[Blends-commit] r3888 - in /projects/med/trunk/debian-med: debian-med-tasks.desc debian/changelog debian/control dependency_data/debian-med_1.13.3.json
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Tue Oct 22 07:31:31 UTC 2013
Author: tille
Date: Tue Oct 22 07:31:31 2013
New Revision: 3888
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3888
Log:
Played around with new blends-dev (not to be released for now)
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/dependency_data/debian-med_1.13.3.json
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=3888&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian-med-tasks.desc (original)
+++ projects/med/trunk/debian-med/debian-med-tasks.desc Tue Oct 22 07:31:31 2013
@@ -4,174 +4,184 @@
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences.
Relevance: 10
-Enhances: t-coffee
-Key:
+Key:
med-bio
Packages: list
- altree
- fastdnaml
- njplot
- tree-puzzle
- probalign
- treeviewx
+ abacas
+ acedb-other
+ acedb-other-belvu
+ acedb-other-dotter
+ adun.app
+ 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
- fastlink
- loki
- plink
- r-cran-qtl
- r-cran-genabel
- amap-align
- boxshade
- fastx-toolkit
- gff2aplot
- muscle
- sim4
- sibsim4
- tabix
- tophat
- 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
- bowtie
- bowtie2
- dotur
- transtermhp
- last-align
- maq
- ssake
- velvet
- qiime
- infernal
- rnahybrid
- adun.app
- garlic
- gamgi
- gdpc
- ghemical
+ filo
+ flexbar
+ freecontact
+ gamgi
+ garlic
+ gbrowse
+ gdpc
+ genometools
+ gentle
+ gff2aplot
+ gff2ps
+ ghemical
+ glam2
+ grinder
+ gromacs
+ hhsuite
+ hmmer
+ hmmer2
+ infernal
+ jalview
+ jellyfish
jmol
- pymol
- r-other-bio3d
- massxpert
- gromacs
- rasmol
- plasmidomics
- gff2ps
- ncbi-epcr
- ncbi-tools-bin
- ncbi-tools-x11
- perlprimer
- readseq
- tigr-glimmer
- melting
+ kalign
+ kissplice
+ last-align
+ librg-utils-perl
+ logol-bin
+ loki
+ ltrsift
+ macs
+ mafft
+ maq
+ maqview
+ massxpert
+ melting
+ metastudent
+ microbiomeutil
mipe
- primer3
- gbrowse
- biomaj
- glam2
- raster3d
- phyml
- autodock
- autogrid
- autodock-vina
- mustang
- theseus
- staden-io-lib-utils
- samtools
- bedtools
- filo
- r-bioc-hilbertvis
- r-other-mott-happy
- mira-assembler
- alien-hunter
- ncoils
- gentle
- picard-tools
- acedb-other-dotter
- acedb-other-belvu
- acedb-other
- python-cogent
- mrbayes
- squizz
- clonalframe
- dssp
- jellyfish
- ballview
- pynast
- raxml
- mlv-smile
- cd-hit
- r-bioc-cummerbund
- grinder
- jalview
- reprof
- tm-align
+ 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
norsnet
norsp
+ perlprimer
+ phyml
+ picard-tools
+ plasmidomics
+ plink
+ poa
+ populations
predictnls
- proftmb
+ predictprotein
+ primer3
+ proalign
+ probalign
+ probcons
+ proda
profbval
profisis
- hhsuite
- ffindex
- neobio
- ray
- logol-bin
- soapdenovo
- aragorn
- cdbfasta
- edtsurf
- fasttree
- genometools
- hmmer2
- ltrsift
- macs
- ncbi-seg
- predictprotein
- r-cran-vegan
- uc-echo
- zalign
- concavity
- conservation-code
- abacas
- profnet-bval
- profnet-chop
- profnet-con
- profnet-isis
- profnet-md
- profnet-norsnet
- profnet-prof
- profnet-snapfun
- profphd-net
- profphd-utils
+ profnet-bval
+ profnet-chop
+ profnet-con
+ profnet-isis
+ profnet-md
+ profnet-norsnet
+ profnet-prof
+ profnet-snapfun
profphd
- ampliconnoise
- disulfinder
- populations
- librg-utils-perl
- vcftools
+ 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
Task: med-bio-dev
Section: debian-med
@@ -179,56 +189,61 @@
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
- libncbi6-dev
- mcl
- biosquid
- libvibrant6-dev
- python-biopython
- python-cogent
- ruby-bio
+ biosquid
+ libace-perl
+ libai-fann-perl
+ libbio-graphics-perl
+ libbio-mage-perl
+ libbio-mage-utils-perl
+ libbio-primerdesigner-perl
+ libbiococoa-dev
libbiojava-java
libbiojava3-java
- libgenome-1.3-0-dev
- libai-fann-perl
- libbio-mage-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
+ libjebl2-java
+ libncbi6-dev
libnhgri-blastall-perl
- libtfbs-perl
- libgo-perl
+ 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-htseq
+ python-mmtk
+ r-bioc-biobase
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
- librcsb-core-wrapper0-dev
+ r-cran-haplo.stats
+ ruby-bio
seqan-dev
- libbio-mage-utils-perl
- libchado-perl
- libpal-java
- libjebl2-java
- r-bioc-biobase
- libffindex0-dev
- librostlab3-dev
- librostlab-doc
- librostlab-blast0-dev
- librostlab-blast-doc
- librg-blast-parser-perl
- libsort-key-top-perl
- libhmsbeagle-dev
- libgenometools0-dev
- python-biom-format
- libgenome-perl
- pyfai
Task: med-bio-ngs
Section: debian-med
@@ -237,10 +252,27 @@
sequences produced by next generation sequencing.
Relevance: 10
Packages: list
- mothur
- qiime
- mira-assembler
- uc-echo
+ 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
Task: med-bio-phylogeny
Section: debian-med
@@ -251,31 +283,31 @@
related software.
Relevance: 10
Packages: list
- 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
+ clustalw
+ clustalx
+ dialign
+ dialign-tx
+ exonerate
+ fastdnaml
figtree
- populations
+ hmmer
+ kalign
+ mrbayes
+ muscle
+ mustang
+ njplot
+ phyml
+ poa
+ populations
+ proalign
+ probalign
+ probcons
+ proda
+ sigma-align
+ t-coffee
+ tm-align
+ tree-puzzle
+ treeviewx
Task: med-cloud
Section: debian-med
@@ -285,13 +317,39 @@
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
- clustalw
- autodock
- raster3d
- python-cogent
+ 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
Task: med-cms
Section: debian-med
@@ -308,10 +366,10 @@
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
@@ -321,11 +379,11 @@
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
@@ -336,16 +394,30 @@
"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
+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
+ out there which might be interesting targets for inclusion into Debian
+ and so we provide a list of these projects which might be included
+ at a later point in time provided somebody is willing to take over
+ the packaging work.
+Relevance: 10
+Key:
+ med-his
+Packages: list
Task: med-imaging
Section: debian-med
@@ -368,56 +440,44 @@
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
- amide
- ctsim
- ctn
- dicomnifti
+ aeskulap
+ amide
+ biosig-tools
+ caret
+ ctn
+ ctsim
+ dcmtk
+ dicom3tools
+ dicomnifti
+ dicomscope
+ gwyddion
imagej
- minc-tools
- medcon
- python-nifti
- xmedcon
- dcmtk
- nifti-bin
- aeskulap
- via-bin
- gwyddion
- sofa-apps
+ imagevis3d
+ king
+ medcon
+ mialmpick
+ minc-tools
+ mriconvert
+ mricron
+ mrtrix
+ nifti-bin
+ openmeeg-tools
+ openslide-tools
+ python-dipy
python-mvpa
+ python-nifti
python-nipy
python-nipype
- caret
- libgdcm-tools
- dicom3tools
- imagevis3d
- odin
- dicomscope
- pixelmed-java
- gofigure2
- ginkgocadx
- openslide-tools
- volview
- camitk-imp
- invesalius
- mricron
- voxbo
- mrtrix
- ants
- itksnap
- mriconvert
- mialmpick
- sigviewer
- tifffile
- openmeeg-tools
- plastimatch
- biosig-tools
+ python-nitime
python-surfer
- king
- python-nitime
- python-dipy
+ sigviewer
+ teem-apps
+ via-bin
+ voxbo
+ xmedcon
Task: med-imaging-dev
Section: debian-med
@@ -425,44 +485,40 @@
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
- libminc-dev
- libmdc2-dev
- libvtk5-dev
- libnifti-dev
- libigstk4-dev
- libinsighttoolkit3-dev
- libvolpack1-dev
- libgdcm2-dev
- python-gdcm
+ 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
+ python-cfflib
+ python-dicom
+ python-dipy
python-mvpa
+ python-nibabel
python-nipy
python-nipype
python-nitime
- python-casmoothing
- libvia-dev
- odin
- libcv-dev
- libvxl1-dev
- gmic
- libgiftiio-dev
- libactiviz.net-cil
- libvistaio-dev
- libopenigtlink1-dev
- python-dicom
- libopenmeeg-dev
- python-nibabel
- libgdf-dev
python-pyxnat
- python-dipy
- libbiosig-dev
- python-cfflib
- libopenslide-dev
- libcamitk3-dev
+ r-cran-rniftilib
Task: med-oncology
Section: debian-med
@@ -470,7 +526,7 @@
This metapackage will install tools that are useful for radiation
oncology.
Relevance: 10
-Key:
+Key:
med-oncology
Packages: list
dicompyler
@@ -482,10 +538,10 @@
collection of software and documentation which is useful for
pharmaceutical research.
Relevance: 10
-Key:
+Key:
med-pharmacy
Packages: list
- chemtool
+ chemtool
Task: med-physics
Section: debian-med
@@ -495,12 +551,12 @@
medical physicists in radiation oncology, diagnostics imaging
and related fields.
Relevance: 10
-Key:
+Key:
med-physics
Packages: list
- paw++
- paw
- octave
+ octave
+ paw
+ paw++
r-base
Task: med-practice
@@ -509,19 +565,18 @@
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
- ginkgocadx
- freediams
- freemedforms-emr
- r-cran-medadherence
- clinica
- entangle
- qrisk2
+ libchipcard-tools
+ qrisk2
+ r-cran-medadherence
Task: med-psychology
Section: debian-med
@@ -529,16 +584,16 @@
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
Relevance: 10
-Key:
+Key:
med-psychology
Packages: list
- python-pyepl
- praat
- r-cran-foreign
- psignifit
- python-pypsignifit
+ praat
+ psignifit
+ psychopy
+ python-pyepl
+ python-pypsignifit
+ r-cran-foreign
r-cran-psy
- psychopy
Task: med-rehabilitation
Section: debian-med
@@ -546,10 +601,10 @@
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
@@ -557,14 +612,14 @@
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
@@ -572,18 +627,18 @@
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
- hunspell-de-med
- quitcount
- workrave
- edfbrowser
- hunspell-en-med
- python-clips
+ workrave
Task: med-typesetting
Section: debian-med
@@ -592,10 +647,10 @@
for typesetting and publishing in medical care and structural
biology.
Relevance: 10
-Key:
+Key:
med-typesetting
Packages: list
+ king
+ texlive-latex-extra
texlive-science
- texlive-latex-extra
- king
-
+
Modified: projects/med/trunk/debian-med/debian/changelog
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/debian/changelog?rev=3888&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog (original)
+++ projects/med/trunk/debian-med/debian/changelog Tue Oct 22 07:31:31 2013
@@ -2,6 +2,58 @@
* debian/control:
- 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
-- 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=3888&op=diff
==============================================================================
--- projects/med/trunk/debian-med/debian/control (original)
+++ projects/med/trunk/debian-med/debian/control Tue Oct 22 07:31:31 2013
@@ -55,338 +55,269 @@
Debian by simply installing the relevant metapackage
Package: med-bio
-Architecture: all
+Architecture: any
+Priority: extra
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: abacas,
- acedb-other,
- acedb-other-belvu,
- acedb-other-dotter,
- adun.app,
+ acedb-other [!hurd-i386],
+ acedb-other-belvu [!hurd-i386],
+ acedb-other-dotter [!hurd-i386],
+ adun.app [!hurd-i386],
alien-hunter,
- altree,
- amap-align,
- ampliconnoise,
- aragorn,
- autodock,
- autodock-vina,
- autogrid,
- ballview,
- bedtools,
+ 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],
biomaj,
- blast2,
- bowtie,
- bowtie2,
- boxshade,
- bwa,
- cd-hit,
- cdbfasta,
- clonalframe,
- clustalo,
- clustalw,
- clustalx,
- concavity,
+ 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],
+ chimeraslayer,
+ clonalframe [!hurd-i386],
+ clustalo [!hurd-i386],
+ clustalw [!hurd-i386],
+ clustalx [!hurd-i386],
+ concavity [!hurd-i386],
conservation-code,
- dialign,
- dialign-tx,
- disulfinder,
- dotur,
- dssp,
- edtsurf,
- embassy-domainatrix,
- embassy-domalign,
- embassy-domsearch,
- emboss,
- exonerate,
- fastdnaml,
- fastlink,
- fasttree,
- fastx-toolkit,
- ffindex,
+ 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],
+ fastqc,
+ fasttree [!hurd-i386],
+ fastx-toolkit [!hurd-i386],
+ ffindex [!hurd-i386],
figtree,
- filo,
- gamgi,
- garlic,
+ 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],
gbrowse,
- gdpc,
- genometools,
- gentle,
- gff2aplot,
+ gdpc [!hurd-i386],
+ genometools [!sparc !hurd-i386 !armel],
+ gentle [!hurd-i386],
+ gff2aplot [!hurd-i386],
gff2ps,
- ghemical,
- glam2,
+ ghemical [!hurd-i386],
+ glam2 [!hurd-i386],
grinder,
- gromacs,
- hhsuite,
- hmmer,
- hmmer2,
- infernal,
+ 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],
jalview,
- jellyfish,
+ jellyfish [!s390 !hurd-i386 !s390x !sparc !powerpc !i386 !armel !armhf !ia64 !mips !kfreebsd-i386 !mipsel],
jmol,
- kalign,
- last-align,
+ kalign [!hurd-i386],
+ kissplice [!hurd-i386],
+ last-align [!hurd-i386],
librg-utils-perl,
- logol-bin,
- loki,
- ltrsift,
- macs,
- mafft,
- maq,
- maqview,
- massxpert,
- melting,
+ 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],
+ metastudent,
+ microbiomeutil,
mipe,
- mira-assembler,
- mlv-smile,
- mothur,
- mrbayes,
- mummer,
- muscle,
- mustang,
- ncbi-blast+,
- ncbi-epcr,
- ncbi-seg,
- ncbi-tools-bin,
- ncbi-tools-x11,
- ncoils,
+ 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],
neobio,
- njplot,
+ njplot [!hurd-i386],
norsnet,
norsp,
perlprimer,
- phyml,
+ phyml [!hurd-i386],
picard-tools,
plasmidomics,
- plink,
- poa,
- populations,
+ plink [!hurd-i386],
+ poa [!hurd-i386],
+ populations [!hurd-i386],
predictnls,
predictprotein,
- primer3,
- probalign,
- probcons,
- proda,
+ primer3 [!hurd-i386],
+ proalign [!hurd-i386],
+ probalign [!hurd-i386],
+ probcons [!hurd-i386],
+ proda [!hurd-i386],
profbval,
profisis,
- profnet-bval,
- profnet-chop,
- profnet-con,
- profnet-isis,
- profnet-md,
- profnet-norsnet,
- profnet-prof,
- profnet-snapfun,
+ 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],
profphd,
- profphd-net,
- profphd-utils,
- proftmb,
- pymol,
+ profphd-net [!hurd-i386],
+ profphd-utils [!hurd-i386],
+ proftmb [!hurd-i386],
+ pymol [!hurd-i386],
pynast,
- python-cogent,
- qiime,
+ python-cogent [!hurd-i386],
+ qiime [!ia64 !hurd-i386],
+ r-bioc-biostrings [!hurd-i386],
r-bioc-cummerbund,
- r-bioc-hilbertvis,
- r-cran-genabel,
- r-cran-qtl,
- r-cran-vegan,
+ r-bioc-hilbertvis [!hurd-i386],
+ r-cran-genabel [!hurd-i386],
+ r-cran-qtl [!hurd-i386],
+ r-cran-vegan [!hurd-i386],
r-other-bio3d,
- r-other-mott-happy,
- rasmol,
- raster3d,
- raxml,
- ray,
- readseq,
+ 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],
reprof,
- rnahybrid,
- samtools,
- sibsim4,
- sigma-align,
- sim4,
- soapdenovo,
- squizz,
- sra-toolkit,
+ 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],
ssake,
- staden-io-lib-utils,
- t-coffee,
- tabix,
- theseus,
- tigr-glimmer,
- tm-align,
- tophat,
- transtermhp,
- tree-puzzle | tree-ppuzzle,
- treeviewx,
- uc-echo,
- vcftools,
- velvet,
- wise,
- zalign
+ 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],
+ trimmomatic,
+ uc-echo [!hurd-i386 !armel !armhf !ia64 !mips !kfreebsd-i386 !mipsel],
+ vcftools [!hurd-i386],
+ velvet [!hurd-i386],
+ wigeon,
+ wise [!hurd-i386],
+ zalign [!s390 !s390x !hurd-i386 !mipsel !mips]
Suggests: abyss,
- act,
+ aevol,
+ altree,
amos-assembler,
- amoscmp,
anfo,
apollo,
- arachne,
arb,
- artemis,
- asap,
- augustus,
autodocktools,
axparafit,
axpcoords,
bagpipe,
- bambus,
bamtools,
- beads,
beast-mcmc,
- big-blast,
bigsdb,
bitseq,
blimps-utils,
- blixem,
- btk-core,
- cactus,
- caftools,
cain,
- cap3,
- 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,
ensembl,
- est-db,
- estferret,
- estscan,
- exalt,
- excavator,
- fas,
- fasta,
- fastqc,
- figaro,
- finex,
- flexbar,
- fluctuate,
forester,
- forge,
- galaxy,
gassst,
- gbioseq,
- gbrowse-syn,
- genemark,
- genesplicer,
- genetrack,
- genezilla,
- genographer,
- glimmerhmm,
gmap,
- gmv,
+ grabix,
grogui,
haploview,
hawkeye,
- hexamer,
- hilbertvisgui,
igv,
jbrowse,
- jigsaw,
- jstreeview,
kempbasu,
lagan,
- lamarc,
logomat-m,
- lucy,
mach-haplotyper,
mage2tab,
- maker2,
martj,
maude,
mauvealigner,
- maxd,
melting-gui,
meme,
- mesquite,
- metarep,
- metastudent,
- microbiomeutil,
- migrate,
- minimus,
- mirbase,
mobyle,
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,
plato,
prank,
- proalign,
profit,
- prot4est,
pscan-tfbs,
psipred,
- pyrophosphate-tools,
- python-orange,
python-rdkit,
python-reaper,
- qtlcart,
- r-ape,
+ r-bioc-gviz,
+ r-bioc-rtracklayer,
r-cran-boolnet,
r-other-valdar-bagphenotype.library,
raccoon,
- rbs-finder,
+ rate4site,
rdp-classifier,
- recombine,
- repeatmasker,
- rmblast,
- roche454ace2caf,
- rose,
rosetta,
sap,
seaview,
@@ -396,124 +327,140 @@
sequenceconverter.app,
sga,
sift,
- smalt,
+ situs,
snap,
snpeff,
- spice,
- splitstree,
spread-phy,
ssaha,
+ staden,
strap,
strap-base,
tacg,
- taverna,
- taxinspector,
- tetra,
- tigr-assembler,
tigr-glimmer-mg,
- trace2dbest,
- tracetuner,
- treebuilder3d,
- treetime,
treeview,
- tripal,
- trnascan-se,
- twain,
ugene,
- 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: all
+Architecture: any
+Priority: extra
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: bioperl,
bioperl-run,
- biosquid,
- libace-perl,
- libai-fann-perl,
+ biosquid [!hurd-i386],
+ libace-perl [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
+ libai-fann-perl [!hurd-i386],
libbio-graphics-perl,
libbio-mage-perl,
libbio-mage-utils-perl,
libbio-primerdesigner-perl,
- libbiococoa-dev,
+ libbiococoa-dev [!hurd-i386],
libbiojava-java,
libbiojava3-java,
libchado-perl,
- libffindex0-dev,
- libgenome-1.3-0-dev,
+ libffindex0-dev [!hurd-i386],
+ libfreecontact-doc,
+ libfreecontact0-dev [!mips !hurd-i386],
+ libgenome-1.3-0-dev [!hurd-i386],
+ libgenome-model-tools-music-perl,
libgenome-perl,
- libgenometools0-dev,
+ libgenometools0-dev [!sparc !hurd-i386 !armel],
libgo-perl,
- libhmsbeagle-dev,
+ libhmsbeagle-dev [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
libjebl2-java,
- libncbi6-dev,
+ libncbi6-dev [!hurd-i386],
libnhgri-blastall-perl,
libpal-java,
- librcsb-core-wrapper0-dev,
- librg-blast-parser-perl,
+ 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,
+ librostlab-blast0-dev [!hurd-i386],
librostlab-doc,
- librostlab3-dev,
- libsort-key-top-perl,
- libsrf-dev,
- libstaden-read-dev,
- libtfbs-perl,
- libvibrant6-dev,
- libzerg-perl,
- libzerg0-dev,
- mcl,
- pyfai,
- python-biom-format,
- python-biopython,
- python-cogent,
- r-bioc-biobase,
+ 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,
+ r-cran-haplo.stats [!hurd-i386],
ruby-bio,
seqan-dev
-Suggests: bioclipse,
- biostrings,
- iranges,
- libbamtools-dev,
+Suggests: libbamtools-dev,
libbio-das-perl,
libforester-java,
- libgbfp-dev,
- libgenome-model-tools-music-perl,
- libgff-perl,
- libmems-1.5-1,
libopenmm4-dev,
- libqsearch-dev,
libsbml5-dev,
libswarm2-dev,
- octace-bioinfo,
+ libtfbs-perl,
octave-bioinfo,
- python-librcsb-core-wrapper,
- python-mmtk,
python-pysam,
+ r-bioc-affy,
+ r-bioc-affyio,
+ r-bioc-altcdfenvs,
r-bioc-biocgenerics,
+ r-bioc-iranges,
+ r-bioc-makecdfenv,
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,
- clustalw,
- python-cogent,
- raster3d
-Suggests: bagpipe,
+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,
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,
@@ -522,42 +469,42 @@
in cloud computing clusters, where space can be limited.
Package: med-data
-Architecture: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: freediams,
+Architecture: any
+Priority: extra
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: freediams [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
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: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: entangle,
+Architecture: any
+Priority: extra
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: entangle [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
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
+Architecture: any
+Priority: extra
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: epigrass,
r-cran-diagnosismed,
- r-cran-epi,
- r-cran-epibasix,
+ r-cran-epi [!hurd-i386],
+ r-cran-epibasix [!hurd-i386],
r-cran-epicalc,
r-cran-epir,
r-cran-epitools
Suggests: netepi-analysis,
netepi-collection,
r-cran-msm,
- r-cran-surveillance,
- repast
+ r-cran-surveillance
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
@@ -565,124 +512,111 @@
"A short introduction to R for Epidemiology" at
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:
+Suggests: care2x,
+ ewd-920,
+ fis-gtm,
+ gnuhealth,
+ openmrs,
+ 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
+ out there which might be interesting targets for inclusion into Debian
+ and so we provide a list of these projects which might be included
+ at a later point in time provided somebody is willing to take over
+ the packaging work.
+
Package: med-imaging
-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,
+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],
imagej,
- imagevis3d,
- invesalius,
- itksnap,
+ imagevis3d [!hurd-i386],
king,
- libgdcm-tools,
- medcon,
- mialmpick,
- minc-tools,
- mriconvert,
- mricron,
- mrtrix,
- nifti-bin,
- odin,
- openmeeg-tools,
- openslide-tools,
- pixelmed-java,
- plastimatch,
+ 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],
python-dipy,
python-mvpa,
- python-nifti,
+ python-nifti [!hurd-i386],
python-nipy,
python-nipype,
python-nitime,
python-surfer,
- sigviewer,
- sofa-apps,
- tifffile,
- via-bin,
- volview,
- voxbo,
- xmedcon
+ sigviewer [!hurd-i386],
+ teem-apps [!hurd-i386],
+ via-bin [!hurd-i386],
+ voxbo [!hurd-i386],
+ xmedcon [!hurd-i386]
Suggests: afni,
+ ants,
bioimagesuite,
bioimagexd,
- blox,
- brainvisa,
- cdmedicpacs,
+ camitk-imp,
cellprofiler,
cmtk,
connectomeviewer,
conquest-dicom-server,
crea,
- dcm4chee,
- devide,
- dicom4j,
dicoogle,
- drjekyll,
- dti-query,
- dtitk,
- ecg2png,
- eeglab,
elastix,
- fiji,
freesurfer,
fsl,
fslview,
- gimias,
- hid,
+ ginkgocadx,
+ gofigure2,
imagemagick,
imview,
- incf-nidash-oneclick-clients,
insightapplications,
- isis,
- jemris,
+ invesalius,
+ itksnap,
jist,
kradview,
libdcm4che-java,
+ libgdcm-tools,
lipsia,
- maris,
mayam,
- medisnap,
- mesa-test-tools,
mia-tools,
+ mia-viewit,
micromanager,
mipav,
- miview,
- mni-autoreg,
mni-colin27-nifti,
- mni-icbm152-nlin-2009,
- mni-n3,
- mrisim,
- omero,
- opendicom.net,
+ odin,
openelectrophy,
- opensourcepacs,
openwalnut-qt4,
orthanc,
paraview,
- piano,
+ pixelmed-java,
+ plastimatch,
pngquant,
- pymeg,
python-pyxid,
slicer,
- stabilitycalc,
- stir,
- tempo,
- visit,
+ sofa-apps,
+ tifffile,
vmtk,
- xnat
+ volview
Description: Debian Med imaging packages
This metapackage will install Debian packages which might be useful in
medical image processing.
@@ -703,57 +637,56 @@
ftp://medical.nema.org/medical/dicom/2008/ .
Package: med-imaging-dev
-Architecture: all
+Architecture: any
+Priority: extra
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: cimg-dev,
- ctn-dev,
- gmic,
- libactiviz.net-cil,
- libbiosig-dev,
- libcamitk3-dev,
- libcv-dev,
- libgdcm2-dev,
- libgdf-dev,
- libgiftiio-dev,
- libigstk4-dev,
- libinsighttoolkit3-dev,
- libmdc2-dev,
- libminc-dev,
- libnifti-dev,
- libopenigtlink1-dev,
- libopenmeeg-dev,
- libopenslide-dev,
- libvia-dev,
- libvistaio-dev,
- libvolpack1-dev,
- libvtk5-dev,
- libvxl1-dev,
- odin,
- python-casmoothing,
+ 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],
python-cfflib,
python-dicom,
python-dipy,
- python-gdcm,
python-mvpa,
python-nibabel,
python-nipy,
python-nipype,
python-nitime,
- python-pyxnat
-Suggests: emokit,
- igstk-examples,
+ 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,
- libmni-perllib-perl,
+ libmiaviewit-dev,
libnifti-doc,
libopenslide-java,
- libteem1-dev,
libvtk5.4,
libxdffileio-dev,
- octave-dicom,
+ odin,
+ python-gdcm,
python-libavg,
python-openslide
Description: Debian Med packages for medical image development
@@ -761,19 +694,20 @@
for developing applications for medical image processing.
Package: med-oncology
-Architecture: all
+Architecture: any
+Priority: extra
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: dicompyler
-Suggests: planunc,
- uw-prism
+Suggests: uw-prism
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
oncology.
Package: med-pharmacy
-Architecture: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: chemtool
+Architecture: any
+Priority: extra
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: chemtool [!hurd-i386]
Suggests: raccoon
Description: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
@@ -781,16 +715,14 @@
pharmaceutical research.
Package: med-physics
-Architecture: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: octave,
- paw,
- paw++,
+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],
r-base
-Suggests: biosig,
- gate,
- openvibe,
- paw-demos
+Suggests: paw-demos
Description: Debian Med packages for medical physicists
This metapackage contains dependencies for a
collection of software and documentation which is useful for
@@ -798,80 +730,62 @@
and related fields.
Package: med-practice
-Architecture: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: clinica,
- entangle,
- freediams,
- freemedforms-emr,
- ginkgocadx,
+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],
gnumed-client,
gnumed-server,
- libchipcard-tools,
- qrisk2,
- r-cran-medadherence
-Suggests: clearhealth,
- elementalclinic,
- elexis,
- freeb,
- freeicd,
- freemed,
- freeshim,
+ libchipcard-tools [!hurd-i386],
+ qrisk2 [!hurd-i386],
+ r-cran-medadherence [!hurd-i386]
+Suggests: ginkgocadx,
libctapimkt0,
- medintux,
- mirrormed,
- mirth,
openemr,
- openpms,
- openrep,
- proteus,
- remitt,
- resmedicinae,
- sqlclinic,
- thera-pi,
- tinyheb
+ thera-pi
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: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: praat,
- psignifit,
+Architecture: any
+Priority: extra
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: praat [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64],
+ psignifit [!hurd-i386],
psychopy,
- python-pyepl,
- python-pypsignifit,
- r-cran-foreign,
+ python-pyepl [!hurd-i386],
+ python-pypsignifit [!s390 !hurd-i386 !mips],
+ r-cran-foreign [!hurd-i386],
r-cran-psy
-Suggests: miscpsycho,
- psych,
- psychometric,
- psychotree,
- psyphy,
- python-visionegg,
+Suggests: 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: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: sitplus
+Architecture: any
+Priority: extra
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: sitplus [!kfreebsd-i386 !hurd-i386 !kfreebsd-amd64]
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: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: r-bioc-edger,
- r-bioc-limma,
+Architecture: any
+Priority: extra
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: r-bioc-edger [!hurd-i386],
+ r-bioc-limma [!hurd-i386],
r-bioc-qvalue,
r-cran-pvclust,
- r-cran-randomforest
+ r-cran-randomforest [!hurd-i386]
Suggests: r-cran-beeswarm,
science-statistics
Description: Debian Med statistics
@@ -879,17 +793,18 @@
with a special focus on tasks in medical care.
Package: med-tools
-Architecture: all
-Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: edfbrowser,
+Architecture: any
+Priority: extra
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: edfbrowser [!hurd-i386],
hunspell-de-med,
hunspell-en-med,
pcalendar,
pondus,
- python-clips,
- quitcount,
+ python-clips [!hurd-i386],
+ quitcount [!hurd-i386],
wgerman-medical,
- workrave
+ workrave [!hurd-i386]
Suggests: cl-pubmed,
cycle,
entangle,
@@ -900,7 +815,8 @@
Currently it contains some simple programs for Personal Health.
Package: med-typesetting
-Architecture: all
+Architecture: any
+Priority: extra
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: king,
texlive-latex-extra,
Modified: projects/med/trunk/debian-med/dependency_data/debian-med_1.13.3.json
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/dependency_data/debian-med_1.13.3.json?rev=3888&op=diff
==============================================================================
--- projects/med/trunk/debian-med/dependency_data/debian-med_1.13.3.json (original)
+++ projects/med/trunk/debian-med/dependency_data/debian-med_1.13.3.json Tue Oct 22 07:31:31 2013
@@ -1 +1 @@
-{"oncology": {"ignore": [], "suggests": [], "depends": ["uw-prism", "planunc", "dicompyler"], "recommends": [], "avoid": []}, "laboratory": {"ignore": [], "suggests": [], "depends": ["openelis", "openfreezer", "catissuesuite"], "recommends": [], "avoid": []}, "pharmacy": {"ignore": [], "suggests": [], "depends": ["chemtool", "raccoon"], "recommends": [], "avoid": []}, "tools": {"ignore": [], "suggests": ["cycle", "mencal", "cl-pubmed", "entangle"], "depends": ["pcalendar", "pondus", "mssstest", "wgerman-medical", "hunspell-de-med", "quitcount", "workrave", "edfbrowser", "hunspell-en-med", "python-clips"], "recommends": [], "avoid": []}, "cloud": {"ignore": [], "suggests": [], "depends": ["altree", "fastdnaml", "phyml", "tree-puzzle | tree-ppuzzle", "alien-hunter", "fastlink", "loki", "plink", "r-cran-qtl", "r-other-mott-happy", "bagpipe", "r-other-valdar-bagphenotype.library", "clustalw | clustalw-mpi", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "bedtools", "bwa", "filo", "last-align", "maq", "picard-tools", "r-bioc-hilbertvis", "samtools", "ssake", "tophat", "velvet", "infernal", "rnahybrid", "autodock", "raster3d", "python-cogent"], "recommends": [], "avoid": []}, "statistics": {"ignore": [], "suggests": ["science-statistics"], "depends": ["r-bioc-edger", "r-bioc-limma", "r-bioc-qvalue", "r-cran-randomforest", "r-cran-beeswarm", "r-cran-pvclust"], "recommends": [], "avoid": []}, "psychology": {"ignore": [], "suggests": ["science-psychophysics", "python-visionegg"], "depends": ["python-pyepl", "praat", "r-cran-foreign", "psignifit", "python-pypsignifit", "r-cran-psy", "psychopy", "miscpsycho", "psych", "psychometric", "psychotree", "psyphy"], "recommends": [], "avoid": []}, "research": {"ignore": [], "suggests": [], "depends": ["openclinica"], "recommends": [], "avoid": []}, "typesetting": {"ignore": [], "suggests": ["kbibtex", "biber", "bibus", "referencer", "jabref-plugin-oo"], "depends": ["texlive-science", "texlive-latex-extra", "king"], "recommends": [], "avoid": []}, "bio-ngs": {"ignore": [], "suggests": [], "depends": ["bedtools", "bwa", "bowtie", "fastx-toolkit", "filo", "last-align", "maq", "picard-tools", "r-bioc-edger", "r-bioc-hilbertvis", "samtools", "sra-toolkit", "ssake", "tabix", "tophat", "vcftools", "velvet", "mothur", "qiime", "cufflinks", "mira-assembler", "kissplice", "mosaik-aligner", "forge", "uc-echo", "annovar"], "recommends": [], "avoid": []}, "bio": {"ignore": ["riso", "catissuecore", "trapss"], "suggests": ["emboss-explorer", "melting-gui", "mozilla-biofox", "seqan-apps", "pdb2pqr", "cain", "eigensoft", "blimps-utils", "r-cran-boolnet", "circos", "mobyle", "maude", "python-rdkit"], "depends": ["altree", "beast-mcmc", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle", "probalign", "treeviewx", "figtree", "spread-phy", "phylip", "fastlink", "loki", "plink", "r-cran-qtl", "r-cran-genabel", "amap-align", "boxshade", "fastx-toolkit", "gff2aplot", "muscle", "sim4", "sibsim4", "tabix", "tophat", "wise", "maqview", "bwa", "mummer", "blast2", "ncbi-blast+", "mafft", "sra-toolkit", "t-coffee", "kalign", "hmmer", "exonerate", "dialign", "dialign-tx", "poa", "probcons", "proda", "seaview", "sigma-align", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "arb", "clustalx", "clustalo", "clustalw | clustalw-mpi", "mothur", "bowtie", "bowtie2", "dotur", "transtermhp", "last-align", "maq", "ssake", "velvet", "qiime", "infernal", "rnahybrid", "adun.app", "garlic", "gamgi", "gdpc", "ghemical", "jmol", "pymol", "r-other-bio3d", "massxpert", "gromacs", "rasmol", "modeller", "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", "autodocktools", "mustang", "theseus", "staden-io-lib-utils", "samtools", "bedtools", "filo", "gassst", "r-bioc-hilbertvis", "r-other-mott-happy", "seq-gen", "mira-assembler", "alien-hunter", "ncoils", "gentle", "gmap", "igv", "picard-tools", "acedb-other-dotter", "acedb-other-belvu", "acedb-other", "python-cogent", "paml", "ensembl", "mrbayes", "squizz", "clonalframe", "dssp", "jellyfish", "ballview", "pynast", "raxml", "mlv-smile", "cd-hit", "cufflinks", "r-bioc-cummerbund", "grinder", "jalview", "reprof", "tm-align", "norsnet", "norsp", "predictnls", "proftmb", "profbval", "profisis", "hhsuite", "ffindex", "sift", "neobio", "ray", "ugene", "logol-bin", "soapdenovo", "microbiomeutil", "chimeraslayer", "nast-ier", "wigeon", "trimmomatic", "aevol", "amos-assembler", "hawkeye", "anfo", "apollo", "aragorn", "axparafit", "axpcoords", "bamtools", "bagpipe", "bigsdb", "bitseq", "cdbfasta", "cinema", "clonalorigin", "cluster3", "crossbow", "cytoscape", "dazzle", "ecell", "edtsurf", "emmax", "fasttree", "fastqc", "flexbar", "forester", "freecontact", "genometools", "grabix", "grogui", "haploview", "hmmer2", "jbrowse", "kempbasu", "kissplice", "klust", "lagan", "ltrsift", "logomat-m", "mach-haplotyper", "macs", "mage2tab", "martj", "mauvealigner", "meme", "metastudent", "molekel", "mosaik-aligner", "mpsqed", "mrs", "mugsy", "murasaki", "ncbi-seg", "ngila", "nw-align", "oases", "pal2nal", "patman", "patristic", "pcma", "phyloviz-core", "plato", "prank", "predictprotein", "proalign", "pscan-tfbs", "psipred", "python-reaper", "r-bioc-rtracklayer", "r-bioc-gviz", "r-bioc-biostrings", "r-cran-vegan", "r-other-valdar-bagphenotype.library", "rdp-classifier", "rosetta", "sap", "sga", "seqtk", "sequenceconverter.app", "snpeff", "ssaha", "staden", "strap", "strap-base", "tacg", "treeview", "uc-echo", "vienna-rna", "vmd", "wgs-assembler", "zalign", "zodiac-zeden", "copycat", "btk-core", "asap", "cactus", "contralign", "concavity", "conservation-code", "galaxy", "genographer", "pftools", "phylographer", "phylowin", "gbioseq", "phpphylotree", "tracetuner", "twain", "rose", "glimmerhmm", "genezilla", "exalt", "jigsaw", "genesplicer", "mummergpu", "amoscmp", "minimus", "bambus", "gmv", "pyrophosphate-tools", "figaro", "mirbase", "elph", "uniprime", "genetrack", "operondb", "trnascan-se", "artemis", "act", "cdna-db", "das-proserver", "spice", "decipher", "est-db", "finex", "hexamer", "coot", "r-ape", "caftools", "roche454ace2caf", "big-blast", "blixem", "cap3", "coalesce", "estferret", "estscan", "fasta", "fluctuate", "lamarc", "lucy", "maxd", "mesquite", "migrate", "msatfinder", "mview", "oligoarrayaux", "omegamap", "partigene", "pfaat", "prot4est", "qtlcart", "rbs-finder", "recombine", "splitstree", "taverna", "taxinspector", "tetra", "trace2dbest", "profit", "obo-edit", "jstreeview", "phagefinder", "codonw", "compclust", "treebuilder3d", "excavator", "tigr-assembler", "treetime", "abacas", "profnet-bval", "profnet-chop", "profnet-con", "profnet-isis", "profnet-md", "profnet-norsnet", "profnet-prof", "profnet-snapfun", "profphd-net", "profphd-utils", "profphd", "abyss", "ampliconnoise", "disulfinder", "populations", "raccoon", "librg-utils-perl", "snap", "vcftools", "hilbertvisgui", "fas", "beads", "x-tandem-pipeline", "forge", "metarep", "smalt", "arachne", "maker2", "repeatmasker", "rmblast", "augustus", "e-hive", "cmap", "gbrowse-syn", "tripal", "genemark", "python-orange", "tigr-glimmer-mg"], "recommends": [], "avoid": []}, "his": {"ignore": [], "suggests": [], "depends": ["care2x", "fis-gtm", "vista", "ewd-920", "gnuhealth", "world-vista", "ipath", "patientos", "openmrs", "hkma-cms", "oscar-mcmaster", "openeyes"], "recommends": [], "avoid": []}, "dental": {"ignore": [], "suggests": [], "depends": ["openmolar", "imagetooth", "entangle"], "recommends": [], "avoid": []}, "practice": {"ignore": ["clearhealth"], "suggests": ["libctapimkt0", "openpms", "resmedicinae", "sqlclinic", "openrep"], "depends": ["gnumed-client", "gnumed-server", "libchipcard-tools", "ginkgocadx", "freediams", "freemedforms-emr", "r-cran-medadherence", 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"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", "libtfbs-perl", "libfreecontact0-dev", "libfreecontact-doc", "libgo-perl", "r-cran-genetics", "r-cran-haplo.stats", "octave-bioinfo", "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", "libsbml5-dev", "seqan-dev", "libbio-mage-utils-perl", "libchado-perl", "libpal-java", "libjebl2-java", "r-bioc-biobase", "libffindex0-dev", "librostlab3-dev", "librostlab-doc", "librostlab-blast0-dev", "librostlab-blast-doc", "librg-blast-parser-perl", "libsort-key-top-perl", "libhmsbeagle-dev", "libforester-java", "libbamtools-dev", "libbio-das-perl", "python-mmtk", "libopenmm4-dev", "libgenometools0-dev", "python-biom-format", "libgenome-perl", "libgenome-model-tools-music-perl", "pyfai", "python-htseq", "bioclipse", "biostrings", "iranges", "libgff-perl", "libmems-1.5-1", "python-pysam", "libgbfp-dev", "octace-bioinfo"], "recommends": [], "avoid": []}, "epi": {"ignore": [], "suggests": ["r-cran-msm", "repast"], "depends": ["epigrass", "r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi", "r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "netepi-analysis", "netepi-collection"], "recommends": [], "avoid": []}, "cms": {"ignore": [], "suggests": ["zope-zms", "xnat", "hid"], "depends": [], "recommends": [], "avoid": []}, "rehabilitation": {"ignore": [], "suggests": ["aghermann"], "depends": ["sitplus"], "recommends": [], "avoid": []}}
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