[Blends-commit] [SCM] med branch, master, updated. e7e0a7ca4ce62f1484b74d8a643d91aa19ed1824

[Andreas Tille]

The following commit has been merged in the master branch:
commit e7e0a7ca4ce62f1484b74d8a643d91aa19ed1824
Author: Andreas Tille <tille at debian.org>
Date:   Wed Apr 19 15:33:25 2017 +0200

    Re-render before Stretch release

diff --git a/debian/changelog b/debian/changelog
index 14353c4..e2d5161 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+debian-med (3.0.1) unstable; urgency=medium
+
+  * Re-render before Stretch release
+
+ -- Andreas Tille <tille at debian.org>  Wed, 19 Apr 2017 15:29:37 +0200
+
 debian-med (3.0) unstable; urgency=medium
 
   * Bump version for Stretch release
diff --git a/debian/control b/debian/control
index bfbf99f..0d8145a 100644
--- a/debian/control
+++ b/debian/control
@@ -123,7 +123,6 @@ Recommends: abacas,
  bio-eagle,
  bio-rainbow,
  blasr,
- blast2,
  bowtie,
  bowtie2,
  boxshade,
@@ -148,6 +147,7 @@ Recommends: abacas,
  cutadapt,
  daligner,
  dascrubber,
+ datamash,
  dawg,
  dazzdb,
  dialign,
@@ -219,7 +219,6 @@ Recommends: abacas,
  iqtree,
  iva,
  jaligner,
- jalview,
  jellyfish,
  jmodeltest,
  jmol,
@@ -273,6 +272,7 @@ Recommends: abacas,
  nanopolish,
  nast-ier,
  ncbi-blast+,
+ ncbi-blast+-legacy,
  ncbi-entrez-direct,
  ncbi-epcr,
  ncbi-seg,
@@ -284,7 +284,6 @@ Recommends: abacas,
  njplot,
  norsnet,
  norsp,
- openms,
  paraclu,
  parsinsert,
  parsnp,
@@ -351,7 +350,6 @@ Recommends: abacas,
  pynast,
  pyscanfcs,
  python-cogent,
- qiime,
  qtltools,
  r-bioc-annotate,
  r-bioc-biostrings,
@@ -458,7 +456,6 @@ Recommends: abacas,
  tigr-glimmer,
  tm-align,
  tophat,
- topp,
  toppred,
  transdecoder,
  transrate-tools,
@@ -496,6 +493,7 @@ Suggests: acacia,
  biceps,
  big-blast,
  bigsdb,
+ bio-tradis,
  biomaj,
  biomaj-watcher,
  bitseq,
@@ -515,6 +513,7 @@ Suggests: acacia,
  clonalorigin,
  cluster3,
  cmap,
+ cnvkit,
  coalesce,
  compclust,
  condetri,
@@ -544,7 +543,9 @@ Suggests: acacia,
  estscan,
  euler-sr,
  euler2,
+ exabayes,
  exalt,
+ examl,
  excavator,
  fasta,
  fasta3,
@@ -565,6 +566,7 @@ Suggests: acacia,
  genetrack,
  genezilla,
  genographer,
+ getdata,
  glimmerhmm,
  gmap,
  gmv,
@@ -577,12 +579,12 @@ Suggests: acacia,
  htqc,
  igv,
  inspect,
+ jalview,
  jbrowse,
  jigsaw,
  jstreeview,
  kclust,
  kempbasu,
- kronatools,
  lagan,
  lamarc,
  lofreq,
@@ -617,6 +619,7 @@ Suggests: acacia,
  molekel,
  mosaik-aligner,
  mpsqed,
+ mptp,
  mrs,
  msatfinder,
  mugsy,
@@ -632,8 +635,10 @@ Suggests: acacia,
  obo-edit,
  oligoarrayaux,
  omegamap,
+ openms,
  operondb,
  pal2nal,
+ paleomix,
  paml,
  partigene,
  partitionfinder,
@@ -656,10 +661,14 @@ Suggests: acacia,
  prot4est,
  pscan-tfbs,
  psipred,
+ psortb,
  pssh2,
  pyrophosphate-tools,
  python-orange,
  python-reaper,
+ python3-biomaj3,
+ qcumber,
+ qiime,
  qtlcart,
  qualimap,
  r-bioc-annotationhub,
@@ -675,19 +684,25 @@ Suggests: acacia,
  r-other-apmswapp,
  r-other-valdar-bagphenotype.library,
  raccoon,
+ radiant,
+ raxml-ng,
  rbs-finder,
  recombine,
  repeatmasker,
  rmblast,
  roadtrips,
  roche454ace2caf,
+ roguenarok,
  rose,
  rosetta,
  rsat,
+ runcircos-gui,
+ sambamba,
  sap,
  science-workflow,
  segemehl,
  seq-gen,
+ seqsero,
  sequenceconverter.app,
  sift,
  situs,
@@ -704,6 +719,8 @@ Suggests: acacia,
  tetra,
  tide,
  tigr-glimmer-mg,
+ tnseq-transit,
+ topp,
  trace2dbest,
  tracetuner,
  treebuilder3d,
@@ -785,7 +802,6 @@ Recommends: bioperl,
  libngs-java,
  libngs-sdk-dev,
  libnhgri-blastall-perl,
- libopenms-dev,
  libpal-java,
  libpbbam-dev,
  libpbdata-dev,
@@ -804,7 +820,6 @@ Recommends: bioperl,
  libsnp-sites1-dev,
  libsort-key-top-perl,
  libsrf-dev,
- libssm-dev,
  libssw-dev,
  libssw-java,
  libstaden-read-dev,
@@ -853,18 +868,24 @@ Recommends: bioperl,
  ruby-crb-blast,
  sbmltoolbox,
  seqan-dev
-Suggests: bioclipse,
+Suggests: bio-tradis,
+ 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,
@@ -872,15 +893,21 @@ Suggests: bioclipse,
  octace-bioinfo,
  octave-bioinfo,
  python-bd2k,
+ python-biomaj3,
  python-biopython-doc,
+ python-biotools,
  python-bx,
  python-consensuscore2,
  python-hyphy,
  python-misopy,
  python-mmtk,
  python-pyfasta,
+ python-pyflow,
+ python-roadrunner,
  python3-bd2k,
+ python3-biomaj3,
  python3-biopython-sql | python-biopython-sql,
+ python3-biotools,
  python3-bx,
  python3-consensuscore2,
  python3-gffutils,
@@ -912,6 +939,7 @@ Suggests: bioclipse,
  r-bioc-snpstats,
  r-bioc-variantannotation,
  r-bioc-xvector,
+ r-cran-natserv,
  r-cran-rentrez,
  r-cran-rocr,
  ruby-rgfa
@@ -1034,7 +1062,6 @@ Recommends: abyss,
  python-biopython,
  python-cogent,
  python3-biopython,
- qiime,
  r-bioc-edger,
  r-bioc-hilbertvis,
  r-cran-pvclust,
@@ -1072,6 +1099,7 @@ 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,
@@ -1120,8 +1148,10 @@ Recommends: epigrass,
 Suggests: netepi-analysis,
  netepi-collection,
  r-cran-cmprsk,
+ r-cran-lexrankr,
  r-cran-msm,
  repast,
+ shiny-server,
  ushahidi
 Description: Debian Med epidemiology related packages
  This metapackage will install tools that are useful in epidemiological
@@ -1142,6 +1172,7 @@ Suggests: care2x,
  openeyes,
  openmaxims,
  openmrs,
+ orthanc-wsi,
  oscar-mcmaster,
  patientos,
  tryton-modules-health,
@@ -1171,7 +1202,6 @@ Recommends: aeskulap,
  dicom3tools,
  dicomnifti,
  dicomscope,
- fslview,
  gdf-tools,
  ginkgocadx,
  gwyddion,
@@ -1189,10 +1219,7 @@ Recommends: aeskulap,
  minc-tools,
  mriconvert,
  mricron,
- mrtrix,
  nifti-bin,
- odin,
- openmeeg-tools,
  openslide-tools,
  orthanc,
  pixelmed-apps,
@@ -1200,8 +1227,6 @@ Recommends: aeskulap,
  python-dicom,
  python-mvpa2,
  python-nibabel,
- python-nipy,
- python-nipype,
  python-nitime,
  python-surfer,
  python-tifffile,
@@ -1241,6 +1266,7 @@ Suggests: afni,
  fiji,
  freesurfer,
  fsl,
+ fslview,
  fw4spl,
  gimias,
  gofigure2,
@@ -1267,19 +1293,25 @@ 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,
@@ -1330,7 +1362,6 @@ Recommends: cimg-dev,
  libnifti-dev,
  libodil0-dev,
  libopenigtlink-dev,
- libopenmeeg-dev,
  libopenslide-dev,
  libopensurgsim-dev,
  libpapyrus3-dev,
@@ -1342,17 +1373,13 @@ Recommends: cimg-dev,
  libvtk6-dev,
  octave-bart,
  octave-gdf,
- odin,
  python-casmoothing,
  python-cfflib,
  python-dicom,
- python-dipy,
  python-mia | python3-mia,
  python-mne,
  python-mvpa2,
  python-nibabel,
- python-nipy,
- python-nipype,
  python-nitime,
  python-openslide,
  python-pyxnat,
@@ -1361,7 +1388,7 @@ Recommends: cimg-dev,
 Suggests: emokit,
  igstk-examples,
  libbio-formats-java,
- libcamp0.7-dev,
+ libcamp-dev,
  libcifti-dev,
  libctk-dev,
  libeegdev-dev,
@@ -1371,6 +1398,7 @@ Suggests: emokit,
  liblimereg-dev,
  libmni-perllib-perl,
  libnifti-doc,
+ libopenmeeg-dev,
  libopenslide-java,
  libvia-dev,
  libvmtk-dev,
@@ -1379,8 +1407,12 @@ 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
@@ -1395,7 +1427,8 @@ Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${sourc
 Recommends: opencfu
 Suggests: catissuesuite,
  openelis,
- openfreezer
+ openfreezer,
+ orthanc-wsi
 Description: Debian Med suggestions for medical laboratories
  This metapackage contains dependencies for software and that could
  be useful ro run a medical laboratory.
@@ -1405,7 +1438,8 @@ Section: metapackages
 Architecture: all
 Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
 Recommends: dicompyler
-Suggests: planunc,
+Suggests: orthanc-wsi,
+ planunc,
  uw-prism
 Description: Debian Med packages for oncology
  This metapackage will install tools that are useful for radiation
@@ -1474,6 +1508,7 @@ Suggests: clearhealth,
  openemr,
  openpms,
  openrep,
+ orthanc-wsi,
  proteus,
  remitt,
  resmedicinae,
@@ -1491,7 +1526,6 @@ Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${sourc
 Recommends: praat,
  psignifit,
  psychopy,
- python-pyepl,
  r-cran-foreign,
  r-cran-psy
 Suggests: miscpsycho,
@@ -1499,6 +1533,7 @@ Suggests: miscpsycho,
  psychometric,
  psychotree,
  psyphy,
+ python-pyepl,
  python-pypsignifit,
  python-visionegg,
  science-psychophysics

-- 
Debian Med metapackages