmer
- tm-align
- tophat
- transtermhp
- tree-puzzle
- treeviewx
- trimmomatic
- uc-echo
- vcftools
- velvet
- wigeon
- wise
- zalign
+ ampliconnoise
+ disulfinder
+ circos
+ populations
+ librg-utils-perl
+ snap
+ vcftools
Task: med-bio-dev
Section: debian-med
@@ -189,61 +212,64 @@
This metapackage will install Debian packages which might be helpful
for development of applications for micro-biological research.
Relevance: 10
-Key:
+Key:
med-bio-dev
Packages: list
bioperl
bioperl-run
- biosquid
- libace-perl
- libai-fann-perl
- libbio-graphics-perl
- libbio-mage-perl
- libbio-mage-utils-perl
- libbio-primerdesigner-perl
- libbiococoa-dev
+ libncbi6-dev
+ mcl
+ biosquid
+ libvibrant6-dev
+ python-biopython
+ python-cogent
+ ruby-bio
libbiojava-java
libbiojava3-java
+ libgenome-1.3-0-dev
+ libai-fann-perl
+ libbio-mage-perl
+ libnhgri-blastall-perl
+ libfreecontact0-dev
+ libfreecontact-perl
+ libgo-perl
+ r-cran-genetics
+ r-cran-haplo.stats
+ libbio-graphics-perl
+ libbio-primerdesigner-perl
+ libace-perl
+ libbiococoa-dev
+ libstaden-read-dev
+ libsrf-dev
+ libzerg0-dev
+ libzerg-perl
+ librg-reprof-bundle-perl
+ python-corepywrap
+ librcsb-core-wrapper0-dev
+ seqan-dev
+ libbio-mage-utils-perl
libchado-perl
- libffindex0-dev
- libfreecontact-doc
- libfreecontact0-dev
- libgenome-1.3-0-dev
- libgenome-model-tools-music-perl
- libgenome-perl
- libgenometools0-dev
- libgo-perl
- libhmsbeagle-dev
+ libpal-java
libjebl2-java
- libncbi6-dev
- libnhgri-blastall-perl
- libpal-java
- librcsb-core-wrapper0-dev
- librg-blast-parser-perl
- librg-reprof-bundle-perl
+ r-bioc-biobase
+ libffindex0-dev
+ librostlab3-dev
+ librostlab-doc
+ librostlab-blast0-dev
librostlab-blast-doc
- librostlab-blast0-dev
- librostlab-doc
- librostlab3-dev
- libsort-key-top-perl
- libsrf-dev
- libstaden-read-dev
- libvibrant6-dev
- libzerg-perl
- libzerg0-dev
- mcl
- pyfai
- python-biom-format
- python-biopython
- python-cogent
- python-corepywrap
- python-htseq
- python-mmtk
- r-bioc-biobase
- r-cran-genetics
- r-cran-haplo.stats
- ruby-bio
- seqan-dev
+ librg-blast-parser-perl
+ libsort-key-top-perl
+ libhmsbeagle-dev
+ python-mmtk
+ libopenms-dev
+ libgenometools0-dev
+ python-biom-format
+ python-rdkit
+ pyfai
+ python-htseq
+ python-csb
+ python-freecontact
+ python-pysam
Task: med-bio-ngs
Section: debian-med
@@ -252,27 +278,10 @@
sequences produced by next generation sequencing.
Relevance: 10
Packages: list
- bedtools
- bowtie
- bwa
- fastx-toolkit
- filo
- kissplice
- last-align
- maq
- mira-assembler
- picard-tools
- qiime
- r-bioc-edger
- r-bioc-hilbertvis
- samtools
- sra-toolkit
- ssake
- tabix
- tophat
- uc-echo
- vcftools
- velvet
+ mothur
+ mira-assembler
+ kissplice
+ uc-echo
Task: med-bio-phylogeny
Section: debian-med
@@ -283,31 +292,32 @@
related software.
Relevance: 10
Packages: list
- clustalw
- clustalx
- dialign
- dialign-tx
- exonerate
- fastdnaml
+ altree
+ fastdnaml
+ njplot
+ tree-puzzle
+ probalign
+ treeviewx
+ muscle
+ t-coffee
+ kalign
+ hmmer
+ exonerate
+ dialign
+ dialign-tx
+ poa
+ probcons
+ proda
+ sigma-align
+ clustalx
+ clustalw
+ mustang
+ phyml
+ tm-align
+ mrbayes
figtree
- hmmer
- kalign
- mrbayes
- muscle
- mustang
- njplot
- phyml
- poa
- populations
- proalign
- probalign
- probcons
- proda
- sigma-align
- t-coffee
- tm-align
- tree-puzzle
- treeviewx
+ populations
+ proalign
Task: med-cloud
Section: debian-med
@@ -317,39 +327,13 @@
depend on graphical toolkits and therefore can fit on system images for use
in cloud computing clusters, where space can be limited.
Relevance: 10
-Key:
+Key:
med-cloud
Packages: list
- alien-hunter
- autodock
- bedtools
- bwa
- clustalw
- embassy-domainatrix
- embassy-domalign
- embassy-domsearch
- emboss
- fastdnaml
- fastlink
- filo
- infernal
- last-align
- loki
- maq
- phyml
- picard-tools
- plink
- python-cogent
- r-bioc-hilbertvis
- r-cran-qtl
- r-other-mott-happy
- raster3d
- rnahybrid
- samtools
- ssake
- tophat
- tree-puzzle
- velvet
+ clustalw
+ autodock
+ raster3d
+ python-cogent
Task: med-cms
Section: debian-med
@@ -366,10 +350,10 @@
applications. The database can be accessed by any EMR using
the application.
Relevance: 10
-Key:
+Key:
med-data
Packages: list
- freediams
+ freediams
freemedforms-freedata
python-hl7
@@ -379,11 +363,11 @@
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
Relevance: 10
-Key:
+Key:
med-dental
Packages: list
- entangle
imagetooth
+ entangle
Task: med-epi
Section: debian-med
@@ -394,16 +378,16 @@
"A short introduction to R for Epidemiology" at
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
Relevance: 10
-Key:
+Key:
med-epi
Packages: list
epigrass
+ r-cran-epibasix
+ r-cran-epitools
+ r-cran-epi
r-cran-diagnosismed
- r-cran-epi
- r-cran-epibasix
r-cran-epicalc
r-cran-epir
- r-cran-epitools
Task: med-his
Section: debian-med
@@ -415,9 +399,11 @@
at a later point in time provided somebody is willing to take over
the packaging work.
Relevance: 10
-Key:
+Key:
med-his
Packages: list
+ fis-gtm
+ gnuhealth
Task: med-imaging
Section: debian-med
@@ -440,44 +426,51 @@
where you'll find direct links to the most recent yearly edition
ftp://medical.nema.org/medical/dicom/2008/ .
Relevance: 10
-Key:
+Key:
med-imaging
Packages: list
- aeskulap
- amide
- biosig-tools
- caret
- ctn
- ctsim
- dcmtk
- dicom3tools
- dicomnifti
- dicomscope
- gwyddion
+ amide
+ ctsim
+ ctn
+ dicomnifti
imagej
- imagevis3d
+ minc-tools
+ medcon
+ python-nifti
+ xmedcon
+ dcmtk
+ nifti-bin
+ aeskulap
+ gwyddion
+ sofa-apps
+ python-mvpa
+ caret
+ libgdcm-tools
+ dicom3tools
+ imagevis3d
+ dicomscope
+ pixelmed-apps
+ gofigure2
+ ginkgocadx
+ openslide-tools
+ volview
+ camitk-imp
+ teem-apps
+ invesalius
+ mrtrix
+ ants
+ itksnap
+ mriconvert
+ mia-tools
+ mialmpick
+ mia-viewit
+ sigviewer
+ plastimatch
+ biosig-tools
+ python-surfer
king
- medcon
- mialmpick
- minc-tools
- mriconvert
- mricron
- mrtrix
- nifti-bin
- openmeeg-tools
- openslide-tools
+ python-nitime
python-dipy
- python-mvpa
- python-nifti
- python-nipy
- python-nipype
- python-nitime
- python-surfer
- sigviewer
- teem-apps
- via-bin
- voxbo
- xmedcon
Task: med-imaging-dev
Section: debian-med
@@ -485,40 +478,48 @@
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing.
Relevance: 10
-Key:
+Key:
med-imaging-dev
Packages: list
+ ctn-dev
cimg-dev
- ctn-dev
- gmic
- libactiviz.net-cil
- libbiosig-dev
- libcv-dev
- libgdf-dev
- libgiftiio-dev
- libmdc2-dev
- libminc-dev
- libnifti-dev
- libopenigtlink1-dev
- libopenmeeg-dev
- libopenslide-dev
- libteem-dev
- libvia-dev
- libvistaio-dev
- libvolpack1-dev
- libvtk5-dev
- libvxl1-dev
- python-casmoothing
+ libminc-dev
+ libmdc2-dev
+ libvtk5-dev
+ libnifti-dev
+ libigstk4-dev
+ libinsighttoolkit3-dev
+ libvolpack1-dev
+ libgdcm2-dev
+ python-gdcm
+ python-mvpa
+ python-casmoothing
+ libcv-dev
+ libvxl1-dev
+ libteem-dev
+ gmic
+ libgiftiio-dev
+ libactiviz.net-cil
+ libvistaio-dev
+ libmia-2.0-dev
+ libmiaviewit-dev
+ libmialm-dev
+ python-mia
+ r-cran-rniftilib
+ python-dicom
+ python-nibabel
+ libgdf-dev
+ python-pyxnat
+ python-dipy
+ libbiosig-dev
python-cfflib
- python-dicom
- python-dipy
- python-mvpa
- python-nibabel
- python-nipy
- python-nipype
- python-nitime
- python-pyxnat
- r-cran-rniftilib
+ libopenslide-dev
+ python-openslide
+ libcamitk3-dev
+ libpapyrus3-dev
+ python-mne
+ libvigraimpex-dev
+ python-vigra
Task: med-oncology
Section: debian-med
@@ -526,7 +527,7 @@
This metapackage will install tools that are useful for radiation
oncology.
Relevance: 10
-Key:
+Key:
med-oncology
Packages: list
dicompyler
@@ -538,10 +539,11 @@
collection of software and documentation which is useful for
pharmaceutical research.
Relevance: 10
-Key:
+Key:
med-pharmacy
Packages: list
- chemtool
+ chemtool
+ r-cran-dosefinding
Task: med-physics
Section: debian-med
@@ -551,12 +553,12 @@
medical physicists in radiation oncology, diagnostics imaging
and related fields.
Relevance: 10
-Key:
+Key:
med-physics
Packages: list
- octave
- paw
- paw++
+ paw++
+ paw
+ octave
r-base
Task: med-practice
@@ -565,18 +567,19 @@
This metapackage contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
Relevance: 10
-Key:
+Key:
med-practice
Packages: list
- clinica
- entangle
- freediams
- freemedforms-emr
gnumed-client
gnumed-server
- libchipcard-tools
- qrisk2
- r-cran-medadherence
+ libchipcard-tools
+ ginkgocadx
+ freediams
+ freemedforms-emr
+ r-cran-medadherence
+ clinica
+ entangle
+ qrisk2
Task: med-psychology
Section: debian-med
@@ -584,15 +587,14 @@
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
Relevance: 10
-Key:
+Key:
med-psychology
Packages: list
- praat
- psignifit
- psychopy
- python-pyepl
- python-pypsignifit
- r-cran-foreign
+ python-pyepl
+ praat
+ r-cran-foreign
+ psignifit
+ python-pypsignifit
r-cran-psy
Task: med-rehabilitation
@@ -601,10 +603,10 @@
This metapackage will install tools that are useful for
rehabilitation and therapy.
Relevance: 10
-Key:
+Key:
med-rehabilitation
Packages: list
- sitplus
+ sitplus
Task: med-statistics
Section: debian-med
@@ -612,14 +614,14 @@
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
Relevance: 10
-Key:
+Key:
med-statistics
Packages: list
- r-bioc-edger
- r-bioc-limma
+ r-bioc-edger
+ r-bioc-limma
r-bioc-qvalue
+ r-cran-randomforest
r-cran-pvclust
- r-cran-randomforest
Task: med-tools
Section: debian-med
@@ -627,18 +629,20 @@
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
Relevance: 10
-Key:
+Key:
med-tools
Packages: list
- edfbrowser
- hunspell-de-med
- hunspell-en-med
pcalendar
pondus
- python-clips
- quitcount
wgerman-medical
- workrave
+ hunspell-de-med
+ quitcount
+ workrave
+ edfbrowser
+ hunspell-en-med
+ python-clips
+ cronometer
+ python3-fitbitscraper
Task: med-typesetting
Section: debian-med
@@ -647,10 +651,10 @@
for typesetting and publishing in medical care and structural
biology.
Relevance: 10
-Key:
+Key:
med-typesetting
Packages: list
+ texlive-science
+ texlive-latex-extra
king
- texlive-latex-extra
- texlive-science
-
+
Modified: projects/med/trunk/debian-med/debian/changelog
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/changelog?rev=4019&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog (original)
+++ projects/med/trunk/debian-med/debian/changelog Tue Apr 15 15:44:28 2014
@@ -1,59 +1,8 @@
debian-med (1.13.3) UNRELEASED; urgency=low
- * debian/control:
+ * debian/control.stub:
- Build-Depends: blends-dev (>= 0.6.16.3)
-
- * start of automatic changelog entry *
-
- * Changes in metapackage dependencies
- -med-cloud
- added:
- Depends: bagpipe
- removed:
- Depends: bagphenotype
- -med-psychology
- added:
- Depends: python-pypsignifit
- Suggests: python-visionegg
- removed:
- Depends: psignifit3
- Suggests: visionegg
- -med-bio
- added:
- Depends: bagpipe, grabix, freecontact, staden, ray, r-bioc-rtracklayer, kissplice, rtax, metastudent, chimeraslayer, trimmomatic, r-bioc-gviz, spread-phy, rate4site, flexbar, nast-ier, bitseq, mach-haplotyper, aragorn, emmax, klust, aevol, strap-base, uc-echo, wigeon, r-cran-vegan, r-bioc-biostrings, mrs, modeller, situs
- Suggests: r-cran-boolnet
- removed:
- Depends: phy-spread | spread-phy, bagphenotype, sra-sdk, ray-denovoassembler, vegan
- -med-bio-ngs
- added:
- Depends: kissplice
- removed:
- Depends: ssaha2
- -med-practice
- removed:
- Depends: freeicd
- -med-imaging-dev
- added:
- Depends: libmiaviewit-dev, libteem-dev, r-cran-rniftilib
- removed:
- Depends: libteem1-dev
- -med-imaging
- added:
- Depends: teem-apps, mia-viewit, python-surfer
- Suggests: python-pyxid, openwalnut-qt4
- removed:
- Suggests: pysurfer, pyxid, openwalnut
- -med-bio-phylogeny
- added:
- Depends: spread-phy
- removed:
- Depends: phy-spread | spread-phy
- -med-bio-dev
- added:
- Depends: libfreecontact-doc, libgenome-model-tools-music-perl, python-corepywrap, pyfai, python-htseq, libfreecontact0-dev, libgenome-perl
- Suggests: r-bioc-altcdfenvs, r-bioc-affyio, r-bioc-affy, r-bioc-iranges, r-bioc-makecdfenv
- removed:
- Depends: libqsearch-dev, python-librcsb-core-wrapper
+ - cme fix dpkg-control
-- Andreas Tille <tille at debian.org> Thu, 18 Apr 2013 07:42:55 +0200
Modified: projects/med/trunk/debian-med/debian/control
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/control?rev=4019&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control (original)
+++ projects/med/trunk/debian-med/debian/control Tue Apr 15 15:44:28 2014
@@ -1,14 +1,13 @@
# This file is autogenerated via make -f debian/rules dist. Do not edit!
Source: debian-med
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: misc
Priority: extra
-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 (>= 0.6.16.3)
-Standards-Version: 3.9.3
-Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/
-Vcs-Svn: svn://svn.debian.org/blends/projects/med/trunk/debian-med/
+Standards-Version: 3.9.5
+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/
Package: med-tasks
Architecture: all
@@ -55,412 +54,518 @@
Debian by simply installing the relevant metapackage
Package: med-bio
-Architecture: any
-Priority: extra
+Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: abacas,
- acedb-other [!hurd-i386],
- acedb-other-belvu [!hurd-i386],
- acedb-other-dotter [!hurd-i386],
- adun.app [!hurd-i386],
+ acedb-other,
+ acedb-other-belvu,
+ acedb-other-dotter,
+ adun.app,
+ aevol,
alien-hunter,
- amap-align [!hurd-i386],
- ampliconnoise [!s390 !s390x !hurd-i386 !mipsel !mips],
- aragorn [!hurd-i386],
- autodock [!hurd-i386],
- autodock-vina [!hurd-i386],
- autogrid [!hurd-i386],
- ballview [!hurd-i386],
- bedtools [!hurd-i386],
+ altree,
+ amap-align,
+ ampliconnoise,
+ anfo,
+ aragorn,
+ arden,
+ autodock,
+ autodock-vina,
+ autogrid,
+ bedtools,
biomaj,
- blast2 [!hurd-i386],
- bowtie [!hurd-i386],
- bowtie2 [!s390 !hurd-i386 !s390x !powerpc !sparc !armel !armhf !ia64 !mips !mipsel],
- boxshade [!hurd-i386],
- bwa [!hurd-i386],
- cd-hit [!hurd-i386],
- cdbfasta [!hurd-i386],
+ blast2,
+ bowtie2,
+ boxshade,
+ bwa,
+ cd-hit,
+ cdbfasta,
chimeraslayer,
- clonalframe [!hurd-i386],
- clustalo [!hurd-i386],
- clustalw [!hurd-i386],
- clustalx [!hurd-i386],
- concavity [!hurd-i386],
+ circos,
+ clearcut,
+ clonalframe,
+ clustalo,
+ clustalw,
+ clustalx,
+ concavity,
conservation-code,
- dialign [!hurd-i386],
- dialign-tx [!hurd-i386],
- disulfinder [!hurd-i386],
- dotur [!hurd-i386],
- dssp [!hurd-i386],
- edtsurf [!hurd-i386],
- embassy-domainatrix [!hurd-i386],
- embassy-domalign [!hurd-i386],
- embassy-domsearch [!hurd-i386],
- emboss [!hurd-i386],
- exonerate [!hurd-i386],
- fastdnaml [!hurd-i386],
- fastlink [!hurd-i386],
+ dialign,
+ dialign-tx,
+ discosnp,
+ disulfinder,
+ dnaclust,
+ dssp,
+ edtsurf,
+ embassy-domainatrix,
+ embassy-domalign,
+ embassy-domsearch,
+ emboss,
+ exonerate,
+ fastdnaml,
+ fastlink,
fastqc,
- fasttree [!hurd-i386],
- fastx-toolkit [!hurd-i386],
- ffindex [!hurd-i386],
+ fasttree,
+ fastx-toolkit,
+ ffindex,
figtree,
- filo [!hurd-i386],
- flexbar [!s390 !hurd-i386 !kfreebsd-amd64 !s390x !sparc !armel !armhf !mips !kfreebsd-i386 !mipsel],
- freecontact [!mips !hurd-i386],
- gamgi [!hurd-i386],
- garlic [!hurd-i386],
+ filo,
+ flexbar,
+ freecontact,
+ gamgi,
+ garlic,
gbrowse,
- gdpc [!hurd-i386],
- genometools [!sparc !hurd-i386 !armel],
- gentle [!hurd-i386],
- gff2aplot [!hurd-i386],
+ gdpc,
+ genometools,
+ gentle,
+ gff2aplot,
gff2ps,
- ghemical [!hurd-i386],
- glam2 [!hurd-i386],
+ glam2,
grinder,
- gromacs [!hurd-i386],
- hhsuite [!s390 !hurd-i386 !kfreebsd-amd64 !s390x !powerpc !sparc !armel !armhf !ia64 !mips !kfreebsd-i386 !mipsel !i386],
- hmmer [!hurd-i386],
- hmmer2 [!hurd-i386],
- infernal [!hurd-i386],
+ gromacs,
+ hhsuite,
+ hmmer,
+ hmmer2,
+ idba,
+ infernal,
+ ipig,
jalview,
- jellyfish [!s390 !hurd-i386 !s390x !sparc !powerpc !i386 !armel !armhf !ia64 !mips !kfreebsd-i386 !mipsel],
+ jellyfish,
jmol,
- kalign [!hurd-i386],
- kissplice [!hurd-i386],
- last-align [!hurd-i386],
+ kalign,
+ kissplice,
+ last-align,
librg-utils-perl,
- logol-bin [!s390 !hurd-i386 !kfreebsd-amd64 !s390x !armel !armhf !mips !kfreebsd-i386 !mipsel],
- loki [!hurd-i386],
- ltrsift [!ia64 !sparc !hurd-i386 !armel],
- macs [!hurd-i386],
- mafft [!hurd-i386],
- maq [!hurd-i386],
- maqview [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- massxpert [!hurd-i386],
- melting [!hurd-i386],
+ logol-bin,
+ loki,
+ ltrsift,
+ macs,
+ mafft,
+ mapsembler2,
+ maq,
+ maqview,
+ massxpert,
+ melting,
metastudent,
microbiomeutil,
+ minia,
mipe,
- mira-assembler [!hurd-i386],
- mlv-smile [!hurd-i386],
- mrbayes [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- mrs [!s390 !hurd-i386 !kfreebsd-amd64 !s390x !powerpc !sparc !armel !armhf !ia64 !mips !kfreebsd-i386 !mipsel !i386],
- mummer [!hurd-i386],
- muscle [!hurd-i386],
- mustang [!hurd-i386],
- nast-ier [!hurd-i386],
- ncbi-blast+ [!hurd-i386],
- ncbi-epcr [!hurd-i386],
- ncbi-seg [!hurd-i386],
- ncbi-tools-bin [!hurd-i386],
- ncbi-tools-x11 [!hurd-i386],
- ncoils [!hurd-i386],
+ mira-assembler,
+ mlv-smile,
+ mothur,
+ mrbayes,
+ mrs,
+ mummer,
+ muscle,
+ mustang,
+ nast-ier,
+ ncbi-blast+,
+ ncbi-epcr,
+ ncbi-seg,
+ ncbi-tools-bin,
+ ncbi-tools-x11,
+ ncoils,
neobio,
- njplot [!hurd-i386],
+ njplot,
norsnet,
norsp,
+ openms,
+ parsinsert,
+ pdb2pqr,
perlprimer,
- phyml [!hurd-i386],
+ phyml,
picard-tools,
plasmidomics,
- plink [!hurd-i386],
- poa [!hurd-i386],
- populations [!hurd-i386],
+ plink,
+ poa,
+ populations,
+ prank,
predictnls,
predictprotein,
- primer3 [!hurd-i386],
- proalign [!hurd-i386],
- probalign [!hurd-i386],
- probcons [!hurd-i386],
- proda [!hurd-i386],
+ prime-phylo,
+ primer3,
+ proalign,
+ probalign,
+ probcons,
+ proda,
profbval,
profisis,
- profnet-bval [!hurd-i386],
- profnet-chop [!hurd-i386],
- profnet-con [!hurd-i386],
- profnet-isis [!hurd-i386],
- profnet-md [!hurd-i386],
- profnet-norsnet [!hurd-i386],
- profnet-prof [!hurd-i386],
- profnet-snapfun [!hurd-i386],
+ profnet-bval,
+ profnet-chop,
+ profnet-con,
+ profnet-isis,
+ profnet-md,
+ profnet-norsnet,
+ profnet-prof,
+ profnet-snapfun,
profphd,
- profphd-net [!hurd-i386],
- profphd-utils [!hurd-i386],
- proftmb [!hurd-i386],
- pymol [!hurd-i386],
+ profphd-net,
+ profphd-utils,
+ proftmb,
+ pycorrfit,
+ pymol,
pynast,
- python-cogent [!hurd-i386],
- qiime [!ia64 !hurd-i386],
- r-bioc-biostrings [!hurd-i386],
+ python-cogent,
+ r-bioc-biostrings,
r-bioc-cummerbund,
- r-bioc-hilbertvis [!hurd-i386],
- r-cran-genabel [!hurd-i386],
- r-cran-qtl [!hurd-i386],
- r-cran-vegan [!hurd-i386],
+ r-bioc-gviz,
+ r-bioc-hilbertvis,
+ r-bioc-rtracklayer,
+ r-cran-genabel,
+ r-cran-qtl,
+ r-cran-vegan,
r-other-bio3d,
- r-other-mott-happy [!hurd-i386],
- rasmol [!hurd-i386],
- raster3d [!hurd-i386],
- raxml [!s390 !hurd-i386 !s390x !powerpc !sparc !armel !armhf !ia64 !mips !mipsel],
- ray [!hurd-i386],
- readseq [!hurd-i386],
+ rasmol,
+ raster3d,
+ rate4site,
+ raxml,
+ ray,
+ readseq,
reprof,
- rnahybrid [!hurd-i386],
- samtools [!sparc !hurd-i386 !armel],
- sibsim4 [!hurd-i386],
- sigma-align [!hurd-i386],
- sim4 [!hurd-i386],
- soapdenovo [!s390 !hurd-i386 !s390x !sparc !powerpc !i386 !armel !armhf !mips !kfreebsd-i386 !mipsel],
- squizz [!hurd-i386],
- sra-toolkit [!s390 !hurd-i386 !s390x !powerpc !sparc !armel !armhf !ia64 !mips !mipsel],
+ rnahybrid,
+ rtax,
+ saint,
+ samtools,
+ seqan-apps,
+ seqtk,
+ sibsim4,
+ sigma-align,
+ sim4,
+ snap,
+ soapdenovo,
+ soapdenovo2,
+ squizz,
+ sra-toolkit,
ssake,
- staden-io-lib-utils [!hurd-i386],
- t-coffee [!hurd-i386],
- tabix [!hurd-i386],
- theseus [!hurd-i386],
- tigr-glimmer [!hurd-i386],
- tm-align [!hurd-i386],
- tophat [!sparc !hurd-i386 !armel],
- transtermhp [!hurd-i386],
- tree-puzzle [!s390 !s390x !hurd-i386 !mipsel !mips] | tree-ppuzzle [!s390 !s390x !hurd-i386 !mipsel !mips],
- treeviewx [!hurd-i386],
+ staden-io-lib-utils,
+ t-coffee,
+ tabix,
+ theseus,
+ tigr-glimmer,
+ tm-align,
+ topp,
+ transtermhp,
+ tree-puzzle | tree-ppuzzle,
+ treeviewx,
trimmomatic,
- uc-echo [!hurd-i386 !armel !armhf !ia64 !mips !kfreebsd-i386 !mipsel],
- vcftools [!hurd-i386],
- velvet [!hurd-i386],
+ uc-echo,
+ vcftools,
+ velvet,
wigeon,
- wise [!hurd-i386],
- zalign [!s390 !s390x !hurd-i386 !mipsel !mips]
+ wise,
+ zalign
Suggests: abyss,
- aevol,
- altree,
+ acacia,
+ act,
amos-assembler,
- anfo,
+ amoscmp,
apollo,
+ arachne,
arb,
+ artemis,
+ asap,
+ augustus,
autodocktools,
axparafit,
axpcoords,
bagpipe,
+ ballview,
+ bambus,
bamtools,
+ beads,
beast-mcmc,
+ biceps,
+ big-blast,
bigsdb,
+ biomaj-watcher,
bitseq,
+ blat,
blimps-utils,
+ blixem,
+ bowtie,
+ btk-core,
+ cactus,
+ caftools,
cain,
+ cap3,
+ cassiopee,
+ cdna-db,
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,
emmax,
+ emperor,
ensembl,
+ est-db,
+ estferret,
+ estscan,
+ exalt,
+ excavator,
+ fas,
+ fasta,
+ fastaq,
+ figaro,
+ finex,
+ fitgcp,
+ fluctuate,
forester,
+ forge,
+ freebayes,
+ galaxy,
+ gasic,
gassst,
+ gbioseq,
+ gbrowse-syn,
+ genemark,
+ genesplicer,
+ genetrack,
+ genezilla,
+ genographer,
+ ghemical,
+ giira,
+ glimmerhmm,
gmap,
+ gmv,
grabix,
grogui,
haploview,
hawkeye,
+ hexamer,
+ hilbertvisgui,
igv,
jbrowse,
+ jigsaw,
+ jstreeview,
+ kclust,
kempbasu,
lagan,
+ lamarc,
logomat-m,
+ lucy,
mach-haplotyper,
mage2tab,
+ maker2,
martj,
maude,
mauvealigner,
+ maxd,
melting-gui,
meme,
+ mesquite,
+ metarep,
+ migrate,
+ minimus,
+ mirbase,
mobyle,
+ mobyle-programs,
+ mobyle-tutorials,
+ modeller,
molekel,
mosaik-aligner,
- mothur,
- mozilla-biofox,
mpsqed,
+ msatfinder,
mugsy,
+ mummergpu,
murasaki,
+ mview,
ngila,
nw-align,
oases,
+ obo-edit,
+ oligoarrayaux,
+ omegamap,
+ operondb,
pal2nal,
paml,
+ partigene,
patman,
patristic,
pcma,
- pdb2pqr,
+ pfaat,
+ pftools,
+ phagefinder,
+ phpphylotree,
phylip,
+ phylographer,
phyloviz-core,
+ phylowin,
+ phyutility,
plato,
- prank,
profit,
+ prot4est,
pscan-tfbs,
psipred,
- python-rdkit,
+ pyrophosphate-tools,
+ python-orange,
python-reaper,
- r-bioc-gviz,
- r-bioc-rtracklayer,
+ qiime,
+ qtlcart,
+ r-cran-ape,
r-cran-boolnet,
+ r-other-mott-happy,
r-other-valdar-bagphenotype.library,
raccoon,
- rate4site,
+ rbs-finder,
rdp-classifier,
+ recombine,
+ repeatmasker,
+ rmblast,
+ roche454ace2caf,
+ rose,
rosetta,
sap,
seaview,
seq-gen,
- seqan-apps,
- seqtk,
sequenceconverter.app,
sga,
sift,
situs,
- snap,
+ smalt,
snpeff,
+ spades,
+ spice,
+ splitstree,
spread-phy,
ssaha,
staden,
strap,
strap-base,
tacg,
+ taverna,
+ taxinspector,
+ tetra,
+ tigr-assembler,
tigr-glimmer-mg,
+ tophat,
+ trace2dbest,
+ tracetuner,
+ treebuilder3d,
+ treetime,
treeview,
+ tripal,
+ trnascan-se,
+ twain,
ugene,
+ unc-fish,
+ uniprime,
vienna-rna,
vmd,
wgs-assembler,
+ x-tandem-pipeline,
zodiac-zeden
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.
Package: med-bio-dev
-Architecture: any
-Priority: extra
+Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: bioperl,
bioperl-run,
- biosquid [!hurd-i386],
- libace-perl [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- libai-fann-perl [!hurd-i386],
+ biosquid,
+ libace-perl,
+ libai-fann-perl,
libbio-graphics-perl,
libbio-mage-perl,
libbio-mage-utils-perl,
libbio-primerdesigner-perl,
- libbiococoa-dev [!hurd-i386],
+ libbiococoa-dev,
libbiojava-java,
libbiojava3-java,
libchado-perl,
- libffindex0-dev [!hurd-i386],
+ libffindex0-dev,
+ libfreecontact-perl,
+ libfreecontact0-dev,
+ libgenome-1.3-0-dev,
+ libgenometools0-dev,
+ libgo-perl,
+ libhmsbeagle-dev,
+ libjebl2-java,
+ libncbi6-dev,
+ libnhgri-blastall-perl,
+ libopenms-dev,
+ libpal-java,
+ librcsb-core-wrapper0-dev,
+ librg-blast-parser-perl,
+ librg-reprof-bundle-perl,
+ librostlab-blast-doc,
+ librostlab-blast0-dev,
+ librostlab-doc,
+ librostlab3-dev,
+ libsort-key-top-perl,
+ libsrf-dev,
+ libstaden-read-dev,
+ libvibrant6-dev,
+ libzerg-perl,
+ libzerg0-dev,
+ mcl,
+ pyfai,
+ python-biom-format,
+ python-biopython,
+ python-cogent,
+ python-corepywrap,
+ python-csb | python3-csb,
+ python-freecontact,
+ python-htseq,
+ python-mmtk,
+ python-pysam,
+ python-rdkit,
+ r-bioc-biobase,
+ r-cran-genetics,
+ r-cran-haplo.stats,
+ ruby-bio,
+ seqan-dev
+Suggests: bioclipse,
+ libbambamc-dev,
+ libbamtools-dev,
+ libbio-das-perl,
+ libforester-java,
libfreecontact-doc,
- libfreecontact0-dev [!mips !hurd-i386],
- libgenome-1.3-0-dev [!hurd-i386],
+ libgbfp-dev,
libgenome-model-tools-music-perl,
libgenome-perl,
- libgenometools0-dev [!sparc !hurd-i386 !armel],
- libgo-perl,
- libhmsbeagle-dev [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- libjebl2-java,
- libncbi6-dev [!hurd-i386],
- libnhgri-blastall-perl,
- libpal-java,
- librcsb-core-wrapper0-dev [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- librg-blast-parser-perl [!hurd-i386],
- librg-reprof-bundle-perl,
- librostlab-blast-doc,
- librostlab-blast0-dev [!hurd-i386],
- librostlab-doc,
- librostlab3-dev [!hurd-i386],
- libsort-key-top-perl [!hurd-i386],
- libsrf-dev [!hurd-i386],
- libstaden-read-dev [!hurd-i386],
- libvibrant6-dev [!hurd-i386],
- libzerg-perl [!hurd-i386],
- libzerg0-dev [!hurd-i386],
- mcl [!hurd-i386],
- pyfai [!hurd-i386],
- python-biom-format [!hurd-i386],
- python-biopython [!hurd-i386],
- python-cogent [!hurd-i386],
- python-corepywrap [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- python-htseq [!hurd-i386],
- python-mmtk [!hurd-i386],
- r-bioc-biobase [!hurd-i386],
- r-cran-genetics,
- r-cran-haplo.stats [!hurd-i386],
- ruby-bio,
- seqan-dev
-Suggests: libbamtools-dev,
- libbio-das-perl,
- libforester-java,
- libopenmm4-dev,
+ libgff-perl,
+ libgtextutils-dev,
+ libmems-1.5-1,
libsbml5-dev,
libswarm2-dev,
libtfbs-perl,
- octave-bioinfo,
- python-pysam,
+ octace-bioinfo,
r-bioc-affy,
- r-bioc-affyio,
- r-bioc-altcdfenvs,
- r-bioc-biocgenerics,
- r-bioc-iranges,
- r-bioc-makecdfenv,
- r-cran-rocr
+ r-cran-rocr,
+ sbmltoolbox
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: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: alien-hunter,
- autodock [!hurd-i386],
- bedtools [!hurd-i386],
- bwa [!hurd-i386],
- clustalw [!hurd-i386],
- embassy-domainatrix [!hurd-i386],
- embassy-domalign [!hurd-i386],
- embassy-domsearch [!hurd-i386],
- emboss [!hurd-i386],
- fastdnaml [!hurd-i386],
- fastlink [!hurd-i386],
- filo [!hurd-i386],
- infernal [!hurd-i386],
- last-align [!hurd-i386],
- loki [!hurd-i386],
- maq [!hurd-i386],
- phyml [!hurd-i386],
- picard-tools,
- plink [!hurd-i386],
- python-cogent [!hurd-i386],
- r-bioc-hilbertvis [!hurd-i386],
- r-cran-qtl [!hurd-i386],
- r-other-mott-happy [!hurd-i386],
- raster3d [!hurd-i386],
- rnahybrid [!hurd-i386],
- samtools [!sparc !hurd-i386 !armel],
- ssake,
- tophat [!sparc !hurd-i386 !armel],
- tree-puzzle [!s390 !s390x !hurd-i386 !mipsel !mips] | tree-ppuzzle [!s390 !s390x !hurd-i386 !mipsel !mips],
- velvet [!hurd-i386]
-Suggests: altree,
- bagpipe,
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: autodock,
+ clustalw,
+ python-cogent,
+ raster3d
+Suggests: bagpipe,
clustalw-mpi,
- embassy-phylip,
r-other-valdar-bagphenotype.library
Description: Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
@@ -469,42 +574,42 @@
in cloud computing clusters, where space can be limited.
Package: med-data
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: freediams [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: freediams,
freemedforms-freedata,
python-hl7
+Suggests: drugref.org
Description: Debian Med drug databases
This metapackage will install free drug databases and related
applications. The database can be accessed by any EMR using
the application.
Package: med-dental
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: entangle [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: entangle,
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: any
-Priority: extra
+Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: epigrass,
r-cran-diagnosismed,
- r-cran-epi [!hurd-i386],
- r-cran-epibasix [!hurd-i386],
+ 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
+ r-cran-surveillance,
+ repast
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
@@ -513,16 +618,20 @@
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
Package: med-his
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends:
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: fis-gtm,
+ gnuhealth
Suggests: care2x,
ewd-920,
- fis-gtm,
- gnuhealth,
+ hkma-cms,
+ ipath,
+ openeyes,
openmrs,
- vista
+ oscar-mcmaster,
+ patientos,
+ vista-foia,
+ world-vista
Description: Debian Med suggestions for Hospital Information Systems
Currently Debian Med does not yet contain any software which can be
regarded as Hospital Information System. There is some Free Software
@@ -532,91 +641,127 @@
the packaging work.
Package: med-imaging
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: aeskulap [!hurd-i386],
- amide [!hurd-i386],
- biosig-tools [!hurd-i386],
- caret [!hurd-i386],
- ctn [!hurd-i386],
- ctsim [!hurd-i386],
- dcmtk [!hurd-i386],
- dicom3tools [!hurd-i386],
- dicomnifti [!hurd-i386],
- dicomscope [!hurd-i386],
- gwyddion [!hurd-i386],
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: aeskulap,
+ amide,
+ ants,
+ biosig-tools,
+ camitk-imp,
+ caret,
+ ctn,
+ ctsim,
+ dcmtk,
+ dicom3tools,
+ dicomnifti,
+ dicomscope,
+ ginkgocadx,
+ gofigure2,
+ gwyddion,
imagej,
- imagevis3d [!hurd-i386],
+ imagevis3d,
+ invesalius,
+ itksnap,
king,
- medcon [!hurd-i386],
- mialmpick [!hurd-i386],
- minc-tools [!hurd-i386],
- mriconvert [!hurd-i386],
- mricron [!s390 !hurd-i386 !kfreebsd-amd64 !s390x !ia64 !mips !kfreebsd-i386 !mipsel],
- mrtrix [!hurd-i386],
- nifti-bin [!hurd-i386],
- openmeeg-tools [!mips !hurd-i386],
- openslide-tools [!hurd-i386],
+ libgdcm-tools,
+ medcon,
+ mia-tools,
+ mia-viewit,
+ mialmpick,
+ minc-tools,
+ mriconvert,
+ mrtrix,
+ nifti-bin,
+ openslide-tools,
+ pixelmed-apps,
+ plastimatch,
python-dipy,
python-mvpa,
- python-nifti [!hurd-i386],
- python-nipy,
- python-nipype,
- python-nitime,
+ python-nifti,
python-surfer,
- sigviewer [!hurd-i386],
- teem-apps [!hurd-i386],
- via-bin [!hurd-i386],
- voxbo [!hurd-i386],
- xmedcon [!hurd-i386]
+ sigviewer,
+ sofa-apps,
+ teem-apps,
+ volview,
+ xmedcon
Suggests: afni,
- ants,
bioimagesuite,
bioimagexd,
- camitk-imp,
+ blox,
+ brainvisa,
+ cdmedicpacs,
cellprofiler,
cmtk,
connectomeviewer,
conquest-dicom-server,
crea,
+ dcm4chee,
+ devide,
+ dicom4j,
dicoogle,
+ drjekyll,
+ dti-query,
+ dtitk,
+ ecg2png,
+ eeglab,
elastix,
+ fiji,
freesurfer,
fsl,
fslview,
- ginkgocadx,
- gofigure2,
+ gimias,
+ hid,
imagemagick,
imview,
+ incf-nidash-oneclick-clients,
insightapplications,
- invesalius,
- itksnap,
+ isis,
+ jemris,
jist,
kradview,
libdcm4che-java,
- libgdcm-tools,
lipsia,
+ maris,
mayam,
- mia-tools,
- mia-viewit,
+ medisnap,
+ mesa-test-tools,
micromanager,
mipav,
+ miview,
+ mni-autoreg,
mni-colin27-nifti,
+ mni-icbm152-nlin-2009,
+ mni-n3,
+ mricron,
+ mrisim,
odin,
+ omero,
+ opendicom.net,
openelectrophy,
+ openmeeg-tools,
+ opensourcepacs,
openwalnut-qt4,
orthanc,
paraview,
- pixelmed-java,
- plastimatch,
+ piano,
pngquant,
+ pymeg,
+ python-nipy,
+ python-nipype,
+ python-nitime,
python-pyxid,
slicer,
- sofa-apps,
+ stabilitycalc,
+ stir,
+ tempo,
tifffile,
+ trimage,
+ via-bin,
+ visit,
vmtk,
- volview
+ voxbo,
+ vtk-dicom-tools,
+ xnat
Description: Debian Med imaging packages
This metapackage will install Debian packages which might be useful in
medical image processing.
@@ -637,77 +782,92 @@
ftp://medical.nema.org/medical/dicom/2008/ .
Package: med-imaging-dev
-Architecture: any
-Priority: extra
+Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: cimg-dev,
- ctn-dev [!hurd-i386],
- gmic [!hurd-i386],
- libactiviz.net-cil [!s390 !hurd-i386 !mipsel !armhf !mips],
- libbiosig-dev [!hurd-i386],
- libcv-dev [!hurd-i386],
- libgdf-dev [!hurd-i386],
- libgiftiio-dev [!hurd-i386],
- libmdc2-dev [!hurd-i386],
- libminc-dev [!hurd-i386],
- libnifti-dev [!hurd-i386],
- libopenigtlink1-dev [!hurd-i386],
- libopenmeeg-dev [!mips !hurd-i386],
- libopenslide-dev [!hurd-i386],
- libteem-dev [!hurd-i386],
- libvia-dev [!hurd-i386],
- libvistaio-dev [!hurd-i386],
- libvolpack1-dev [!hurd-i386],
- libvtk5-dev [!hurd-i386],
- libvxl1-dev [!hurd-i386],
- python-casmoothing [!hurd-i386],
+ ctn-dev,
+ gmic,
+ libactiviz.net-cil,
+ libbiosig-dev,
+ libcamitk3-dev,
+ libcv-dev,
+ libgdcm2-dev,
+ libgdf-dev,
+ libgiftiio-dev,
+ libigstk4-dev,
+ libinsighttoolkit3-dev | libinsighttoolkit4-dev,
+ libmdc2-dev,
+ libmia-2.0-dev,
+ libmialm-dev,
+ libmiaviewit-dev,
+ libminc-dev,
+ libnifti-dev,
+ libopenslide-dev,
+ libpapyrus3-dev,
+ libteem-dev,
+ libvigraimpex-dev,
+ libvistaio-dev,
+ libvolpack1-dev,
+ libvtk5-dev,
+ libvxl1-dev,
+ python-casmoothing,
python-cfflib,
python-dicom,
python-dipy,
+ python-gdcm,
+ python-mia | python3-mia,
+ python-mne,
python-mvpa,
python-nibabel,
+ python-openslide,
+ python-pyxnat,
+ python-vigra,
+ r-cran-rniftilib
+Suggests: emokit,
+ igstk-examples,
+ insighttoolkit3-examples,
+ libbio-formats-java,
+ libctk-dev,
+ libeegdev-dev,
+ libics-dev,
+ libmni-perllib-perl,
+ libnifti-doc,
+ libopenigtlink1-dev,
+ libopenmeeg-dev,
+ libopenslide-java,
+ libvia-dev,
+ libvmtk-dev,
+ libvtk-dicom0.4-dev,
+ libvtk5.4,
+ libvtkedge-dev,
+ libxdffileio-dev,
+ octave-dicom,
+ odin,
+ python-libavg,
python-nipy,
python-nipype,
python-nitime,
- python-pyxnat,
- r-cran-rniftilib [!hurd-i386]
-Suggests: igstk-examples,
- insighttoolkit3-examples,
- libbio-formats-java,
- libcamitk3-dev,
- libctk-dev,
- libeegdev-dev,
- libigstk4-dev,
- libinsighttoolkit3-dev,
- libmia-2.0-dev,
- libmiaviewit-dev,
- libnifti-doc,
- libopenslide-java,
- libvtk5.4,
- libxdffileio-dev,
- odin,
- python-gdcm,
- python-libavg,
- python-openslide
+ python-tifffile,
+ python-vmtk
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: any
-Priority: extra
+Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: dicompyler
-Suggests: uw-prism
+Suggests: planunc,
+ uw-prism
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
oncology.
Package: med-pharmacy
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: chemtool [!hurd-i386]
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: chemtool,
+ r-cran-dosefinding
Suggests: raccoon
Description: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
@@ -715,14 +875,16 @@
pharmaceutical research.
Package: med-physics
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: octave [!hurd-i386],
- paw [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- paw++ [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: octave,
+ paw,
+ paw++,
r-base
-Suggests: paw-demos
+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
@@ -730,62 +892,79 @@
and related fields.
Package: med-practice
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: clinica [!hurd-i386],
- entangle [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- freediams [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- freemedforms-emr [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: clinica,
+ entangle,
+ freediams,
+ freemedforms-emr,
+ ginkgocadx,
gnumed-client,
gnumed-server,
- libchipcard-tools [!hurd-i386],
- qrisk2 [!hurd-i386],
- r-cran-medadherence [!hurd-i386]
-Suggests: ginkgocadx,
- libctapimkt0,
+ libchipcard-tools,
+ qrisk2,
+ r-cran-medadherence
+Suggests: clearhealth,
+ elementalclinic,
+ elexis,
+ freeb,
+ freemed,
+ freeshim,
+ libctapimkt1,
+ medintux,
+ mirrormed,
+ mirth,
openemr,
- thera-pi
+ openpms,
+ openrep,
+ proteus,
+ remitt,
+ 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.
Package: med-psychology
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: praat [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
- psignifit [!hurd-i386],
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: praat,
+ psignifit,
+ python-pyepl,
+ python-pypsignifit,
+ r-cran-foreign,
+ r-cran-psy
+Suggests: miscpsycho,
+ psych,
+ psychometric,
psychopy,
- python-pyepl [!hurd-i386],
- python-pypsignifit [!s390 !hurd-i386 !mips],
- r-cran-foreign [!hurd-i386],
- r-cran-psy
-Suggests: python-visionegg,
+ psychotree,
+ psyphy,
+ python-visionegg,
science-psychophysics
Description: Debian Med packages for psychology
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
Package: med-rehabilitation
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: sitplus [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64]
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: sitplus
Suggests: aghermann
Description: Debian Med packages for rehabilitation technologies
This metapackage will install tools that are useful for
rehabilitation and therapy.
Package: med-statistics
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: r-bioc-edger [!hurd-i386],
- r-bioc-limma [!hurd-i386],
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: r-bioc-edger,
+ r-bioc-limma,
r-bioc-qvalue,
r-cran-pvclust,
- r-cran-randomforest [!hurd-i386]
+ r-cran-randomforest
Suggests: r-cran-beeswarm,
science-statistics
Description: Debian Med statistics
@@ -793,30 +972,31 @@
with a special focus on tasks in medical care.
Package: med-tools
-Architecture: any
-Priority: extra
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: edfbrowser [!hurd-i386],
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: cronometer,
+ edfbrowser,
hunspell-de-med,
hunspell-en-med,
pcalendar,
pondus,
- python-clips [!hurd-i386],
- quitcount [!hurd-i386],
+ python-clips,
+ python3-fitbitscraper,
+ quitcount,
wgerman-medical,
- workrave [!hurd-i386]
-Suggests: cl-pubmed,
- cycle,
+ workrave
+Suggests: cycle,
entangle,
+ goldencheetah,
mencal,
- mssstest
+ mssstest,
+ python-fitbit
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
-Architecture: any
-Priority: extra
+Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: king,
texlive-latex-extra,
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=4019&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control.stub (original)
+++ projects/med/trunk/debian-med/debian/control.stub Tue Apr 15 15:44:28 2014
@@ -1,13 +1,12 @@
Source: debian-med
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: misc
Priority: extra
-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 (>= 0.6.16.3)
-Standards-Version: 3.9.3
-Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/
-Vcs-Svn: svn://svn.debian.org/blends/projects/med/trunk/debian-med/
+Standards-Version: 3.9.5
+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/
Package: med-tasks
Architecture: all
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