The following commit has been merged in the master branch:
commit 297709d48218fb3609f169cccf092f37bf35eed2
Author: Andreas Tille <ti...@debian.org>
Date: Sat Aug 5 04:44:21 2017 +0200
Update control file after Squeeze release, should be now valid for Buster
diff --git a/debian/control b/debian/control
index 0d8145a..6158c05 100644
--- a/debian/control
+++ b/debian/control
@@ -111,6 +111,7 @@ Recommends: abacas,
autodock-vina,
autogrid,
axe-demultiplexer,
+ baitfisher,
ballview,
bamtools,
barrnap,
@@ -118,16 +119,21 @@ Recommends: abacas,
beagle,
beast-mcmc,
beast2-mcmc,
+ bedops,
bedtools,
berkeley-express,
bio-eagle,
bio-rainbow,
+ bio-tradis,
blasr,
bowtie,
bowtie2,
boxshade,
+ bppphyview,
+ bppsuite,
brig,
bwa,
+ canu,
cassiopee,
cd-hit,
cdbfasta,
@@ -146,18 +152,20 @@ Recommends: abacas,
crac,
cutadapt,
daligner,
- dascrubber,
datamash,
dawg,
dazzdb,
+ deepnano,
dialign,
dialign-tx,
+ diamond-aligner,
dindel,
discosnp,
disulfinder,
dnaclust,
dssp,
dwgsim,
+ e-mem,
ea-utils,
ecopcr,
edtsurf,
@@ -166,6 +174,7 @@ Recommends: abacas,
embassy-domalign,
embassy-domsearch,
emboss,
+ examl,
exonerate,
falcon,
fastahack,
@@ -183,6 +192,7 @@ Recommends: abacas,
fitgcp,
flexbar,
fml-asm,
+ freebayes,
freecontact,
fsa,
fsm-lite,
@@ -219,6 +229,7 @@ Recommends: abacas,
iqtree,
iva,
jaligner,
+ jalview,
jellyfish,
jmodeltest,
jmol,
@@ -264,6 +275,7 @@ Recommends: abacas,
mira-assembler,
mlv-smile,
mothur,
+ mptp,
mrbayes,
mummer,
murasaki,
@@ -284,6 +296,9 @@ Recommends: abacas,
njplot,
norsnet,
norsp,
+ openms,
+ paleomix,
+ paml,
paraclu,
parsinsert,
parsnp,
@@ -299,6 +314,7 @@ Recommends: abacas,
pdb2pqr,
perlprimer,
perm,
+ pftools,
phipack,
phybin,
phylip,
@@ -345,12 +361,18 @@ Recommends: abacas,
progressivemauve,
proteinortho,
prottest,
+ psortb,
pycorrfit,
pymol,
pynast,
pyscanfcs,
python-cogent,
+ python-treetime,
+ python3-biomaj3,
+ qcumber,
+ qiime,
qtltools,
+ quorum,
r-bioc-annotate,
r-bioc-biostrings,
r-bioc-cummerbund,
@@ -381,6 +403,7 @@ Recommends: abacas,
r-cran-treescape,
r-cran-vegan,
r-other-mott-happy.hbrem,
+ radiant,
rambo-k,
rapmap,
rasmol,
@@ -400,8 +423,10 @@ Recommends: abacas,
rna-star,
rnahybrid,
roary,
+ roguenarok,
rsem,
rtax,
+ runcircos-gui,
saint,
salmon,
samtools,
@@ -411,6 +436,7 @@ Recommends: abacas,
seer,
seqan-apps,
seqprep,
+ seqsero,
seqtk,
sga,
sibsim4,
@@ -455,7 +481,9 @@ Recommends: abacas,
theseus,
tigr-glimmer,
tm-align,
+ tnseq-transit,
tophat,
+ topp,
toppred,
transdecoder,
transrate-tools,
@@ -486,14 +514,11 @@ Suggests: acacia,
axparafit,
axpcoords,
bagpipe,
- baitfisher,
bambus,
beads,
- bedops,
biceps,
big-blast,
bigsdb,
- bio-tradis,
biomaj,
biomaj-watcher,
bitseq,
@@ -505,8 +530,8 @@ Suggests: acacia,
cactus,
caftools,
cain,
- canu,
cap3,
+ card-rgi,
ccs,
cdna-db,
cinema,
@@ -526,10 +551,9 @@ Suggests: acacia,
cufflinks,
cytoscape,
das-proserver,
+ dascrubber,
dazzle,
decipher,
- deepnano,
- diamond-aligner,
e-hive,
ecell,
elph,
@@ -545,7 +569,6 @@ Suggests: acacia,
euler2,
exabayes,
exalt,
- examl,
excavator,
fasta,
fasta3,
@@ -555,7 +578,6 @@ Suggests: acacia,
fluctuate,
forester,
forge,
- freebayes,
galaxy,
gassst,
gatk,
@@ -579,7 +601,6 @@ Suggests: acacia,
htqc,
igv,
inspect,
- jalview,
jbrowse,
jigsaw,
jstreeview,
@@ -619,7 +640,6 @@ Suggests: acacia,
molekel,
mosaik-aligner,
mpsqed,
- mptp,
mrs,
msatfinder,
mugsy,
@@ -635,18 +655,14 @@ Suggests: acacia,
obo-edit,
oligoarrayaux,
omegamap,
- openms,
operondb,
pal2nal,
- paleomix,
- paml,
partigene,
partitionfinder,
patman,
patristic,
pcma,
pfaat,
- pftools,
phagefinder,
phast,
phpphylotree,
@@ -661,14 +677,10 @@ Suggests: acacia,
prot4est,
pscan-tfbs,
psipred,
- psortb,
pssh2,
pyrophosphate-tools,
python-orange,
python-reaper,
- python3-biomaj3,
- qcumber,
- qiime,
qtlcart,
qualimap,
r-bioc-annotationhub,
@@ -684,7 +696,6 @@ Suggests: acacia,
r-other-apmswapp,
r-other-valdar-bagphenotype.library,
raccoon,
- radiant,
raxml-ng,
rbs-finder,
recombine,
@@ -692,17 +703,14 @@ Suggests: acacia,
rmblast,
roadtrips,
roche454ace2caf,
- roguenarok,
rose,
rosetta,
rsat,
- runcircos-gui,
sambamba,
sap,
science-workflow,
segemehl,
seq-gen,
- seqsero,
sequenceconverter.app,
sift,
situs,
@@ -719,8 +727,7 @@ Suggests: acacia,
tetra,
tide,
tigr-glimmer-mg,
- tnseq-transit,
- topp,
+ tn-seqexplorer,
trace2dbest,
tracetuner,
treebuilder3d,
@@ -746,7 +753,8 @@ Package: med-bio-dev
Section: metapackages
Architecture: all
Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (=
${source:Version})
-Recommends: bioperl,
+Recommends: bio-tradis,
+ bioperl,
bioperl-run,
biosquid,
libace-perl,
@@ -755,11 +763,13 @@ Recommends: bioperl,
libbamtools-dev,
libbio-coordinate-perl,
libbio-das-lite-perl,
+ libbio-eutilities-perl,
libbio-graphics-perl,
libbio-mage-perl,
libbio-mage-utils-perl,
libbio-primerdesigner-perl,
libbiococoa-dev,
+ libbiod-dev,
libbiojava-java,
libbiojava4-java,
libblasr-dev,
@@ -802,6 +812,7 @@ Recommends: bioperl,
libngs-java,
libngs-sdk-dev,
libnhgri-blastall-perl,
+ libopenms-dev,
libpal-java,
libpbbam-dev,
libpbdata-dev,
@@ -816,10 +827,12 @@ Recommends: bioperl,
librostlab-blast0-dev,
librostlab3-dev,
libsbml5-dev,
+ libseqlib-dev,
libsmithwaterman-dev,
libsnp-sites1-dev,
libsort-key-top-perl,
libsrf-dev,
+ libssm-dev,
libssw-dev,
libssw-java,
libstaden-read-dev,
@@ -844,15 +857,18 @@ Recommends: bioperl,
python-pbh5tools,
python-pysam,
python-rdkit,
- python-screed,
+ python3-biomaj3 | python-biomaj3,
python3-biopython | python-biopython,
+ python3-biotools | python-biotools,
python3-csb | python-csb,
python3-cutadapt | python-cutadapt,
python3-dendropy | python-dendropy,
python3-fast5 | python-fast5,
+ python3-gffutils,
python3-intervaltree-bio | python-intervaltree-bio,
python3-ngs | python-ngs,
python3-pbconsensuscore | python-pbconsensuscore,
+ python3-pybedtools,
python3-pyfaidx | python-pyfaidx,
python3-pymummer,
python3-pyvcf | python-pyvcf,
@@ -868,24 +884,18 @@ Recommends: bioperl,
ruby-crb-blast,
sbmltoolbox,
seqan-dev
-Suggests: bio-tradis,
- bioclipse,
+Suggests: bioclipse,
libbam-dev,
- libbio-eutilities-perl,
- libbiod-dev,
libdisorder-dev,
libforester-java,
libfreecontact-doc,
libgff-perl,
libgtextutils-dev,
- libopenms-dev,
libpbcopper-dev,
libqcpp-dev,
libroadrunner-dev,
librostlab-blast-doc,
librostlab-doc,
- libseqlib-dev,
- libssm-dev,
libswarm2-dev,
mgltools-networkeditor,
mgltools-pybabel,
@@ -893,9 +903,7 @@ Suggests: bio-tradis,
octace-bioinfo,
octave-bioinfo,
python-bd2k,
- python-biomaj3,
python-biopython-doc,
- python-biotools,
python-bx,
python-consensuscore2,
python-hyphy,
@@ -904,16 +912,13 @@ Suggests: bio-tradis,
python-pyfasta,
python-pyflow,
python-roadrunner,
+ python-screed,
python3-bd2k,
- python3-biomaj3,
python3-biopython-sql | python-biopython-sql,
- python3-biotools,
python3-bx,
python3-consensuscore2,
- python3-gffutils,
python3-hyphy,
python3-misopy,
- python3-pybedtools,
python3-pyfasta,
r-bioc-affy,
r-bioc-affyio,
@@ -1062,6 +1067,7 @@ Recommends: abyss,
python-biopython,
python-cogent,
python3-biopython,
+ qiime,
r-bioc-edger,
r-bioc-hilbertvis,
r-cran-pvclust,
@@ -1099,7 +1105,6 @@ Suggests: bagpipe,
cufflinks,
embassy-phylip,
gmap,
- qiime,
r-other-valdar-bagphenotype.library
Description: Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
@@ -1137,18 +1142,19 @@ Section: metapackages
Architecture: all
Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (=
${source:Version})
Recommends: epigrass,
+ python-treetime,
r-cran-diagnosismed,
r-cran-epi,
r-cran-epibasix,
r-cran-epicalc,
r-cran-epir,
r-cran-epitools,
+ r-cran-lexrankr,
r-cran-seroincidence,
r-cran-surveillance
Suggests: netepi-analysis,
netepi-collection,
r-cran-cmprsk,
- r-cran-lexrankr,
r-cran-msm,
repast,
shiny-server,
@@ -1164,7 +1170,8 @@ Package: med-his
Section: metapackages
Architecture: all
Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (=
${source:Version})
-Recommends: fis-gtm
+Recommends: fis-gtm,
+ orthanc-wsi
Suggests: care2x,
ewd-920,
hkma-cms,
@@ -1172,7 +1179,6 @@ Suggests: care2x,
openeyes,
openmaxims,
openmrs,
- orthanc-wsi,
oscar-mcmaster,
patientos,
tryton-modules-health,
@@ -1202,6 +1208,7 @@ Recommends: aeskulap,
dicom3tools,
dicomnifti,
dicomscope,
+ fw4spl,
gdf-tools,
ginkgocadx,
gwyddion,
@@ -1219,14 +1226,20 @@ Recommends: aeskulap,
minc-tools,
mriconvert,
mricron,
+ mrtrix,
nifti-bin,
+ odin,
+ openmeeg-tools,
openslide-tools,
orthanc,
+ orthanc-wsi,
pixelmed-apps,
plastimatch,
python-dicom,
python-mvpa2,
python-nibabel,
+ python-nipy,
+ python-nipype,
python-nitime,
python-surfer,
python-tifffile,
@@ -1267,7 +1280,6 @@ Suggests: afni,
freesurfer,
fsl,
fslview,
- fw4spl,
gimias,
gofigure2,
hid,
@@ -1293,25 +1305,19 @@ Suggests: afni,
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
- mrtrix,
- odin,
omero,
opendicom.net,
openelectrophy,
- openmeeg-tools,
opensourcepacs,
openwalnut-qt4,
orthanc-dicomweb,
orthanc-imagej,
orthanc-postgresql,
orthanc-webviewer,
- orthanc-wsi,
paraview,
piano,
pngquant,
pymeg,
- python-nipy,
- python-nipype,
python-pyxid,
science-workflow,
slicer,
@@ -1346,6 +1352,7 @@ Recommends: cimg-dev,
libbart-dev,
libbiosig-dev,
libcamitk-dev,
+ libcifti-dev,
libcv-dev,
libedf-dev,
libgdcm2-dev,
@@ -1362,6 +1369,7 @@ Recommends: cimg-dev,
libnifti-dev,
libodil0-dev,
libopenigtlink-dev,
+ libopenmeeg-dev,
libopenslide-dev,
libopensurgsim-dev,
libpapyrus3-dev,
@@ -1373,13 +1381,18 @@ Recommends: cimg-dev,
libvtk6-dev,
octave-bart,
octave-gdf,
+ odin,
python-casmoothing,
python-cfflib,
python-dicom,
+ python-dipy,
+ python-imageio,
python-mia | python3-mia,
python-mne,
python-mvpa2,
python-nibabel,
+ python-nipy,
+ python-nipype,
python-nitime,
python-openslide,
python-pyxnat,
@@ -1389,7 +1402,6 @@ Suggests: emokit,
igstk-examples,
libbio-formats-java,
libcamp-dev,
- libcifti-dev,
libctk-dev,
libeegdev-dev,
libfreeimage-dev,
@@ -1398,7 +1410,6 @@ Suggests: emokit,
liblimereg-dev,
libmni-perllib-perl,
libnifti-doc,
- libopenmeeg-dev,
libopenslide-java,
libvia-dev,
libvmtk-dev,
@@ -1407,12 +1418,7 @@ Suggests: emokit,
libvxl1-dev,
libxdffileio-dev,
octave-dicom,
- odin,
- python-dipy,
- python-imageio,
python-libavg,
- python-nipy,
- python-nipype,
python-tifffile,
python-vmtk
Description: Debian Med image processing and visualization packages development
@@ -1424,11 +1430,11 @@ Package: med-laboratory
Section: metapackages
Architecture: all
Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (=
${source:Version})
-Recommends: opencfu
+Recommends: opencfu,
+ orthanc-wsi
Suggests: catissuesuite,
openelis,
- openfreezer,
- orthanc-wsi
+ openfreezer
Description: Debian Med suggestions for medical laboratories
This metapackage contains dependencies for software and that could
be useful ro run a medical laboratory.
@@ -1437,9 +1443,9 @@ Package: med-oncology
Section: metapackages
Architecture: all
Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (=
${source:Version})
-Recommends: dicompyler
-Suggests: orthanc-wsi,
- planunc,
+Recommends: dicompyler,
+ orthanc-wsi
+Suggests: planunc,
uw-prism
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
@@ -1492,6 +1498,7 @@ Recommends: entangle,
gnumed-server,
libchipcard-tools,
orthanc,
+ orthanc-wsi,
qrisk2,
r-cran-medadherence,
sleepyhead
@@ -1508,7 +1515,6 @@ Suggests: clearhealth,
openemr,
openpms,
openrep,
- orthanc-wsi,
proteus,
remitt,
resmedicinae,
@@ -1526,6 +1532,7 @@ Depends: med-tasks (= ${source:Version}),
${misc:Depends}, med-config (= ${sourc
Recommends: praat,
psignifit,
psychopy,
+ python-pyepl,
r-cran-foreign,
r-cran-psy
Suggests: miscpsycho,
@@ -1533,7 +1540,6 @@ Suggests: miscpsycho,
psychometric,
psychotree,
psyphy,
- python-pyepl,
python-pypsignifit,
python-visionegg,
science-psychophysics
--
Debian Med metapackages
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