[Blends-commit] [SCM] med branch, master, updated. a3178c464548deda36e64f97281ee70cdd148b0e
Michael R. Crusoe
michael.crusoe at gmail.com
Wed May 18 09:26:10 UTC 2016
The following commit has been merged in the master branch:
commit a3178c464548deda36e64f97281ee70cdd148b0e
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed May 18 02:24:31 2016 -0700
make dist
diff --git a/debian-med-tasks.desc b/debian-med-tasks.desc
index eceabf1..b7b623a 100644
--- a/debian-med-tasks.desc
+++ b/debian-med-tasks.desc
@@ -1,522 +1,91 @@
+Task: debian-med
+Relevance: 7
+Section: debian-med
+Description: Debian Med Pure Blend
+ .
+
Task: med-bio
+Parent: debian-med
Section: debian-med
-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.
-Relevance: 10
+Description: Debian Med bioinformatics packages
+ This metapackage will install Debian packages for use in molecular biology,
+ structural biology and other biological sciences.
Enhances: t-coffee
+Test-new-install: mark show
Key:
med-bio
-Packages: list
- abacas
- acedb-other
- acedb-other-belvu
- acedb-other-dotter
- aegean
- aevol
- alien-hunter
- altree
- amap-align
- ampliconnoise
- anfo
- aragorn
- arden
- autodock
- autodock-vina
- autogrid
- bamtools
- barrnap
- 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
- ecopcr
- edtsurf
- embassy-domainatrix
- embassy-domalign
- embassy-domsearch
- emboss
- exonerate
- fastaq
- fastdnaml
- fastlink
- fastqc
- fasttree
- fastx-toolkit
- ffindex
- figtree
- filo
- flexbar
- freecontact
- gamgi
- garlic
- gbrowse
- gdpc
- genometools
- gentle
- gff2aplot
- gff2ps
- ghemical
- giira
- glam2
- grinder
- gromacs
- gwama
- hhsuite
- hmmer
- hmmer2
- hyphy-mpi
- hyphygui
- idba
- infernal
- ipig
- jalview
- jellyfish
- jmol
- kalign
- kissplice
- kmer
- last-align
- librg-utils-perl
- logol-bin
- loki
- ltrsift
- macs
- macsyfinder
- mafft
- mapsembler2
- maq
- maqview
- massxpert
- mauve-aligner
- melting
- metastudent
- microbegps
- microbiomeutil
- minia
- mipe
- mira-assembler
- mlv-smile
- mothur
- mrbayes
- mrs
- mummer
- murasaki
- muscle
- mustang
- nast-ier
- ncbi-blast+
- ncbi-epcr
- ncbi-seg
- ncbi-tools-bin
- ncbi-tools-x11
- ncoils
- neobio
- njplot
- norsnet
- norsp
- 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
- progressivemauve
- pycorrfit
- pymol
- pynast
- pyscanfcs
- python-cogent
- qiime
- r-bioc-annotate
- r-bioc-biostrings
- r-bioc-cummerbund
- r-bioc-edger
- r-bioc-genefilter
- r-bioc-gviz
- r-bioc-hilbertvis
- r-bioc-limma
- r-bioc-rtracklayer
- r-cran-ape
- r-cran-genabel
- r-cran-phangorn
- r-cran-qtl
- r-cran-seqinr
- r-cran-vegan
- r-other-bio3d
- r-other-mott-happy.hbrem
- rasmol
- raster3d
- rate4site
- raxml
- ray
- rdp-alignment
- rdp-classifier
- rdp-readseq
- readseq
- relion-bin
- relion-bin+gui
- reprof
- rna-star
- rnahybrid
- rtax
- saint
- samtools
- scythe
- seaview
- seqan-apps
- seqtk
- sibsim4
- sickle
- sigma-align
- sim4
- smalt
- snap
- snp-sites
- soapdenovo
- soapdenovo2
- spread-phy
- squizz
- sra-toolkit
- ssake
- staden
- staden-io-lib-utils
- subread
- sumatra
- swarm
- t-coffee
- tabix
- theseus
- tigr-glimmer
- tm-align
- tophat
- toppred
- transdecoder
- transtermhp
- tree-puzzle
- treeviewx
- trimmomatic
- uc-echo
- vcftools
- velvet
- velvetoptimiser
- vsearch
- wigeon
- wise
- zalign
Task: med-bio-dev
+Parent: debian-med
Section: debian-med
-Description: Debian Med packages for development of micro-biology applications
+Description: Debian Med packages for development of bioinformatics applications
This metapackage will install Debian packages which might be helpful
- for development of applications for micro-biological research.
-Relevance: 10
+ for development of applications for biological research.
+Test-new-install: mark show
Key:
med-bio-dev
-Packages: list
- 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
- libbiojava4-java
- libchado-perl
- libdivsufsort-dev
- 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
- libkmer-dev
- libmems-1.6-dev
- libmuscle-3.7-dev
- libncbi6-dev
- libnhgri-blastall-perl
- libpal-java
- librcsb-core-wrapper0-dev
- librdp-taxonomy-tree-java
- 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
- python-cobra
- python-cogent
- python-corepywrap
- python-csb
- python-freecontact
- python-htseq
- python-mmtk
- python-rdkit
- python-screed
- python3-hyphy
- python3-ruffus
- r-bioc-biobase
- r-cran-genetics
- r-cran-haplo.stats
- ruby-bio
- sbmltoolbox
- seqan-dev
Task: med-bio-ngs
+Parent: debian-med
Section: debian-med
Description: Debian Med bioinformatics applications usable in Next Generation Sequencing
It aims at gettting packages which specializes in alignment of
sequences produced by next generation sequencing.
-Relevance: 10
-Packages: list
- kissplice
- mira-assembler
- mothur
- qiime
- uc-echo
+Test-new-install: mark show
Task: med-bio-phylogeny
+Parent: debian-med
Section: debian-med
Description: Debian Med phylogeny packages
This lists Debian packages related to phylogeny for use in life sciences.
The purpose of this compilation of packages is to have a handy subset of
from the med-bio metapackage which contains a lot more than only phylogeny
related software.
-Relevance: 10
-Packages: list
- altree
- clustalw
- clustalx
- dialign
- dialign-tx
- exonerate
- fastdnaml
- figtree
- hmmer
- kalign
- mrbayes
- muscle
- mustang
- njplot
- phylip
- phyml
- poa
- populations
- proalign
- probalign
- probcons
- proda
- seaview
- sigma-align
- spread-phy
- t-coffee
- tm-align
- tree-puzzle
- treeviewx
+Test-new-install: mark show
Task: med-cloud
+Parent: debian-med
Section: debian-med
Description: Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences, that do not
depend on graphical toolkits and therefore can fit on system images for use
in cloud computing clusters, where space can be limited.
-Relevance: 10
+Test-new-install: mark show
Key:
med-cloud
-Packages: list
- 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
- flexbar
- freecontact
- 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
Task: med-cms
+Parent: debian-med
Section: debian-med
Description: Debian Med content management systems
Here you can find software that is useful to build a
content management system for medical care.
-Relevance: 10
-Packages: list
+Test-new-install: mark show
Task: med-data
+Parent: debian-med
Section: debian-med
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.
-Relevance: 10
+Test-new-install: mark show
Key:
med-data
-Packages: list
- freediams
- freemedforms-freedata
- python-hl7
Task: med-dental
+Parent: debian-med
Section: debian-med
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.
-Relevance: 10
+Test-new-install: mark show
Key:
med-dental
-Packages: list
- imagetooth
- openmolar
Task: med-epi
+Parent: debian-med
Section: debian-med
Description: Debian Med epidemiology related packages
This metapackage will install tools that are useful in epidemiological
@@ -524,21 +93,12 @@ Description: Debian Med epidemiology related packages
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
-Relevance: 10
+Test-new-install: mark show
Key:
med-epi
-Packages: list
- epigrass
- r-cran-diagnosismed
- r-cran-epi
- r-cran-epibasix
- r-cran-epicalc
- r-cran-epir
- r-cran-epitools
- r-cran-seroincidence
- r-cran-surveillance
Task: med-his
+Parent: debian-med
Section: debian-med
Description: Debian Med suggestions for Hospital Information Systems
This metapackage contains dependencies for software and that could
@@ -546,13 +106,12 @@ Description: Debian Med suggestions for Hospital Information Systems
continuous work going on to package a ready to install system currently
only preconditions are finished but hopefully helpful in hospitals
anyway.
-Relevance: 10
+Test-new-install: mark show
Key:
med-his
-Packages: list
- fis-gtm
Task: med-imaging
+Parent: debian-med
Section: debian-med
Description: Debian Med image processing and visualization packages
This metapackage will install Debian packages which might be useful in
@@ -565,263 +124,122 @@ Description: Debian Med image processing and visualization packages
software packages that can be used for visualization and for image processing
- either from a graphical user interface, the command line, or implemented in
workflows.
-Relevance: 10
+Test-new-install: mark show
Key:
med-imaging
-Packages: list
- aeskulap
- amide
- biosig-tools
- caret
- conquest-common
- ctn
- ctsim
- dcmtk
- dicom3tools
- dicomnifti
- dicomscope
- fslview
- gdf-tools
- gwyddion
- imagej
- imagevis3d
- invesalius
- ismrmrd-tools
- 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-mvpa2
- python-nibabel
- python-nipy
- python-nipype
- python-surfer
- sigviewer
- sofa-apps
- teem-apps
- voxbo
- vtk-dicom-tools
- xmedcon
- python-dipy
- python-nitime
Task: med-imaging-dev
+Parent: debian-med
Section: debian-med
Description: Debian Med image processing and visualization packages development
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing and
visualization.
-Relevance: 10
+Test-new-install: mark show
Key:
med-imaging-dev
-Packages: list
- cimg-dev
- ctn-dev
- gmic
- libactiviz.net-cil
- libbiosig-dev
- libcv-dev
- libedf-dev
- libgdcm2-dev
- libgdf-dev
- libgiftiio-dev
- libinsighttoolkit3-dev
- libismrmrd-dev
- libmaxflow-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
- libvtk-dicom-java
- libvtk-dicom0.5-dev
- libvtk5-dev
- libvxl1-dev
- octave-gdf
- odin
- python-casmoothing
- python-cfflib
- python-dicom
- python-dipy
- python-gdcm
- python-mia
- python-mne
- python-mvpa2
- python-nibabel
- python-nipy
- python-nipype
- python-nitime
- python-openslide
- python-pyxnat
- python-vigra
- r-cran-rniftilib
Task: med-laboratory
+Parent: debian-med
Section: debian-med
Description: Debian Med suggestions for medical laboratories
This metapackage contains dependencies for software and that could
be useful ro run a medical laboratory.
-Relevance: 10
+Test-new-install: mark show
Key:
med-laboratory
-Packages: list
- opencfu
Task: med-oncology
+Parent: debian-med
Section: debian-med
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
oncology.
-Relevance: 10
+Test-new-install: mark show
Key:
med-oncology
-Packages: list
- dicompyler
Task: med-pharmacy
+Parent: debian-med
Section: debian-med
Description: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
collection of software and documentation which is useful for
pharmaceutical research.
-Relevance: 10
+Test-new-install: mark show
Key:
med-pharmacy
-Packages: list
- chemtool
- r-cran-dosefinding
Task: med-physics
+Parent: debian-med
Section: debian-med
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.
-Relevance: 10
+Test-new-install: mark show
Key:
med-physics
-Packages: list
- biosig-tools
- gdf-tools
- octave
- paw
- paw++
- r-base
Task: med-practice
+Parent: debian-med
Section: debian-med
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.
-Relevance: 10
+Test-new-install: mark show
Key:
med-practice
-Packages: list
- freediams
- freemedforms-emr
- gnumed-client
- gnumed-server
- libchipcard-tools
- qrisk2
- r-cran-medadherence
Task: med-psychology
+Parent: debian-med
Section: debian-med
Description: Debian Med packages for psychology
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
-Relevance: 10
+Test-new-install: mark show
Key:
med-psychology
-Packages: list
- praat
- psignifit
- psychopy
- python-pyepl
- r-cran-foreign
- r-cran-psy
Task: med-rehabilitation
+Parent: debian-med
Section: debian-med
Description: Debian Med packages for rehabilitation technologies
This metapackage will install tools that are useful for
rehabilitation and therapy.
-Relevance: 10
+Test-new-install: mark show
Key:
med-rehabilitation
-Packages: list
- sitplus
Task: med-statistics
+Parent: debian-med
Section: debian-med
Description: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
-Relevance: 10
+Test-new-install: mark show
Key:
med-statistics
-Packages: list
- r-bioc-edger
- r-bioc-limma
- r-bioc-qvalue
- r-cran-beeswarm
- r-cran-pvclust
- r-cran-randomforest
Task: med-tools
+Parent: debian-med
Section: debian-med
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.
-Relevance: 10
+Test-new-install: mark show
Key:
med-tools
-Packages: list
- cronometer
- edfbrowser
- hunspell-de-med
- hunspell-en-med
- nut-nutrition
- pcalendar
- pondus
- python-clips
- python-fitbit
- quitcount
- wgerman-medical
- workrave
Task: med-typesetting
+Parent: debian-med
Section: debian-med
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.
-Relevance: 10
+Test-new-install: mark show
Key:
med-typesetting
-Packages: list
- king
- texlive-latex-extra
- texlive-science
diff --git a/debian/control b/debian/control
index 78fa5ee..1e61f01 100644
--- a/debian/control
+++ b/debian/control
@@ -5,9 +5,9 @@ Uploaders: Andreas Tille <tille at debian.org>
Section: misc
Priority: extra
Build-Depends-Indep: blends-dev (>= 0.6.92.3)
-Standards-Version: 3.9.6
+Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/blends/projects/med.git
-Vcs-Git: git://anonscm.debian.org/blends/projects/med.git
+Vcs-Git: https://anonscm.debian.org/git/blends/projects/med.git
Package: med-tasks
Architecture: all
@@ -53,6 +53,32 @@ Description: Debian Med general config package
you will conveniently get all free medical software which is available for
Debian by simply installing the relevant metapackage
+Package: med-all
+Section: metapackages
+Architecture: all
+Recommends: med-bio,
+ med-bio-dev,
+ med-cloud,
+ med-data,
+ med-dental,
+ med-epi,
+ med-his,
+ med-imaging,
+ med-imaging-dev,
+ med-laboratory,
+ med-oncology,
+ med-pharmacy,
+ med-physics,
+ med-practice,
+ med-psychology,
+ med-rehabilitation,
+ med-statistics,
+ med-tools,
+ med-typesetting
+Description: Default selection of tasks for Debian Med
+ This package is part of the Debian Med Pure Blend and installs all
+ tasks for a default installation of this blend.
+
Package: med-bio
Section: metapackages
Architecture: all
@@ -61,45 +87,65 @@ Recommends: abacas,
acedb-other,
acedb-other-belvu,
acedb-other-dotter,
+ adun-core,
aegean,
aevol,
alien-hunter,
+ alter-sequence-alignment,
altree,
amap-align,
ampliconnoise,
- anfo,
+ andi,
aragorn,
- arden,
+ artemis,
+ artfastqgenerator,
+ augustus,
autodock,
autodock-vina,
autogrid,
+ axe-demultiplexer,
bamtools,
barrnap,
+ bcftools,
+ beagle,
bedtools,
+ berkeley-express,
+ bio-rainbow,
biomaj,
+ blasr,
blast2,
bowtie,
bowtie2,
boxshade,
+ brig,
bwa,
cassiopee,
cd-hit,
cdbfasta,
+ cgview,
chimeraslayer,
+ circlator,
circos,
clearcut,
clonalframe,
clustalo,
clustalw,
clustalx,
+ codonw,
concavity,
conservation-code,
+ daligner,
+ dawg,
+ dazzdb,
dialign,
dialign-tx,
+ dindel,
discosnp,
disulfinder,
dnaclust,
dssp,
+ dwgsim,
+ ea-utils,
ecopcr,
edtsurf,
embassy-domainatrix,
@@ -107,19 +153,23 @@ Recommends: abacas,
embassy-domsearch,
emboss,
exonerate,
+ falconkit,
fastaq,
fastdnaml,
fastlink,
+ fastml,
fastqc,
fasttree,
fastx-toolkit,
ffindex,
figtree,
filo,
+ fitgcp,
flexbar,
freecontact,
gamgi,
garlic,
+ gasic,
gbrowse,
gdpc,
genometools,
@@ -131,22 +181,34 @@ Recommends: abacas,
glam2,
grinder,
gromacs,
+ gubbins,
gwama,
+ harvest-tools,
hhsuite,
hmmer,
hmmer2,
hyphy-mpi | hyphy-pt,
hyphygui,
idba,
+ indelible,
infernal,
ipig,
+ iqtree,
+ iva,
+ jaligner,
jalview,
jellyfish,
jmol,
kalign,
+ khmer,
+ kineticstools,
+ king-probe,
kissplice,
+ kmc,
kmer,
+ kraken,
last-align,
+ leaff,
librg-utils-perl,
logol-bin,
loki,
@@ -154,32 +216,36 @@ Recommends: abacas,
macs,
macsyfinder,
mafft,
- mapsembler2,
maq,
maqview,
massxpert,
mauve-aligner,
melting,
+ meryl,
metastudent,
+ mhap,
microbegps,
microbiomeutil,
minia,
+ miniasm,
+ minimap,
mipe,
mira-assembler,
mlv-smile,
mothur,
mrbayes,
- mrs,
mummer,
murasaki,
muscle,
mustang,
+ nanopolish,
nast-ier,
ncbi-blast+,
ncbi-epcr,
ncbi-seg,
ncbi-tools-bin,
ncbi-tools-x11,
+ ncl-tools,
ncoils,
neobio,
njplot,
@@ -187,17 +253,32 @@ Recommends: abacas,
norsp,
paraclu,
parsinsert,
+ pbalign,
+ pbbarcode,
+ pbdagcon,
+ pbgenomicconsensus,
+ pbhoney,
+ pbjelly,
+ pbsim,
+ pbsuite,
pdb2pqr,
perlprimer,
perm,
+ phybin,
phylip,
phyml,
phyutility,
picard-tools,
+ piler,
+ placnet,
plasmidomics,
+ plast,
plink,
+ plink1.9,
+ plip,
poa,
populations,
+ poretools,
prank,
predictnls,
predictprotein,
@@ -224,15 +305,17 @@ Recommends: abacas,
profphd-utils,
proftmb,
progressivemauve,
+ proteinortho,
+ prottest,
pycorrfit,
pymol,
pynast,
pyscanfcs,
python-cogent,
- qiime,
r-bioc-annotate,
r-bioc-biostrings,
r-bioc-cummerbund,
+ r-bioc-ebseq,
r-bioc-edger,
r-bioc-genefilter,
r-bioc-gviz,
@@ -240,12 +323,12 @@ Recommends: abacas,
r-bioc-limma,
r-bioc-rtracklayer,
r-cran-ape,
+ r-cran-bio3d,
r-cran-genabel,
r-cran-phangorn,
r-cran-qtl,
r-cran-seqinr,
r-cran-vegan,
- r-other-bio3d,
r-other-mott-happy.hbrem,
rasmol,
raster3d,
@@ -256,51 +339,76 @@ Recommends: abacas,
rdp-classifier,
rdp-readseq,
readseq,
+ reapr,
relion-bin | relion-bin+mpi,
relion-bin+gui | relion-bin+mpi+gui,
+ repeatmasker-recon,
reprof,
rna-star,
rnahybrid,
+ roary,
+ rsem,
rtax,
saint,
+ salmon,
samtools,
+ scrm,
scythe,
seaview,
+ seer,
seqan-apps,
+ seqprep,
seqtk,
sibsim4,
sickle,
sigma-align,
sim4,
+ sim4db,
smalt,
snap,
+ snap-aligner,
snp-sites,
+ snpomatic,
soapdenovo,
soapdenovo2,
+ sortmerna,
+ spaced,
+ spades,
+ sprai,
spread-phy,
squizz,
sra-toolkit,
ssake,
+ stacks,
staden,
staden-io-lib-utils,
subread,
+ suitename,
+ sumaclust,
sumatra,
+ sumtrees,
+ surankco,
swarm,
t-coffee,
tabix,
+ tantan,
theseus,
tigr-glimmer,
tm-align,
tophat,
toppred,
transdecoder,
+ transrate-tools,
transtermhp,
tree-puzzle | tree-ppuzzle,
+ treeview,
treeviewx,
trimmomatic,
+ trinityrnaseq,
uc-echo,
+ varna,
vcftools,
- velvet,
+ velvet | velvet-long,
velvetoptimiser,
vsearch,
wigeon,
@@ -308,19 +416,18 @@ Recommends: abacas,
zalign
Suggests: abyss,
acacia,
- act,
- adun-core,
adun.app,
amos-assembler,
amoscmp,
+ anfo,
apollo,
arachne,
arb,
- artemis,
+ arden,
+ ariba,
+ art-nextgen-simulation-tools,
asap,
- augustus,
autodocktools,
- axe-demultiplexer,
axparafit,
axpcoords,
bagpipe,
@@ -328,14 +435,11 @@ Suggests: abyss,
bambus,
beads,
beast-mcmc,
- berkeley-express,
biceps,
big-blast,
bigsdb,
- bio-rainbow,
biomaj-watcher,
bitseq,
- blasr,
blat,
blimps-utils,
blixem,
@@ -343,29 +447,28 @@ Suggests: abyss,
cactus,
caftools,
cain,
+ canu,
cap3,
cdna-db,
cinema,
clonalorigin,
- clustalw-mpi,
cluster3,
cmap,
coalesce,
- codonw,
compclust,
+ condetri,
contralign,
coot,
copycat,
crac,
crossbow,
+ crux-toolkit,
cufflinks,
cytoscape,
- daligner,
das-proserver,
dazzle,
decipher,
e-hive,
- ea-utils,
ecell,
eigensoft,
elph,
@@ -381,17 +484,18 @@ Suggests: abyss,
excavator,
fasta,
fasta3,
- fastml2,
+ fastqtl,
+ ffp,
figaro,
finex,
- fitgcp,
fluctuate,
forester,
forge,
freebayes,
fsa,
+ fsm-lite,
galaxy,
- gasic,
+ garli,
gassst,
gatk,
gbioseq,
@@ -406,29 +510,29 @@ Suggests: abyss,
gmv,
grabix,
grogui,
- gubbins,
haploview,
hawkeye,
hexamer,
hilbertvisgui,
htqc,
igv,
- iqtree,
- iva,
- jaligner,
+ inspect,
jbrowse,
jigsaw,
+ jmodeltest,
jstreeview,
kclust,
kempbasu,
- khmer,
lagan,
lamarc,
+ lofreq,
logomat-m,
lucy,
mach-haplotyper,
+ maffilter,
mage2tab,
maker2,
+ mapsembler2,
martj,
maude,
maxd,
@@ -439,7 +543,6 @@ Suggests: abyss,
metastudent-data,
metastudent-data-2,
metastudent-data-3,
- mhap,
migrate,
minimus,
mirbase,
@@ -450,10 +553,12 @@ Suggests: abyss,
molekel,
mosaik-aligner,
mpsqed,
+ mrs,
msatfinder,
mugsy,
mummergpu,
mview,
+ ncbi-entrez-direct,
ngila,
ngsqctoolkit,
nw-align,
@@ -466,80 +571,77 @@ Suggests: abyss,
operondb,
pal2nal,
paml,
+ parsnp,
partigene,
+ partitionfinder,
patman,
patristic,
- pbdagcon,
pcma,
pfaat,
pftools,
phagefinder,
+ phast,
+ phipack,
phpphylotree,
phylographer,
phyloviz-core,
phylowin,
+ pipasic,
plato,
- plip,
profit,
prokka,
prot4est,
pscan-tfbs,
psipred,
+ pssh2,
pyrophosphate-tools,
- python-kineticstools,
python-orange,
- python-pbalign,
python-reaper,
+ qiime,
qtlcart,
- r-bioc-ebseq,
+ qualimap,
+ r-bioc-aroma.light,
r-cran-boolnet,
r-cran-metamix,
+ r-cran-treescape,
r-other-apmswapp,
r-other-valdar-bagphenotype.library,
- r8s,
raccoon,
+ rambo-k,
rbs-finder,
recombine,
repeatmasker,
- repeatmasker-recon,
rmblast,
+ roadtrips,
roche454ace2caf,
rose,
rosetta,
- rsem,
sap,
+ science-workflow,
seq-gen,
- seqprep,
sequenceconverter.app,
sga,
sift,
situs,
smrtanalysis,
snpeff,
- sortmerna,
- spades,
spice,
splitstree,
+ srst2,
ssaha,
- stacks,
strap,
strap-base,
- suitename,
- sumtrees,
tacg,
- tantan,
taverna,
taxinspector,
tetra,
- tigr-assembler,
+ tide,
tigr-glimmer-mg,
topp,
trace2dbest,
tracetuner,
treebuilder3d,
treetime,
- treeview,
- trinityrnaseq,
tripal,
trnascan-se,
twain,
@@ -549,13 +651,11 @@ Suggests: abyss,
varscan,
vienna-rna,
vmd,
- wgs-assembler,
- wgsim,
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.
+Description: Debian Med bioinformatics packages
+ This metapackage will install Debian packages for use in molecular biology,
+ structural biology and other biological sciences.
Package: med-bio-dev
Section: metapackages
@@ -568,6 +668,7 @@ Recommends: bioperl,
libai-fann-perl,
libbambamc-dev,
libbamtools-dev,
+ libbio-das-lite-perl,
libbio-graphics-perl,
libbio-mage-perl,
libbio-mage-utils-perl,
@@ -576,25 +677,45 @@ Recommends: bioperl,
libbiojava-java,
libbiojava3-java,
libbiojava4-java,
+ libblasr-dev,
+ libbpp-core-dev,
+ libbpp-phyl-dev,
+ libbpp-phyl-omics-dev,
+ libbpp-popgen-dev,
+ libbpp-qt-dev,
+ libbpp-raa-dev,
+ libbpp-seq-dev,
+ libbpp-seq-omics-dev,
libchado-perl,
libdivsufsort-dev,
+ libfast5-dev,
libffindex0-dev,
libfreecontact-perl,
- libfreecontact0-dev,
libgenome-1.3-dev,
libgenome-model-tools-music-perl,
libgenome-perl,
libgenometools0-dev,
+ libgff-dev,
libgo-perl,
libhmsbeagle-dev,
libhts-dev,
+ libhtsjdk-java,
libjebl2-java,
libkmer-dev,
libmems-1.6-dev,
+ libminimap-dev,
libmuscle-3.7-dev,
libncbi6-dev,
+ libncl-dev,
+ libngs-java,
+ libngs-sdk-dev,
libnhgri-blastall-perl,
libpal-java,
+ libpbbam-dev,
+ libpbdata-dev,
+ libpbihdf-dev,
+ libpbseq-dev,
+ libqes-dev,
librcsb-core-wrapper0-dev,
librdp-taxonomy-tree-java,
librelion-dev,
@@ -608,62 +729,77 @@ Recommends: bioperl,
libsrf-dev,
libssm-dev,
libstaden-read-dev,
+ libtabixpp-dev,
libtfbs-perl,
libvibrant6-dev,
libzerg-perl,
libzerg0-dev,
mcl,
pyfai,
- python-biom-format,
- python-biopython | python3-biopython,
python-cobra,
python-cogent,
python-corepywrap,
- python-csb | python3-csb,
python-freecontact,
- python-htseq,
- python-mmtk,
- python-rdkit,
+ python-kineticstools,
+ python-ngs,
+ python-pbcommand,
+ python-pbcore,
+ python-pbh5tools,
+ python-pysam,
python-screed,
+ python3-biopython | python-biopython,
+ python3-csb | python-csb,
+ python3-cutadapt | python-cutadapt,
+ python3-dendropy | python-dendropy,
python3-hyphy | python-hyphy,
+ python3-ngs,
+ python3-pbconsensuscore | python-pbconsensuscore,
+ python3-pyfaidx | python-pyfaidx,
+ python3-pymummer,
+ python3-pyvcf | python-pyvcf,
python3-ruffus | python-ruffus,
r-bioc-biobase,
r-cran-genetics,
r-cran-haplo.stats,
+ r-cran-rncl,
+ r-cran-rnexml,
ruby-bio,
+ ruby-crb-blast,
sbmltoolbox,
seqan-dev
Suggests: bioclipse,
- libbio-das-perl,
+ libbam-dev,
libforester-java,
libfreecontact-doc,
- libgbfp-dev,
+ libfreecontact0-dev,
libgff-perl,
libgtextutils-dev,
libopenms-dev,
+ libqcpp-dev,
librostlab-blast-doc,
librostlab-doc,
libswarm2-dev,
- libtabixpp,
libvcflib,
octace-bioinfo,
+ octave-bioinfo,
+ python-biom-format,
python-biopython-doc,
- python-biopython-sql | python3-biopython-sql,
- python-cutadapt,
- python-dendropy,
+ python-htseq,
+ python-intervaltree-bio,
python-miso,
- python-pbcore,
- python-pbh5tools,
- python-pysam,
+ python-mmtk,
+ python-pyfasta,
+ python-rdkit,
python-skbio,
- python3-cutadapt,
- python3-dendropy,
+ python3-biopython-sql | python-biopython-sql,
+ python3-intervaltree-bio,
+ python3-pyfasta,
python3-skbio,
r-bioc-affy,
r-cran-rocr
-Description: Debian Med packages for development of micro-biology applications
+Description: Debian Med packages for development of bioinformatics applications
This metapackage will install Debian packages which might be helpful
- for development of applications for micro-biological research.
+ for development of applications for biological research.
Package: med-cloud
Section: metapackages
@@ -675,9 +811,7 @@ Recommends: acedb-other,
altree,
amap-align,
ampliconnoise,
- anfo,
aragorn,
- arden,
autodock,
autodock-vina,
autogrid,
@@ -711,8 +845,10 @@ Recommends: acedb-other,
fasttree,
fastx-toolkit,
filo,
+ fitgcp,
flexbar,
freecontact,
+ gasic,
genometools,
giira,
grinder,
@@ -722,7 +858,6 @@ Recommends: acedb-other,
last-align,
loki,
macs,
- mapsembler2,
maq,
melting,
minia,
@@ -748,10 +883,11 @@ Recommends: acedb-other,
tophat,
velvet
Suggests: abyss,
+ anfo,
+ arden,
bagpipe,
cufflinks,
- fitgcp,
- gasic
+ mapsembler2
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
@@ -765,7 +901,8 @@ Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: freediams,
freemedforms-freedata,
python-hl7
-Suggests: drugref.org
+Suggests: drugref.org,
+ sleepyhead
Description: Debian Med drug databases
This metapackage will install free drug databases and related
applications. The database can be accessed by any EMR using
@@ -775,9 +912,9 @@ Package: med-dental
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: imagetooth,
+Recommends: entangle,
+ imagetooth,
openmolar
-Suggests: entangle
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.
@@ -797,6 +934,7 @@ Recommends: epigrass,
r-cran-surveillance
Suggests: netepi-analysis,
netepi-collection,
+ r-cran-cmprsk,
r-cran-msm,
repast,
ushahidi
@@ -817,6 +955,7 @@ Suggests: care2x,
hkma-cms,
ipath,
openeyes,
+ openmaxims,
openmrs,
oscar-mcmaster,
patientos,
@@ -836,8 +975,10 @@ Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: aeskulap,
amide,
+ ants,
+ bart,
biosig-tools,
- caret,
+ camitk-imp,
conquest-common,
ctn,
ctsim,
@@ -845,13 +986,13 @@ Recommends: aeskulap,
dicom3tools,
dicomnifti,
dicomscope,
- fslview,
gdf-tools,
+ ginkgocadx,
gwyddion,
imagej,
imagevis3d,
- invesalius,
ismrmrd-tools,
+ itksnap,
king,
libgdcm-tools,
medcon,
@@ -860,7 +1001,6 @@ Recommends: aeskulap,
mialmpick,
minc-tools,
mriconvert,
- mricron,
mrtrix,
nifti-bin,
odin,
@@ -872,23 +1012,19 @@ Recommends: aeskulap,
python-dipy,
python-mvpa2,
python-nibabel,
- python-nipy,
- python-nipype,
python-nitime,
python-surfer,
sigviewer,
- sofa-apps,
teem-apps,
voxbo,
vtk-dicom-tools,
xmedcon
Suggests: afni,
- ants,
bioimagesuite,
bioimagexd,
blox,
brainvisa,
- camitk-imp,
+ caret,
cdmedicpacs,
cellprofiler,
cmtk,
@@ -911,16 +1047,17 @@ Suggests: afni,
fiji,
freesurfer,
fsl,
+ fslview,
+ fw4spl,
gimias,
- ginkgocadx,
gofigure2,
hid,
imagemagick,
imview,
incf-nidash-oneclick-clients,
insightapplications,
+ invesalius,
isis,
- itksnap,
jemris,
jist,
kradview,
@@ -937,6 +1074,7 @@ Suggests: afni,
mni-colin27-nifti,
mni-icbm152-nlin-2009,
mni-n3,
+ mricron,
mrisim,
omero,
opendicom.net,
@@ -944,13 +1082,20 @@ Suggests: afni,
openmeeg-tools,
opensourcepacs,
openwalnut-qt4,
+ orthanc-dicomweb,
+ orthanc-imagej,
+ orthanc-postgresql,
orthanc-webviewer,
paraview,
piano,
pngquant,
pymeg,
+ python-nipy,
+ python-nipype,
python-pyxid,
+ science-workflow,
slicer,
+ sofa-apps,
stabilitycalc,
stir,
tempo,
@@ -965,20 +1110,13 @@ Description: Debian Med image processing and visualization packages
This metapackage will install Debian packages which might be useful in
medical image processing and visualization.
.
- It installs several packages supporting DICOM (Digital Imaging and
+ On one hand, it installs several packages supporting various image file
+ formats and image management, like 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/ .
+ image management, and NIFTI. On the other hand, it provides a variety of
+ software packages that can be used for visualization and for image processing
+ - either from a graphical user interface, the command line, or implemented in
+ workflows.
Package: med-imaging-dev
Section: metapackages
@@ -987,14 +1125,14 @@ Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: cimg-dev,
ctn-dev,
gmic,
- libactiviz.net-cil,
+ libbart-dev,
libbiosig-dev,
libcv-dev,
libedf-dev,
libgdcm2-dev,
libgdf-dev,
libgiftiio-dev,
- libinsighttoolkit3-dev | libinsighttoolkit4-dev,
+ libinsighttoolkit4-dev,
libismrmrd-dev,
libmaxflow-dev,
libmdc2-dev,
@@ -1003,16 +1141,17 @@ Recommends: cimg-dev,
libmiaviewit-dev,
libminc-dev,
libnifti-dev,
+ libodil0-dev,
libopenslide-dev,
+ libopensurgsim-dev,
libpapyrus3-dev,
libteem-dev,
libvigraimpex-dev,
libvistaio-dev,
libvolpack1-dev,
- libvtk-dicom-java,
- libvtk-dicom0.5-dev,
- libvtk5-dev,
+ libvtk6-dev,
libvxl1-dev,
+ octave-bart,
octave-gdf,
odin,
python-casmoothing,
@@ -1024,8 +1163,6 @@ Recommends: cimg-dev,
python-mne,
python-mvpa2,
python-nibabel,
- python-nipy,
- python-nipype,
python-nitime,
python-openslide,
python-pyxnat,
@@ -1033,11 +1170,13 @@ Recommends: cimg-dev,
r-cran-rniftilib
Suggests: emokit,
igstk-examples,
- insighttoolkit3-examples,
+ libactiviz.net-cil,
libbio-formats-java,
libcamitk3-dev,
+ libcamp0.7-dev,
libctk-dev,
libeegdev-dev,
+ libfreeimage-dev,
libics-dev,
libigstk4-dev,
liblimereg-dev,
@@ -1046,15 +1185,17 @@ Suggests: emokit,
libopenigtlink1-dev,
libopenmeeg-dev,
libopenslide-java,
- libopensurgsim-dev,
libvia-dev,
libvmtk-dev,
- libvtk5.4,
+ libvtk-dicom-java,
+ libvtk-dicom0.5-dev,
libvtkedge-dev,
libxdffileio-dev,
octave-dicom,
python-imageio,
python-libavg,
+ python-nipy,
+ python-nipype,
python-tifffile,
python-vmtk
Description: Debian Med image processing and visualization packages development
@@ -1124,22 +1265,23 @@ Package: med-practice
Section: metapackages
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: freediams,
+Recommends: entangle,
+ freediams,
freemedforms-emr,
+ ginkgocadx,
gnumed-client,
gnumed-server,
libchipcard-tools,
+ orthanc,
qrisk2,
- r-cran-medadherence
+ r-cran-medadherence,
+ sleepyhead
Suggests: clearhealth,
- clinica,
elementalclinic,
elexis,
- entangle,
freeb,
freemed,
freeshim,
- ginkgocadx,
libctapimkt1,
medintux,
mirrormed,
@@ -1195,11 +1337,14 @@ Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: r-bioc-edger,
r-bioc-limma,
+ r-bioc-multtest,
r-bioc-qvalue,
+ r-cran-ade4,
r-cran-beeswarm,
r-cran-pvclust,
r-cran-randomforest
-Suggests: science-statistics
+Suggests: rstudio,
+ 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.
@@ -1218,13 +1363,15 @@ Recommends: cronometer,
python-clips,
python-fitbit,
quitcount,
+ r-cran-fitbitscraper,
wgerman-medical,
workrave
Suggests: cycle,
entangle,
goldencheetah,
mencal,
- mssstest
+ mssstest,
+ sleepyhead
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.
--
Debian Med metapackages
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