[Blends-commit] [SCM] med branch, master, updated. 251eda07708f86b03df9afebb8ec3d93c47400b3

Andreas Tille tille at debian.org
Sun Aug 13 02:05:39 UTC 2017


The following commit has been merged in the master branch:
commit 297709d48218fb3609f169cccf092f37bf35eed2
Author: Andreas Tille <tille at 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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