[Blends-commit] [SCM] med branch, master, updated. 995e5823a960673507aac016512c079179dc6e04

[Andreas Tille]

The following commit has been merged in the master branch:
commit 995e5823a960673507aac016512c079179dc6e04
Author: Andreas Tille <tille at debian.org>
Date:   Tue Sep 1 22:42:39 2015 +0200

    Preparation of version 2.2

diff --git a/debian-med-tasks.desc b/debian-med-tasks.desc
index dde7554..e292476 100644
--- a/debian-med-tasks.desc
+++ b/debian-med-tasks.desc
@@ -24,12 +24,10 @@ Packages: list
  autodock
  autodock-vina
  autogrid
- ballview
  bamtools
  barrnap
  bedtools
  biomaj
- blasr
  blast2
  bowtie
  bowtie2
@@ -53,7 +51,6 @@ Packages: list
  disulfinder
  dnaclust
  dssp
- ea-utils
  ecopcr
  edtsurf
  embassy-domainatrix
@@ -70,12 +67,10 @@ Packages: list
  ffindex
  figtree
  filo
- fitgcp
  flexbar
  freecontact
  gamgi
  garlic
- gasic
  gbrowse
  gdpc
  genometools
@@ -141,7 +136,6 @@ Packages: list
  njplot
  norsnet
  norsp
- openms
  paraclu
  parsinsert
  pdb2pqr
@@ -224,7 +218,6 @@ Packages: list
  scythe
  seaview
  seqan-apps
- seqprep
  seqtk
  sibsim4
  sickle
@@ -235,12 +228,10 @@ Packages: list
  snp-sites
  soapdenovo
  soapdenovo2
- sortmerna
  spread-phy
  squizz
  sra-toolkit
  ssake
- stacks
  staden
  staden-io-lib-utils
  subread
@@ -248,12 +239,10 @@ Packages: list
  swarm
  t-coffee
  tabix
- tantan
  theseus
  tigr-glimmer
  tm-align
  tophat
- topp
  toppred
  transdecoder
  transtermhp
@@ -311,7 +300,6 @@ Packages: list
  libmuscle-3.7-dev
  libncbi6-dev
  libnhgri-blastall-perl
- libopenms-dev
  libpal-java
  librcsb-core-wrapper0-dev
  librdp-taxonomy-tree-java
@@ -341,14 +329,10 @@ Packages: list
  python-freecontact
  python-htseq
  python-mmtk
- python-pbcore
- python-pbh5tools
- python-pysam
  python-rdkit
  python-screed
  python3-hyphy
  python3-ruffus
- python3-skbio
  r-bioc-biobase
  r-cran-genetics
  r-cran-haplo.stats
@@ -461,10 +445,8 @@ Packages: list
  fasttree
  fastx-toolkit
  filo
- fitgcp
  flexbar
  freecontact
- gasic
  genometools
  giira
  grinder
@@ -531,7 +513,6 @@ Relevance: 10
 Key: 
  med-dental
 Packages: list
- entangle
  imagetooth
  openmolar
 
@@ -597,9 +578,7 @@ Key:
 Packages: list
  aeskulap
  amide
- ants
  biosig-tools
- camitk-imp
  caret
  conquest-common
  ctn
@@ -610,14 +589,11 @@ Packages: list
  dicomscope
  fslview
  gdf-tools
- ginkgocadx
- gofigure2
  gwyddion
  imagej
  imagevis3d
  invesalius
  ismrmrd-tools
- itksnap
  king
  libgdcm-tools
  medcon
@@ -630,7 +606,6 @@ Packages: list
  mrtrix
  nifti-bin
  odin
- openmeeg-tools
  openslide-tools
  orthanc
  pixelmed-apps
@@ -665,13 +640,11 @@ Packages: list
  gmic
  libactiviz.net-cil
  libbiosig-dev
- libcamitk3-dev
  libcv-dev
  libedf-dev
  libgdcm2-dev
  libgdf-dev
  libgiftiio-dev
- libigstk4-dev
  libinsighttoolkit3-dev
  libismrmrd-dev
  libmaxflow-dev
@@ -681,7 +654,6 @@ Packages: list
  libmiaviewit-dev
  libminc-dev
  libnifti-dev
- libopenmeeg-dev
  libopenslide-dev
  libpapyrus3-dev
  libteem-dev
@@ -773,11 +745,8 @@ Relevance: 10
 Key: 
  med-practice
 Packages: list
- clinica
- entangle
  freediams
  freemedforms-emr
- ginkgocadx
  gnumed-client
  gnumed-server
  libchipcard-tools
diff --git a/debian/changelog b/debian/changelog
index 8a2369a..ab449fc 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-debian-med (2.2) UNRELEASED; urgency=medium
+debian-med (2.2) unstable; urgency=medium
 
   * Moved to Git
 
diff --git a/debian/control b/debian/control
index ae4da97..78fa5ee 100644
--- a/debian/control
+++ b/debian/control
@@ -73,12 +73,10 @@ Recommends: abacas,
  autodock,
  autodock-vina,
  autogrid,
- ballview,
  bamtools,
  barrnap,
  bedtools,
  biomaj,
- blasr,
  blast2,
  bowtie,
  bowtie2,
@@ -102,7 +100,6 @@ Recommends: abacas,
  disulfinder,
  dnaclust,
  dssp,
- ea-utils,
  ecopcr,
  edtsurf,
  embassy-domainatrix,
@@ -119,12 +116,10 @@ Recommends: abacas,
  ffindex,
  figtree,
  filo,
- fitgcp,
  flexbar,
  freecontact,
  gamgi,
  garlic,
- gasic,
  gbrowse,
  gdpc,
  genometools,
@@ -190,7 +185,6 @@ Recommends: abacas,
  njplot,
  norsnet,
  norsp,
- openms,
  paraclu,
  parsinsert,
  pdb2pqr,
@@ -273,7 +267,6 @@ Recommends: abacas,
  scythe,
  seaview,
  seqan-apps,
- seqprep,
  seqtk,
  sibsim4,
  sickle,
@@ -284,12 +277,10 @@ Recommends: abacas,
  snp-sites,
  soapdenovo,
  soapdenovo2,
- sortmerna,
  spread-phy,
  squizz,
  sra-toolkit,
  ssake,
- stacks,
  staden,
  staden-io-lib-utils,
  subread,
@@ -297,12 +288,10 @@ Recommends: abacas,
  swarm,
  t-coffee,
  tabix,
- tantan,
  theseus,
  tigr-glimmer,
  tm-align,
  tophat,
- topp,
  toppred,
  transdecoder,
  transtermhp,
@@ -335,6 +324,7 @@ Suggests: abyss,
  axparafit,
  axpcoords,
  bagpipe,
+ ballview,
  bambus,
  beads,
  beast-mcmc,
@@ -345,6 +335,7 @@ Suggests: abyss,
  bio-rainbow,
  biomaj-watcher,
  bitseq,
+ blasr,
  blat,
  blimps-utils,
  blixem,
@@ -374,6 +365,7 @@ Suggests: abyss,
  dazzle,
  decipher,
  e-hive,
+ ea-utils,
  ecell,
  eigensoft,
  elph,
@@ -392,12 +384,14 @@ Suggests: abyss,
  fastml2,
  figaro,
  finex,
+ fitgcp,
  fluctuate,
  forester,
  forge,
  freebayes,
  fsa,
  galaxy,
+ gasic,
  gassst,
  gatk,
  gbioseq,
@@ -468,6 +462,7 @@ Suggests: abyss,
  obo-edit,
  oligoarrayaux,
  omegamap,
+ openms,
  operondb,
  pal2nal,
  paml,
@@ -514,26 +509,31 @@ Suggests: abyss,
  rsem,
  sap,
  seq-gen,
+ seqprep,
  sequenceconverter.app,
  sga,
  sift,
  situs,
  smrtanalysis,
  snpeff,
+ sortmerna,
  spades,
  spice,
  splitstree,
  ssaha,
+ stacks,
  strap,
  strap-base,
  suitename,
  sumtrees,
  tacg,
+ tantan,
  taverna,
  taxinspector,
  tetra,
  tigr-assembler,
  tigr-glimmer-mg,
+ topp,
  trace2dbest,
  tracetuner,
  treebuilder3d,
@@ -594,7 +594,6 @@ Recommends: bioperl,
  libmuscle-3.7-dev,
  libncbi6-dev,
  libnhgri-blastall-perl,
- libopenms-dev,
  libpal-java,
  librcsb-core-wrapper0-dev,
  librdp-taxonomy-tree-java,
@@ -624,14 +623,10 @@ Recommends: bioperl,
  python-freecontact,
  python-htseq,
  python-mmtk,
- python-pbcore,
- python-pbh5tools,
- python-pysam,
  python-rdkit,
  python-screed,
  python3-hyphy | python-hyphy,
  python3-ruffus | python-ruffus,
- python3-skbio | python-skbio,
  r-bioc-biobase,
  r-cran-genetics,
  r-cran-haplo.stats,
@@ -645,6 +640,7 @@ Suggests: bioclipse,
  libgbfp-dev,
  libgff-perl,
  libgtextutils-dev,
+ libopenms-dev,
  librostlab-blast-doc,
  librostlab-doc,
  libswarm2-dev,
@@ -656,8 +652,13 @@ Suggests: bioclipse,
  python-cutadapt,
  python-dendropy,
  python-miso,
+ python-pbcore,
+ python-pbh5tools,
+ python-pysam,
+ python-skbio,
  python3-cutadapt,
  python3-dendropy,
+ python3-skbio,
  r-bioc-affy,
  r-cran-rocr
 Description: Debian Med packages for development of micro-biology applications
@@ -710,10 +711,8 @@ Recommends: acedb-other,
  fasttree,
  fastx-toolkit,
  filo,
- fitgcp,
  flexbar,
  freecontact,
- gasic,
  genometools,
  giira,
  grinder,
@@ -750,7 +749,9 @@ Recommends: acedb-other,
  velvet
 Suggests: abyss,
  bagpipe,
- cufflinks
+ cufflinks,
+ fitgcp,
+ gasic
 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
@@ -774,9 +775,9 @@ Package: med-dental
 Section: metapackages
 Architecture: all
 Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: entangle,
- imagetooth,
+Recommends: 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.
@@ -835,9 +836,7 @@ Architecture: all
 Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
 Recommends: aeskulap,
  amide,
- ants,
  biosig-tools,
- camitk-imp,
  caret,
  conquest-common,
  ctn,
@@ -848,14 +847,11 @@ Recommends: aeskulap,
  dicomscope,
  fslview,
  gdf-tools,
- ginkgocadx,
- gofigure2,
  gwyddion,
  imagej,
  imagevis3d,
  invesalius,
  ismrmrd-tools,
- itksnap,
  king,
  libgdcm-tools,
  medcon,
@@ -868,7 +864,6 @@ Recommends: aeskulap,
  mrtrix,
  nifti-bin,
  odin,
- openmeeg-tools,
  openslide-tools,
  orthanc,
  pixelmed-apps,
@@ -888,10 +883,12 @@ Recommends: aeskulap,
  vtk-dicom-tools,
  xmedcon
 Suggests: afni,
+ ants,
  bioimagesuite,
  bioimagexd,
  blox,
  brainvisa,
+ camitk-imp,
  cdmedicpacs,
  cellprofiler,
  cmtk,
@@ -915,12 +912,15 @@ Suggests: afni,
  freesurfer,
  fsl,
  gimias,
+ ginkgocadx,
+ gofigure2,
  hid,
  imagemagick,
  imview,
  incf-nidash-oneclick-clients,
  insightapplications,
  isis,
+ itksnap,
  jemris,
  jist,
  kradview,
@@ -941,6 +941,7 @@ Suggests: afni,
  omero,
  opendicom.net,
  openelectrophy,
+ openmeeg-tools,
  opensourcepacs,
  openwalnut-qt4,
  orthanc-webviewer,
@@ -988,13 +989,11 @@ Recommends: cimg-dev,
  gmic,
  libactiviz.net-cil,
  libbiosig-dev,
- libcamitk3-dev,
  libcv-dev,
  libedf-dev,
  libgdcm2-dev,
  libgdf-dev,
  libgiftiio-dev,
- libigstk4-dev,
  libinsighttoolkit3-dev | libinsighttoolkit4-dev,
  libismrmrd-dev,
  libmaxflow-dev,
@@ -1004,7 +1003,6 @@ Recommends: cimg-dev,
  libmiaviewit-dev,
  libminc-dev,
  libnifti-dev,
- libopenmeeg-dev,
  libopenslide-dev,
  libpapyrus3-dev,
  libteem-dev,
@@ -1037,13 +1035,16 @@ Suggests: emokit,
  igstk-examples,
  insighttoolkit3-examples,
  libbio-formats-java,
+ libcamitk3-dev,
  libctk-dev,
  libeegdev-dev,
  libics-dev,
+ libigstk4-dev,
  liblimereg-dev,
  libmni-perllib-perl,
  libnifti-doc,
  libopenigtlink1-dev,
+ libopenmeeg-dev,
  libopenslide-java,
  libopensurgsim-dev,
  libvia-dev,
@@ -1123,22 +1124,22 @@ Package: med-practice
 Section: metapackages
 Architecture: all
 Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: clinica,
- entangle,
- freediams,
+Recommends: freediams,
  freemedforms-emr,
- ginkgocadx,
  gnumed-client,
  gnumed-server,
  libchipcard-tools,
  qrisk2,
  r-cran-medadherence
 Suggests: clearhealth,
+ clinica,
  elementalclinic,
  elexis,
+ entangle,
  freeb,
  freemed,
  freeshim,
+ ginkgocadx,
  libctapimkt1,
  medintux,
  mirrormed,

-- 
Debian Med metapackages