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# This file is autogenerated via make -f debian/rules dist. Do not edit!
Source: debian-med
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: misc
Priority: extra
Build-Depends-Indep: blends-dev (>= 0.6.92)
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/blends/projects/med/trunk/debian-med/
Vcs-Svn: svn://anonscm.debian.org/blends/projects/med/trunk/debian-med/
Package: med-tasks
Architecture: all
Depends: tasksel
Description: Debian Med tasks for tasksel
This package provides Debian Med tasks in tasksel.
.
These tasks are described in detail at
http://debian-med.alioth.debian.org/tasks/
Package: med-config
Architecture: all
Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.15)
Conflicts: med-common
Replaces: med-common
Provides: med-common
Description: Debian Med general config package
This package provides the basic infrastructure of all metapackages assembled
by the Debian Med team.
.
This metapackage provides common features shared between the different
metapackages of the project. Moreover it introduces a method to handle a
'med' system users group using debconf.
.
The Debian Med Project include metapackages for different tasks, which are:
* applications for microbiological research and support for development of
biological applications
* cloud computing in microbiological research
* drug databases
* dental surgery practice
* epidemiology and medical statistics
* image processing and support for imaging application development
* pharmacological research
* radiation oncology, diagnostic imaging and related fields
* medical practice
* psychological research and practice
* rehabilitation
* typesetting and publishing
* miscellaneous tools
.
Each task is represented by a metapackage. Metapackages do not contain
executable programs, but rather dependencies from other packages. This way
you will conveniently get all free medical software which is available for
Debian by simply installing the relevant metapackage
Package: med-bio
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: abacas,
acedb-other,
acedb-other-belvu,
acedb-other-dotter,
adun.app,
aevol,
alien-hunter,
altree,
amap-align,
ampliconnoise,
anfo,
aragorn,
arden,
autodock,
autodock-vina,
autogrid,
ballview,
bamtools,
bedtools,
biomaj,
blast2,
bowtie,
bowtie2,
boxshade,
bwa,
cassiopee,
cd-hit,
cdbfasta,
chimeraslayer,
circos,
clearcut,
clonalframe,
clustalo,
clustalw,
clustalx,
concavity,
conservation-code,
dialign,
dialign-tx,
discosnp,
disulfinder,
dnaclust,
dssp,
edtsurf,
embassy-domainatrix,
embassy-domalign,
embassy-domsearch,
emboss,
exonerate,
fastaq,
fastdnaml,
fastlink,
fastqc,
fasttree,
fastx-toolkit,
ffindex,
figtree,
filo,
fitgcp,
flexbar,
freecontact,
gamgi,
garlic,
gasic,
gbrowse,
gdpc,
genometools,
gentle,
gff2aplot,
gff2ps,
giira,
glam2,
grinder,
gromacs,
hhsuite,
hmmer,
hmmer2,
idba,
infernal,
ipig,
jalview,
jellyfish,
jmol,
kalign,
kissplice,
last-align,
librg-utils-perl,
logol-bin,
loki,
ltrsift,
macs,
mafft,
mapsembler2,
maq,
maqview,
massxpert,
melting,
metastudent,
microbiomeutil,
minia,
mipe,
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,
norsnet,
norsp,
openms,
paraclu,
parsinsert,
pdb2pqr,
perlprimer,
perm,
phylip,
phyml,
phyutility,
picard-tools,
plasmidomics,
plink,
poa,
populations,
prank,
predictnls,
predictprotein,
prime-phylo,
primer3,
proalign,
probabel,
probalign,
probcons,
proda,
prodigal,
profbval,
profisis,
profnet-bval,
profnet-chop,
profnet-con,
profnet-isis,
profnet-md,
profnet-norsnet,
profnet-prof,
profnet-snapfun,
profphd,
profphd-net,
profphd-utils,
proftmb,
pycorrfit,
pymol,
pynast,
pyscanfcs,
python-cogent,
qiime,
r-bioc-biostrings,
r-bioc-cummerbund,
r-bioc-gviz,
r-bioc-hilbertvis,
r-bioc-rtracklayer,
r-cran-ape,
r-cran-genabel,
r-cran-qtl,
r-cran-vegan,
r-other-bio3d,
r-other-mott-happy.hbrem,
rasmol,
raster3d,
rate4site,
raxml,
ray,
readseq,
relion-bin,
reprof,
rnahybrid,
rtax,
saint,
samtools,
seaview,
seqan-apps,
seqtk,
sibsim4,
sigma-align,
sim4,
smalt,
snap,
snp-sites,
soapdenovo,
soapdenovo2,
squizz,
sra-toolkit,
ssake,
staden,
staden-io-lib-utils,
t-coffee,
tabix,
theseus,
tigr-glimmer,
tm-align,
tophat,
topp,
transtermhp,
tree-puzzle | tree-ppuzzle,
treeviewx,
trimmomatic,
uc-echo,
vcftools,
velvet,
velvetoptimiser,
wigeon,
wise,
zalign
Suggests: abyss,
acacia,
act,
amos-assembler,
amoscmp,
apollo,
arachne,
arb,
artemis,
asap,
augustus,
autodocktools,
axparafit,
axpcoords,
bagpipe,
bambus,
beads,
beast-mcmc,
biceps,
big-blast,
bigsdb,
biomaj-watcher,
bitseq,
blat,
blimps-utils,
blixem,
btk-core,
cactus,
caftools,
cain,
cap3,
cdna-db,
cinema,
clonalorigin,
clustalw-mpi,
cluster3,
cmap,
coalesce,
codonw,
compclust,
contralign,
coot,
copycat,
crac,
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,
fasta,
figaro,
finex,
fluctuate,
forester,
forge,
freebayes,
fsa,
galaxy,
gassst,
gbioseq,
gbrowse-syn,
genemark,
genesplicer,
genetrack,
genezilla,
genographer,
ghemical,
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,
mpsqed,
msatfinder,
mugsy,
mummergpu,
murasaki,
mview,
ngila,
ngsqctoolkit,
nw-align,
oases,
obo-edit,
oligoarrayaux,
omegamap,
operondb,
pal2nal,
paml,
partigene,
patman,
patristic,
pcma,
pfaat,
pftools,
phagefinder,
phpphylotree,
phylographer,
phyloviz-core,
phylowin,
plato,
profit,
prot4est,
pscan-tfbs,
psipred,
pyrophosphate-tools,
python-orange,
python-reaper,
qtlcart,
r-cran-boolnet,
r-other-valdar-bagphenotype.library,
raccoon,
rbs-finder,
rdp-classifier,
recombine,
relion-bin-mpi,
relion-gui,
repeatmasker,
rmblast,
roche454ace2caf,
rose,
rosetta,
sap,
seq-gen,
sequenceconverter.app,
sga,
sift,
situs,
snpeff,
spades,
spice,
splitstree,
spread-phy,
ssaha,
strap,
strap-base,
tacg,
taverna,
taxinspector,
tetra,
tigr-assembler,
tigr-glimmer-mg,
trace2dbest,
tracetuner,
treebuilder3d,
treetime,
treeview,
tripal,
trnascan-se,
twain,
ugene,
unc-fish,
uniprime,
varscan,
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
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: bioperl,
bioperl-run,
biosquid,
libace-perl,
libai-fann-perl,
libbambamc-dev,
libbamtools-dev,
libbio-graphics-perl,
libbio-mage-perl,
libbio-mage-utils-perl,
libbio-primerdesigner-perl,
libbiococoa-dev,
libbiojava-java,
libbiojava3-java,
libchado-perl,
libffindex0-dev,
libfreecontact-perl,
libfreecontact0-dev,
libgenome-1.3-dev,
libgenome-model-tools-music-perl,
libgenome-perl,
libgenometools0-dev,
libgo-perl,
libhmsbeagle-dev,
libhts-dev,
libjebl2-java,
libncbi6-dev,
libnhgri-blastall-perl,
libopenms-dev,
libpal-java,
librcsb-core-wrapper0-dev,
librelion-dev,
librg-blast-parser-perl,
librg-reprof-bundle-perl,
librostlab-blast0-dev,
librostlab3-dev,
libsbml5-dev,
libsnp-sites1-dev,
libsort-key-top-perl,
libsrf-dev,
libssm-dev,
libstaden-read-dev,
libtfbs-perl,
libvibrant6-dev,
libzerg-perl,
libzerg0-dev,
mcl,
pyfai,
python-biom-format,
python-biopython | python3-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,
sbmltoolbox,
seqan-dev
Suggests: bioclipse,
libbio-das-perl,
libforester-java,
libfreecontact-doc,
libgbfp-dev,
libgff-perl,
libgtextutils-dev,
libmems-1.5-1,
librostlab-blast-doc,
librostlab-doc,
libswarm2-dev,
octace-bioinfo,
python-biopython-doc,
python-biopython-sql | python3-biopython-sql,
r-bioc-affy,
r-cran-rocr
Description: Debian Med packages for development of micro-biology applications
This metapackage will install Debian packages which might be helpful
for development of applications for micro-biological research.
Package: med-cloud
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: acedb-other,
aevol,
alien-hunter,
altree,
amap-align,
ampliconnoise,
anfo,
aragorn,
arden,
autodock,
autodock-vina,
autogrid,
bamtools,
bedtools,
biomaj,
bioperl,
bioperl-run,
biosquid,
blast2,
bowtie,
bowtie2,
boxshade,
bwa,
cain,
cassiopee,
cd-hit,
cdbfasta,
circos,
clearcut,
clonalframe,
concavity,
datamash,
discosnp,
disulfinder,
dnaclust,
dssp,
fastdnaml,
fastlink,
fastqc,
fasttree,
fastx-toolkit,
filo,
fitgcp,
flexbar,
freecontact,
gasic,
genometools,
giira,
grinder,
idba,
infernal,
kissplice,
last-align,
loki,
macs,
mapsembler2,
maq,
melting,
minia,
mipe,
mira-assembler,
mothur,
ncbi-epcr,
ncbi-tools-bin,
ncoils,
parsinsert,
perm,
phyml,
phyutility,
picard-tools,
plink,
primer3,
python-cogent,
rnahybrid,
rtax,
samtools,
smalt,
ssake,
tophat,
velvet
Suggests: abyss,
bagpipe,
cufflinks
Description: Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences, that do not
depend on graphical toolkits and therefore can fit on system images for use
in cloud computing clusters, where space can be limited.
Package: med-data
Section: metapackages
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
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: entangle,
imagetooth,
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
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: epigrass,
r-cran-diagnosismed,
r-cran-epi,
r-cran-epibasix,
r-cran-epicalc,
r-cran-epir,
r-cran-epitools,
r-cran-surveillance
Suggests: netepi-analysis,
netepi-collection,
r-cran-msm,
repast,
ushahidi
Description: Debian Med epidemiology related packages
This metapackage will install tools that are useful in epidemiological
research. Several packages making use of the GNU R data language for
statistical investigation. It might be a good idea to read the paper
"A short introduction to R for Epidemiology" at
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
Package: med-his
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: fis-gtm
Suggests: care2x,
ewd-920,
gnuhealth,
hkma-cms,
ipath,
openeyes,
openmrs,
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
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
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: aeskulap,
amide,
ants,
biosig-tools,
camitk-imp,
caret,
conquest-common,
ctn,
ctsim,
dcmtk,
dicom3tools,
dicomnifti,
dicomscope,
fslview,
gdf-tools,
ginkgocadx,
gofigure2,
gwyddion,
imagej,
imagevis3d,
invesalius,
itksnap,
king,
libgdcm-tools,
medcon,
mia-tools,
mia-viewit,
mialmpick,
minc-tools,
mriconvert,
mricron,
mrtrix,
nifti-bin,
odin,
openslide-tools,
orthanc,
pixelmed-apps,
plastimatch,
python-dicom,
python-dipy,
python-mvpa2,
python-nibabel,
python-nitime,
python-surfer,
sigviewer,
sofa-apps,
teem-apps,
voxbo,
vtk-dicom-tools,
xmedcon
Suggests: afni,
bioimagesuite,
bioimagexd,
blox,
brainvisa,
cdmedicpacs,
cellprofiler,
cmtk,
connectomeviewer,
conquest-dbase,
conquest-mysql,
conquest-postgres,
conquest-sqlite,
crea,
dcm4chee,
devide,
dicom4j,
dicoogle,
drjekyll,
dti-query,
dtitk,
ecg2png,
eeglab,
elastix,
fiji,
freesurfer,
fsl,
gimias,
hid,
imagemagick,
imview,
incf-nidash-oneclick-clients,
insightapplications,
isis,
jemris,
jist,
kradview,
libdcm4che-java,
lipsia,
maris,
mayam,
medisnap,
mesa-test-tools,
micromanager,
mipav,
miview,
mni-autoreg,
mni-colin27-nifti,
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
omero,
opendicom.net,
openelectrophy,
openmeeg-tools,
opensourcepacs,
openwalnut-qt4,
paraview,
piano,
pngquant,
pymeg,
python-nipy,
python-nipype,
python-pyxid,
slicer,
stabilitycalc,
stir,
tempo,
tifffile,
trimage,
via-bin,
visit,
vmtk,
volview,
xnat
Description: Debian Med imaging packages
This metapackage will install Debian packages which might be useful in
medical image processing.
.
It installs several packages supporting DICOM (Digital Imaging and
Communications in Medicine) which is the de-facto standard for medical
image management. The standard defines data structures and services for
the exchange of medical images and related information. The latest release
has been published in 2008 and consists of 18 parts.
.
For more information, you can visit the NEMA homepage
http://medical.nema.org/ .
.
The status of the official DICOM base standard plus all the
supplements and correction items are summarized at David Clunie's webpage:
http://www.dclunie.com/dicom-status/status.html
where you'll find direct links to the most recent yearly edition
ftp://medical.nema.org/medical/dicom/2008/ .
Package: med-imaging-dev
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: cimg-dev,
ctn-dev,
gmic,
libactiviz.net-cil,
libbiosig-dev,
libcamitk3-dev,
libcv-dev,
libedf-dev,
libgdcm2-dev,
libgdf-dev,
libgiftiio-dev,
libinsighttoolkit3-dev | libinsighttoolkit4-dev,
libmdc2-dev,
libmia-2.2-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,
octave-gdf,
odin,
python-casmoothing,
python-cfflib,
python-dicom,
python-dipy,
python-gdcm,
python-mia | python3-mia,
python-mne,
python-mvpa2,
python-nibabel,
python-nitime,
python-openslide,
python-pyxnat,
python-vigra,
r-cran-rniftilib
Suggests: emokit,
igstk-examples,
insighttoolkit3-examples,
libbio-formats-java,
libctk-dev,
libeegdev-dev,
libics-dev,
libigstk4-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,
python-libavg,
python-nipy,
python-nipype,
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
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: dicompyler
Suggests: planunc,
uw-prism
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
oncology.
Package: med-pharmacy
Section: metapackages
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
collection of software and documentation which is useful for
pharmaceutical research.
Package: med-physics
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: biosig-tools,
gdf-tools,
octave,
paw,
paw++,
r-base
Suggests: gate,
libbiosig-dev,
octave-biosig,
openvibe,
paw-demos,
python-biosig,
python-multipletau
Description: Debian Med packages for medical physicists
This metapackage contains dependencies for a
collection of software and documentation which is useful for
medical physicists in radiation oncology, diagnostics imaging
and related fields.
Package: med-practice
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: clinica,
entangle,
freediams,
freemedforms-emr,
ginkgocadx,
gnumed-client,
gnumed-server,
libchipcard-tools,
qrisk2,
r-cran-medadherence
Suggests: clearhealth,
elementalclinic,
elexis,
freeb,
freemed,
freeshim,
libctapimkt1,
medintux,
mirrormed,
mirth,
openemr,
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
Section: metapackages
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,
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
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends:
Suggests: aghermann,
sitplus
Description: Debian Med packages for rehabilitation technologies
This metapackage will install tools that are useful for
rehabilitation and therapy.
Package: med-statistics
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: r-bioc-edger,
r-bioc-limma,
r-bioc-qvalue,
r-cran-beeswarm,
r-cran-pvclust,
r-cran-randomforest
Suggests: science-statistics
Description: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
Package: med-tools
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: cronometer,
edfbrowser,
hunspell-de-med,
hunspell-en-med,
nut-nutrition,
pcalendar,
pondus,
python-clips,
python-fitbit,
quitcount,
wgerman-medical,
workrave
Suggests: cycle,
entangle,
goldencheetah,
mencal,
mssstest,
python3-fitbitscraper
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
Package: med-typesetting
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: king,
texlive-latex-extra,
texlive-science
Suggests: biber,
bibus,
jabref-plugin-oo,
kbibtex,
referencer
Description: Debian Med support for typesetting and publishing
This metapackage will install Debian packages that might be helpful
for typesetting and publishing in medical care and structural
biology.
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