[Blends-commit] [SCM] med branch, master, updated. b8479fe6fcfb91de98c42eb348c5c372d9f6f05b

[Andreas Tille]

The following commit has been merged in the master branch:
commit b8479fe6fcfb91de98c42eb348c5c372d9f6f05b
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jan 24 10:55:48 2017 +0100

    Upload version 3.0

diff --git a/debian-med-tasks.desc b/debian-med-tasks.desc
index 11e27ed..6108c40 100644
--- a/debian-med-tasks.desc
+++ b/debian-med-tasks.desc
@@ -24,6 +24,17 @@ Test-new-install: mark show
 Key: 
  med-bio-dev
 
+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.
+Key: 
+ med-cloud
+
 Task: med-data
 Parent: debian-med
 Section: debian-med
@@ -34,6 +45,15 @@ Description: Debian Med drug databases
 Key: 
  med-data
 
+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.
+Key: 
+ med-dental
+
 Task: med-epi
 Parent: debian-med
 Section: debian-med
@@ -46,6 +66,18 @@ Description: Debian Med epidemiology related packages
 Key: 
  med-epi
 
+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
+ be useful ro run a Hospital Information System.  While there is
+ continuous work going on to package a ready to install system currently
+ only preconditions are finished but hopefully helpful in hospitals
+ anyway.
+Key: 
+ med-his
+
 Task: med-imaging
 Parent: debian-med
 Section: debian-med
@@ -73,6 +105,34 @@ Description: Debian Med image processing and visualization packages development
 Key: 
  med-imaging-dev
 
+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.
+Key: 
+ med-laboratory
+
+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.
+Key: 
+ med-oncology
+
+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.
+Key: 
+ med-pharmacy
+
 Task: med-physics
 Parent: debian-med
 Section: debian-med
diff --git a/debian/changelog b/debian/changelog
index befc303..14353c4 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-debian-med (3.0) UNRELEASED; urgency=medium
+debian-med (3.0) unstable; urgency=medium
 
   * Bump version for Stretch release
 
@@ -35,7 +35,7 @@ debian-med (3.0) UNRELEASED; urgency=medium
       Depends:  libbiojava3-java, libvcflib, python3-skbio | python-skbio,
                 python-miso, unanimity
 
- -- Andreas Tille <tille at debian.org>  Tue, 24 Jan 2017 09:54:03 +0100
+ -- Andreas Tille <tille at debian.org>  Tue, 24 Jan 2017 10:51:13 +0100
 
 debian-med (2.4) unstable; urgency=medium
 
diff --git a/debian/control b/debian/control
index b46db2f..bfbf99f 100644
--- a/debian/control
+++ b/debian/control
@@ -89,6 +89,7 @@ Recommends: abacas,
  acedb-other-belvu,
  acedb-other-dotter,
  adapterremoval,
+ adun-core,
  aegean,
  aevol,
  alien-hunter,
@@ -104,6 +105,7 @@ Recommends: abacas,
  art-nextgen-simulation-tools,
  artemis,
  artfastqgenerator,
+ atac,
  augustus,
  autodock,
  autodock-vina,
@@ -194,6 +196,7 @@ Recommends: abacas,
  gentle,
  gff2aplot,
  gff2ps,
+ ghemical,
  giira,
  glam2,
  graphlan,
@@ -233,6 +236,7 @@ Recommends: abacas,
  leaff,
  lefse,
  librg-utils-perl,
+ libvcflib-tools,
  logol-bin,
  loki,
  ltrsift,
@@ -269,6 +273,7 @@ Recommends: abacas,
  nanopolish,
  nast-ier,
  ncbi-blast+,
+ ncbi-entrez-direct,
  ncbi-epcr,
  ncbi-seg,
  ncbi-tools-bin,
@@ -279,6 +284,7 @@ Recommends: abacas,
  njplot,
  norsnet,
  norsp,
+ openms,
  paraclu,
  parsinsert,
  parsnp,
@@ -345,6 +351,8 @@ Recommends: abacas,
  pynast,
  pyscanfcs,
  python-cogent,
+ qiime,
+ qtltools,
  r-bioc-annotate,
  r-bioc-biostrings,
  r-bioc-cummerbund,
@@ -357,6 +365,9 @@ Recommends: abacas,
  r-bioc-gviz,
  r-bioc-hilbertvis,
  r-bioc-limma,
+ r-bioc-mergeomics,
+ r-bioc-metagenomeseq,
+ r-bioc-phyloseq,
  r-bioc-rtracklayer,
  r-cran-adegenet,
  r-cran-adephylo,
@@ -367,9 +378,12 @@ Recommends: abacas,
  r-cran-phangorn,
  r-cran-pscbs,
  r-cran-qtl,
+ r-cran-rotl,
  r-cran-seqinr,
+ r-cran-treescape,
  r-cran-vegan,
  r-other-mott-happy.hbrem,
+ rambo-k,
  rapmap,
  rasmol,
  raster3d,
@@ -444,6 +458,7 @@ Recommends: abacas,
  tigr-glimmer,
  tm-align,
  tophat,
+ topp,
  toppred,
  transdecoder,
  transrate-tools,
@@ -463,7 +478,6 @@ Recommends: abacas,
  wise,
  zalign
 Suggests: acacia,
- adun-core,
  adun.app,
  amos-assembler,
  amoscmp,
@@ -471,13 +485,14 @@ Suggests: acacia,
  arachne,
  arb,
  asap,
- atac,
  autodocktools,
  axparafit,
  axpcoords,
  bagpipe,
+ baitfisher,
  bambus,
  beads,
+ bedops,
  biceps,
  big-blast,
  bigsdb,
@@ -494,6 +509,7 @@ Suggests: acacia,
  cain,
  canu,
  cap3,
+ ccs,
  cdna-db,
  cinema,
  clonalorigin,
@@ -514,6 +530,7 @@ Suggests: acacia,
  dazzle,
  decipher,
  deepnano,
+ diamond-aligner,
  e-hive,
  ecell,
  elph,
@@ -525,11 +542,12 @@ Suggests: acacia,
  est-db,
  estferret,
  estscan,
+ euler-sr,
+ euler2,
  exalt,
  excavator,
  fasta,
  fasta3,
- fermi-lite,
  ffp,
  figaro,
  finex,
@@ -547,7 +565,6 @@ Suggests: acacia,
  genetrack,
  genezilla,
  genographer,
- ghemical,
  glimmerhmm,
  gmap,
  gmv,
@@ -606,7 +623,7 @@ Suggests: acacia,
  mummergpu,
  mview,
  nanocall,
- ncbi-entrez-direct,
+ nextsv,
  ngila,
  ngsqctoolkit,
  nw-align,
@@ -615,7 +632,6 @@ Suggests: acacia,
  obo-edit,
  oligoarrayaux,
  omegamap,
- openms,
  operondb,
  pal2nal,
  paml,
@@ -644,22 +660,21 @@ Suggests: acacia,
  pyrophosphate-tools,
  python-orange,
  python-reaper,
- qiime,
  qtlcart,
- qtltools,
  qualimap,
  r-bioc-annotationhub,
  r-bioc-aroma.light,
  r-bioc-ensembldb,
  r-bioc-go.db,
+ r-bioc-savr,
  r-cran-boolnet,
  r-cran-metamix,
  r-cran-pheatmap,
- r-cran-treescape,
+ r-cran-qqman,
+ r-cran-rentrez,
  r-other-apmswapp,
  r-other-valdar-bagphenotype.library,
  raccoon,
- rambo-k,
  rbs-finder,
  recombine,
  repeatmasker,
@@ -689,13 +704,13 @@ Suggests: acacia,
  tetra,
  tide,
  tigr-glimmer-mg,
- topp,
  trace2dbest,
  tracetuner,
  treebuilder3d,
  treetime,
  tripal,
  trnascan-se,
+ tvc,
  twain,
  ugene,
  unc-fish,
@@ -721,6 +736,7 @@ Recommends: bioperl,
  libai-fann-perl,
  libbambamc-dev,
  libbamtools-dev,
+ libbio-coordinate-perl,
  libbio-das-lite-perl,
  libbio-graphics-perl,
  libbio-mage-perl,
@@ -728,7 +744,6 @@ Recommends: bioperl,
  libbio-primerdesigner-perl,
  libbiococoa-dev,
  libbiojava-java,
- libbiojava3-java,
  libbiojava4-java,
  libblasr-dev,
  libbpp-core-dev,
@@ -759,6 +774,7 @@ Recommends: bioperl,
  libhts-dev,
  libhtsjdk-java,
  libjebl2-java,
+ libjloda-java,
  libkmer-dev,
  libmems-1.6-dev,
  libminimap-dev,
@@ -769,6 +785,7 @@ Recommends: bioperl,
  libngs-java,
  libngs-sdk-dev,
  libnhgri-blastall-perl,
+ libopenms-dev,
  libpal-java,
  libpbbam-dev,
  libpbdata-dev,
@@ -791,8 +808,10 @@ Recommends: bioperl,
  libssw-dev,
  libssw-java,
  libstaden-read-dev,
+ libswiss-perl,
  libtabixpp-dev,
  libtfbs-perl,
+ libvcflib-dev,
  libvibrant6-dev,
  libzerg-perl,
  libzerg0-dev,
@@ -812,16 +831,18 @@ Recommends: bioperl,
  python-rdkit,
  python-screed,
  python3-biopython | python-biopython,
- python3-consensuscore2 | python-consensuscore2,
  python3-csb | python-csb,
  python3-cutadapt | python-cutadapt,
  python3-dendropy | python-dendropy,
+ python3-fast5 | python-fast5,
+ python3-intervaltree-bio | python-intervaltree-bio,
  python3-ngs | python-ngs,
  python3-pbconsensuscore | python-pbconsensuscore,
  python3-pyfaidx | python-pyfaidx,
  python3-pymummer,
  python3-pyvcf | python-pyvcf,
  python3-ruffus | python-ruffus,
+ python3-skbio,
  r-bioc-biobase,
  r-cran-genetics,
  r-cran-haplo.stats,
@@ -829,44 +850,51 @@ Recommends: bioperl,
  r-cran-rncl,
  r-cran-rnexml,
  ruby-bio,
+ ruby-crb-blast,
  sbmltoolbox,
  seqan-dev
 Suggests: bioclipse,
  libbam-dev,
+ libbio-eutilities-perl,
  libdisorder-dev,
  libforester-java,
  libfreecontact-doc,
  libgff-perl,
  libgtextutils-dev,
- libopenms-dev,
+ libpbcopper-dev,
  libqcpp-dev,
  librostlab-blast-doc,
  librostlab-doc,
  libswarm2-dev,
- libvcflib,
  mgltools-networkeditor,
  mgltools-pybabel,
  mgltools-vision,
  octace-bioinfo,
  octave-bioinfo,
+ python-bd2k,
  python-biopython-doc,
+ python-bx,
+ python-consensuscore2,
  python-hyphy,
- python-intervaltree-bio,
- python-miso,
+ python-misopy,
  python-mmtk,
  python-pyfasta,
- python-skbio,
+ python3-bd2k,
  python3-biopython-sql | python-biopython-sql,
+ python3-bx,
+ python3-consensuscore2,
+ python3-gffutils,
  python3-hyphy,
- python3-intervaltree-bio,
+ python3-misopy,
+ python3-pybedtools,
  python3-pyfasta,
- python3-skbio,
  r-bioc-affy,
  r-bioc-affyio,
  r-bioc-altcdfenvs,
  r-bioc-annotationdbi,
  r-bioc-biocgenerics,
  r-bioc-biomart,
+ r-bioc-biomformat,
  r-bioc-biovizbase,
  r-bioc-bsgenome,
  r-bioc-genomeinfodb,
@@ -878,14 +906,15 @@ Suggests: bioclipse,
  r-bioc-iranges,
  r-bioc-makecdfenv,
  r-bioc-preprocesscore,
+ r-bioc-rbgl,
  r-bioc-rsamtools,
  r-bioc-shortread,
  r-bioc-snpstats,
  r-bioc-variantannotation,
  r-bioc-xvector,
+ r-cran-rentrez,
  r-cran-rocr,
- ruby-crb-blast,
- unanimity
+ ruby-rgfa
 Description: Debian Med packages for development of bioinformatics applications
  This metapackage will install Debian packages which might be helpful
  for development of applications for biological research.
@@ -1005,6 +1034,7 @@ Recommends: abyss,
  python-biopython,
  python-cogent,
  python3-biopython,
+ qiime,
  r-bioc-edger,
  r-bioc-hilbertvis,
  r-cran-pvclust,
@@ -1042,7 +1072,6 @@ 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,
@@ -1137,15 +1166,18 @@ Recommends: aeskulap,
  camitk-imp,
  ctn,
  ctsim,
+ dcm2niix,
  dcmtk,
  dicom3tools,
  dicomnifti,
  dicomscope,
+ fslview,
  gdf-tools,
  ginkgocadx,
  gwyddion,
  imagej,
  imagevis3d,
+ invesalius,
  ismrmrd-tools,
  itksnap,
  king,
@@ -1156,7 +1188,11 @@ Recommends: aeskulap,
  mialmpick,
  minc-tools,
  mriconvert,
+ mricron,
+ mrtrix,
  nifti-bin,
+ odin,
+ openmeeg-tools,
  openslide-tools,
  orthanc,
  pixelmed-apps,
@@ -1169,11 +1205,14 @@ Recommends: aeskulap,
  python-nitime,
  python-surfer,
  python-tifffile,
+ sigviewer,
+ sofa-apps,
  teem-apps,
  voxbo,
  vtk-dicom-tools,
  xmedcon
 Suggests: afni,
+ bart-view,
  bioimagesuite,
  bioimagexd,
  blox,
@@ -1202,7 +1241,6 @@ Suggests: afni,
  fiji,
  freesurfer,
  fsl,
- fslview,
  fw4spl,
  gimias,
  gofigure2,
@@ -1211,7 +1249,6 @@ Suggests: afni,
  imview,
  incf-nidash-oneclick-clients,
  insightapplications,
- invesalius,
  isis,
  jemris,
  jist,
@@ -1229,14 +1266,10 @@ Suggests: afni,
  mni-colin27-nifti,
  mni-icbm152-nlin-2009,
  mni-n3,
- mricron,
  mrisim,
- mrtrix,
- odin,
  omero,
  opendicom.net,
  openelectrophy,
- openmeeg-tools,
  opensourcepacs,
  openwalnut-qt4,
  orthanc-dicomweb,
@@ -1249,9 +1282,7 @@ Suggests: afni,
  pymeg,
  python-pyxid,
  science-workflow,
- sigviewer,
  slicer,
- sofa-apps,
  stabilitycalc,
  stir,
  tempo,
@@ -1299,6 +1330,7 @@ Recommends: cimg-dev,
  libnifti-dev,
  libodil0-dev,
  libopenigtlink-dev,
+ libopenmeeg-dev,
  libopenslide-dev,
  libopensurgsim-dev,
  libpapyrus3-dev,
@@ -1310,9 +1342,11 @@ 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,
@@ -1337,7 +1371,6 @@ Suggests: emokit,
  liblimereg-dev,
  libmni-perllib-perl,
  libnifti-doc,
- libopenmeeg-dev,
  libopenslide-java,
  libvia-dev,
  libvmtk-dev,
@@ -1346,8 +1379,6 @@ Suggests: emokit,
  libvxl1-dev,
  libxdffileio-dev,
  octave-dicom,
- odin,
- python-dipy,
  python-imageio,
  python-libavg,
  python-tifffile,
@@ -1458,16 +1489,16 @@ Section: metapackages
 Architecture: all
 Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
 Recommends: praat,
+ psignifit,
  psychopy,
+ python-pyepl,
  r-cran-foreign,
  r-cran-psy
 Suggests: miscpsycho,
- psignifit,
  psych,
  psychometric,
  psychotree,
  psyphy,
- python-pyepl,
  python-pypsignifit,
  python-visionegg,
  science-psychophysics
@@ -1519,6 +1550,7 @@ Recommends: cronometer,
  python-fitbit,
  quitcount,
  r-cran-fitbitscraper,
+ r-cran-fitcoach,
  wgerman-medical,
  workrave
 Suggests: cycle,
@@ -1527,6 +1559,7 @@ Suggests: cycle,
  mencal,
  mssstest,
  nut-nutrition,
+ pesco,
  sleepyhead
 Description: Debian Med several tools
  This metapackage will install tools for several purposes in health care.
@@ -1543,6 +1576,7 @@ Suggests: biber,
  bibus,
  jabref-plugin-oo,
  kbibtex,
+ r-cran-qqman,
  referencer
 Description: Debian Med support for typesetting and publishing
  This metapackage will install Debian packages that might be helpful

-- 
Debian Med metapackages