[Blends-commit] [SCM] med branch, master, updated. 6c331288e259517e9f671cd8b761171df48e499a

[Andreas Tille]

The following commit has been merged in the master branch:
commit 2dcc8bc97a9cc05ac11f27a2a0bd2bbc133b2ca5
Author: Andreas Tille <tille at debian.org>
Date:   Mon Sep 12 10:02:57 2016 +0200

    Regenerate dependencies

diff --git a/debian-med-tasks.desc b/debian-med-tasks.desc
index b7b623a..6689025 100644
--- a/debian-med-tasks.desc
+++ b/debian-med-tasks.desc
@@ -25,24 +25,6 @@ Test-new-install: mark show
 Key: 
  med-bio-dev
 
-Task: med-bio-ngs
-Parent: debian-med
-Section: debian-med
-Description: Debian Med bioinformatics applications usable in Next Generation Sequencing
- It aims at gettting packages which specializes in alignment of
- sequences produced by next generation sequencing.
-Test-new-install: mark show
-
-Task: med-bio-phylogeny
-Parent: debian-med
-Section: debian-med
-Description: Debian Med phylogeny packages
- This lists Debian packages related to phylogeny for use in life sciences.
- The purpose of this compilation of packages is to have a handy subset of
- from the med-bio metapackage which contains a lot more than only phylogeny
- related software.
-Test-new-install: mark show
-
 Task: med-cloud
 Parent: debian-med
 Section: debian-med
@@ -51,18 +33,9 @@ Description: Debian Med bioinformatics applications usable in cloud computing
  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.
-Test-new-install: mark show
 Key: 
  med-cloud
 
-Task: med-cms
-Parent: debian-med
-Section: debian-med
-Description: Debian Med content management systems
- Here you can find software that is useful to build a
- content management system for medical care.
-Test-new-install: mark show
-
 Task: med-data
 Parent: debian-med
 Section: debian-med
@@ -70,7 +43,6 @@ Description: Debian Med drug databases
  This metapackage will install free drug databases and related
  applications. The database can be accessed by any EMR using
  the application.
-Test-new-install: mark show
 Key: 
  med-data
 
@@ -80,7 +52,6 @@ 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.
-Test-new-install: mark show
 Key: 
  med-dental
 
@@ -93,7 +64,6 @@ Description: Debian Med epidemiology related packages
  statistical investigation.  It might be a good idea to read the paper
  "A short introduction to R for Epidemiology" at
  http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
-Test-new-install: mark show
 Key: 
  med-epi
 
@@ -106,7 +76,6 @@ Description: Debian Med suggestions for Hospital Information Systems
  continuous work going on to package a ready to install system currently
  only preconditions are finished but hopefully helpful in hospitals
  anyway.
-Test-new-install: mark show
 Key: 
  med-his
 
@@ -124,7 +93,6 @@ Description: Debian Med image processing and visualization packages
  software packages that can be used for visualization and for image processing
  - either from a graphical user interface, the command  line, or implemented in
  workflows.
-Test-new-install: mark show
 Key: 
  med-imaging
 
@@ -135,7 +103,6 @@ Description: Debian Med image processing and visualization packages development
  This metapackage will install Debian packages which might be useful
  for developing applications for medical image processing and
  visualization.
-Test-new-install: mark show
 Key: 
  med-imaging-dev
 
@@ -145,7 +112,6 @@ 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.
-Test-new-install: mark show
 Key: 
  med-laboratory
 
@@ -155,7 +121,6 @@ Section: debian-med
 Description: Debian Med packages for oncology
  This metapackage will install tools that are useful for radiation
  oncology.
-Test-new-install: mark show
 Key: 
  med-oncology
 
@@ -166,7 +131,6 @@ Description: Debian Med packages for pharmaceutical research
  This metapackage contains dependencies for a
  collection of software and documentation which is useful for
  pharmaceutical research.
-Test-new-install: mark show
 Key: 
  med-pharmacy
 
@@ -178,7 +142,6 @@ Description: Debian Med packages for medical physicists
  collection of software and documentation which is useful for
  medical physicists in radiation oncology, diagnostics imaging
  and related fields.
-Test-new-install: mark show
 Key: 
  med-physics
 
@@ -188,7 +151,6 @@ Section: debian-med
 Description: Debian Med packages for practice management
  This metapackage contains dependencies for a collection of software
  which might be helpful for practitioners to manage their practice.
-Test-new-install: mark show
 Key: 
  med-practice
 
@@ -198,7 +160,6 @@ Section: debian-med
 Description: Debian Med packages for psychology
  This metapackage contains dependencies for a collection of software
  which might be helpful for psychological research.
-Test-new-install: mark show
 Key: 
  med-psychology
 
@@ -208,7 +169,6 @@ Section: debian-med
 Description: Debian Med packages for rehabilitation technologies
  This metapackage will install tools that are useful for
  rehabilitation and therapy.
-Test-new-install: mark show
 Key: 
  med-rehabilitation
 
@@ -228,7 +188,6 @@ Section: debian-med
 Description: Debian Med several tools
  This metapackage will install tools for several purposes in health care.
  Currently it contains some simple programs for Personal Health.
-Test-new-install: mark show
 Key: 
  med-tools
 
@@ -239,7 +198,6 @@ Description: Debian Med support for typesetting and publishing
  This metapackage will install Debian packages that might be helpful
  for typesetting and publishing in medical care and structural
  biology.
-Test-new-install: mark show
 Key: 
  med-typesetting
 
diff --git a/debian/control b/debian/control
index 1e61f01..44b490b 100644
--- a/debian/control
+++ b/debian/control
@@ -58,7 +58,8 @@ Section: metapackages
 Architecture: all
 Recommends: med-bio,
  med-bio-dev,
- med-cloud,
+ med-statistics
+Suggests: med-cloud,
  med-data,
  med-dental,
  med-epi,
@@ -72,7 +73,6 @@ Recommends: med-bio,
  med-practice,
  med-psychology,
  med-rehabilitation,
- med-statistics,
  med-tools,
  med-typesetting
 Description: Default selection of tasks for Debian Med
@@ -87,6 +87,7 @@ Recommends: abacas,
  acedb-other,
  acedb-other-belvu,
  acedb-other-dotter,
+ adapterremoval,
  adun-core,
  aegean,
  aevol,
@@ -96,7 +97,11 @@ Recommends: abacas,
  amap-align,
  ampliconnoise,
  andi,
+ anfo,
  aragorn,
+ arden,
+ ariba,
+ art-nextgen-simulation-tools,
  artemis,
  artfastqgenerator,
  augustus,
@@ -104,10 +109,13 @@ Recommends: abacas,
  autodock-vina,
  autogrid,
  axe-demultiplexer,
+ ballview,
  bamtools,
  barrnap,
  bcftools,
  beagle,
+ beast-mcmc,
+ beast2-mcmc,
  bedtools,
  berkeley-express,
  bio-rainbow,
@@ -134,6 +142,7 @@ Recommends: abacas,
  codonw,
  concavity,
  conservation-code,
+ cutadapt,
  daligner,
  dawg,
  dazzdb,
@@ -148,17 +157,20 @@ Recommends: abacas,
  ea-utils,
  ecopcr,
  edtsurf,
+ eigensoft,
  embassy-domainatrix,
  embassy-domalign,
  embassy-domsearch,
  emboss,
  exonerate,
  falconkit,
+ fastahack,
  fastaq,
  fastdnaml,
  fastlink,
  fastml,
  fastqc,
+ fastqtl,
  fasttree,
  fastx-toolkit,
  ffindex,
@@ -166,8 +178,12 @@ Recommends: abacas,
  filo,
  fitgcp,
  flexbar,
+ fml-asm,
  freecontact,
+ fsa,
+ fsm-lite,
  gamgi,
+ garli,
  garlic,
  gasic,
  gbrowse,
@@ -179,12 +195,15 @@ Recommends: abacas,
  ghemical,
  giira,
  glam2,
+ graphlan,
  grinder,
  gromacs,
  gubbins,
  gwama,
  harvest-tools,
  hhsuite,
+ hilive,
+ hisat2,
  hmmer,
  hmmer2,
  hyphy-mpi | hyphy-pt,
@@ -198,6 +217,7 @@ Recommends: abacas,
  jaligner,
  jalview,
  jellyfish,
+ jmodeltest,
  jmol,
  kalign,
  khmer,
@@ -209,15 +229,20 @@ Recommends: abacas,
  kraken,
  last-align,
  leaff,
+ lefse,
  librg-utils-perl,
  logol-bin,
  loki,
  ltrsift,
  macs,
  macsyfinder,
+ maffilter,
  mafft,
+ mapdamage,
+ mapsembler2,
  maq,
  maqview,
+ mash,
  massxpert,
  mauve-aligner,
  melting,
@@ -251,12 +276,14 @@ Recommends: abacas,
  njplot,
  norsnet,
  norsp,
+ openms,
  paraclu,
  parsinsert,
  pbalign,
  pbbarcode,
  pbdagcon,
  pbgenomicconsensus,
+ pbh5tools,
  pbhoney,
  pbjelly,
  pbsim,
@@ -264,9 +291,11 @@ Recommends: abacas,
  pdb2pqr,
  perlprimer,
  perm,
+ phipack,
  phybin,
  phylip,
  phyml,
+ physamp,
  phyutility,
  picard-tools,
  piler,
@@ -312,24 +341,34 @@ Recommends: abacas,
  pynast,
  pyscanfcs,
  python-cogent,
+ qiime,
  r-bioc-annotate,
  r-bioc-biostrings,
  r-bioc-cummerbund,
+ r-bioc-deseq2,
+ r-bioc-dnacopy,
  r-bioc-ebseq,
  r-bioc-edger,
  r-bioc-genefilter,
+ r-bioc-geneplotter,
  r-bioc-gviz,
  r-bioc-hilbertvis,
  r-bioc-limma,
  r-bioc-rtracklayer,
+ r-cran-adegenet,
+ r-cran-adephylo,
  r-cran-ape,
  r-cran-bio3d,
+ r-cran-distory,
  r-cran-genabel,
  r-cran-phangorn,
+ r-cran-pscbs,
  r-cran-qtl,
  r-cran-seqinr,
+ r-cran-treescape,
  r-cran-vegan,
  r-other-mott-happy.hbrem,
+ rapmap,
  rasmol,
  raster3d,
  rate4site,
@@ -359,14 +398,18 @@ Recommends: abacas,
  seqan-apps,
  seqprep,
  seqtk,
+ sga,
  sibsim4,
  sickle,
  sigma-align,
  sim4,
  sim4db,
  smalt,
+ smithwaterman,
+ smrtanalysis,
  snap,
  snap-aligner,
+ sniffles,
  snp-sites,
  snpomatic,
  soapdenovo,
@@ -378,7 +421,10 @@ Recommends: abacas,
  spread-phy,
  squizz,
  sra-toolkit,
+ srst2,
  ssake,
+ sspace,
+ ssw-align,
  stacks,
  staden,
  staden-io-lib-utils,
@@ -396,6 +442,7 @@ Recommends: abacas,
  tigr-glimmer,
  tm-align,
  tophat,
+ topp,
  toppred,
  transdecoder,
  transrate-tools,
@@ -419,22 +466,16 @@ Suggests: abyss,
  adun.app,
  amos-assembler,
  amoscmp,
- anfo,
  apollo,
  arachne,
  arb,
- arden,
- ariba,
- art-nextgen-simulation-tools,
  asap,
  autodocktools,
  axparafit,
  axpcoords,
  bagpipe,
- ballview,
  bambus,
  beads,
- beast-mcmc,
  biceps,
  big-blast,
  bigsdb,
@@ -470,7 +511,6 @@ Suggests: abyss,
  decipher,
  e-hive,
  ecell,
- eigensoft,
  elph,
  embassy-phylip,
  emboss-explorer,
@@ -484,7 +524,7 @@ Suggests: abyss,
  excavator,
  fasta,
  fasta3,
- fastqtl,
+ fermi-lite,
  ffp,
  figaro,
  finex,
@@ -492,10 +532,7 @@ Suggests: abyss,
  forester,
  forge,
  freebayes,
- fsa,
- fsm-lite,
  galaxy,
- garli,
  gassst,
  gatk,
  gbioseq,
@@ -519,30 +556,34 @@ Suggests: abyss,
  inspect,
  jbrowse,
  jigsaw,
- jmodeltest,
  jstreeview,
  kclust,
  kempbasu,
+ kronatools,
  lagan,
  lamarc,
+ lambda-align,
  lofreq,
  logomat-m,
  lucy,
  mach-haplotyper,
- maffilter,
  mage2tab,
  maker2,
- mapsembler2,
  martj,
  maude,
  maxd,
  melting-gui,
  meme,
  mesquite,
+ metabit,
+ metaphlan2,
  metarep,
  metastudent-data,
  metastudent-data-2,
  metastudent-data-3,
+ mgltools-cadd,
+ mgltools-pmv,
+ mgltools-vision,
  migrate,
  minimus,
  mirbase,
@@ -567,7 +608,6 @@ Suggests: abyss,
  obo-edit,
  oligoarrayaux,
  omegamap,
- openms,
  operondb,
  pal2nal,
  paml,
@@ -581,12 +621,13 @@ Suggests: abyss,
  pftools,
  phagefinder,
  phast,
- phipack,
  phpphylotree,
  phylographer,
+ phylophlan,
  phyloviz-core,
  phylowin,
  pipasic,
+ pirs,
  plato,
  profit,
  prokka,
@@ -597,13 +638,15 @@ Suggests: abyss,
  pyrophosphate-tools,
  python-orange,
  python-reaper,
- qiime,
  qtlcart,
  qualimap,
+ r-bioc-annotationhub,
  r-bioc-aroma.light,
+ r-bioc-ensembldb,
+ r-bioc-go.db,
  r-cran-boolnet,
  r-cran-metamix,
- r-cran-treescape,
+ r-cran-pheatmap,
  r-other-apmswapp,
  r-other-valdar-bagphenotype.library,
  raccoon,
@@ -616,18 +659,18 @@ Suggests: abyss,
  roche454ace2caf,
  rose,
  rosetta,
+ rsat,
  sap,
  science-workflow,
+ segemehl,
  seq-gen,
  sequenceconverter.app,
- sga,
  sift,
  situs,
- smrtanalysis,
  snpeff,
+ sparta,
  spice,
  splitstree,
- srst2,
  ssaha,
  strap,
  strap-base,
@@ -637,7 +680,6 @@ Suggests: abyss,
  tetra,
  tide,
  tigr-glimmer-mg,
- topp,
  trace2dbest,
  tracetuner,
  treebuilder3d,
@@ -648,6 +690,7 @@ Suggests: abyss,
  ugene,
  unc-fish,
  uniprime,
+ varmatch,
  varscan,
  vienna-rna,
  vmd,
@@ -687,9 +730,12 @@ Recommends: bioperl,
  libbpp-seq-dev,
  libbpp-seq-omics-dev,
  libchado-perl,
+ libconsensuscore2-dev,
  libdivsufsort-dev,
  libfast5-dev,
+ libfastahack-dev,
  libffindex0-dev,
+ libfml-dev,
  libfreecontact-perl,
  libgenome-1.3-dev,
  libgenome-model-tools-music-perl,
@@ -705,11 +751,13 @@ Recommends: bioperl,
  libmems-1.6-dev,
  libminimap-dev,
  libmuscle-3.7-dev,
+ libncbi-vdb-dev,
  libncbi6-dev,
  libncl-dev,
  libngs-java,
  libngs-sdk-dev,
  libnhgri-blastall-perl,
+ libopenms-dev,
  libpal-java,
  libpbbam-dev,
  libpbdata-dev,
@@ -724,10 +772,13 @@ Recommends: bioperl,
  librostlab-blast0-dev,
  librostlab3-dev,
  libsbml5-dev,
+ libsmithwaterman-dev,
  libsnp-sites1-dev,
  libsort-key-top-perl,
  libsrf-dev,
  libssm-dev,
+ libssw-dev,
+ libssw-java,
  libstaden-read-dev,
  libtabixpp-dev,
  libtfbs-perl,
@@ -736,31 +787,36 @@ Recommends: bioperl,
  libzerg0-dev,
  mcl,
  pyfai,
+ python-biom-format,
  python-cobra,
  python-cogent,
  python-corepywrap,
  python-freecontact,
+ python-htseq,
  python-kineticstools,
- python-ngs,
  python-pbcommand,
  python-pbcore,
  python-pbh5tools,
  python-pysam,
+ 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-hyphy | python-hyphy,
- python3-ngs,
+ 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,
+ r-cran-phylobase,
  r-cran-rncl,
  r-cran-rnexml,
  ruby-bio,
@@ -769,32 +825,31 @@ Recommends: bioperl,
  seqan-dev
 Suggests: bioclipse,
  libbam-dev,
+ libdisorder-dev,
  libforester-java,
  libfreecontact-doc,
  libfreecontact0-dev,
  libgff-perl,
  libgtextutils-dev,
- libopenms-dev,
  libqcpp-dev,
  librostlab-blast-doc,
  librostlab-doc,
  libswarm2-dev,
  libvcflib,
+ mgltools-networkeditor,
+ mgltools-pybabel,
+ mgltools-vision,
  octace-bioinfo,
  octave-bioinfo,
- python-biom-format,
  python-biopython-doc,
- python-htseq,
  python-intervaltree-bio,
  python-miso,
  python-mmtk,
  python-pyfasta,
- python-rdkit,
  python-skbio,
  python3-biopython-sql | python-biopython-sql,
  python3-intervaltree-bio,
  python3-pyfasta,
- python3-skbio,
  r-bioc-affy,
  r-cran-rocr
 Description: Debian Med packages for development of bioinformatics applications
@@ -811,7 +866,9 @@ Recommends: acedb-other,
  altree,
  amap-align,
  ampliconnoise,
+ anfo,
  aragorn,
+ arden,
  autodock,
  autodock-vina,
  autogrid,
@@ -858,6 +915,7 @@ Recommends: acedb-other,
  last-align,
  loki,
  macs,
+ mapsembler2,
  maq,
  melting,
  minia,
@@ -883,11 +941,8 @@ Recommends: acedb-other,
  tophat,
  velvet
 Suggests: abyss,
- anfo,
- arden,
  bagpipe,
- cufflinks,
- mapsembler2
+ cufflinks
 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
@@ -986,11 +1041,13 @@ Recommends: aeskulap,
  dicom3tools,
  dicomnifti,
  dicomscope,
+ fslview,
  gdf-tools,
  ginkgocadx,
  gwyddion,
  imagej,
  imagevis3d,
+ invesalius,
  ismrmrd-tools,
  itksnap,
  king,
@@ -1001,9 +1058,11 @@ Recommends: aeskulap,
  mialmpick,
  minc-tools,
  mriconvert,
+ mricron,
  mrtrix,
  nifti-bin,
  odin,
+ openmeeg-tools,
  openslide-tools,
  orthanc,
  pixelmed-apps,
@@ -1012,9 +1071,12 @@ Recommends: aeskulap,
  python-dipy,
  python-mvpa2,
  python-nibabel,
+ python-nipy,
+ python-nipype,
  python-nitime,
  python-surfer,
  sigviewer,
+ sofa-apps,
  teem-apps,
  voxbo,
  vtk-dicom-tools,
@@ -1047,7 +1109,6 @@ Suggests: afni,
  fiji,
  freesurfer,
  fsl,
- fslview,
  fw4spl,
  gimias,
  gofigure2,
@@ -1056,7 +1117,6 @@ Suggests: afni,
  imview,
  incf-nidash-oneclick-clients,
  insightapplications,
- invesalius,
  isis,
  jemris,
  jist,
@@ -1074,12 +1134,10 @@ Suggests: afni,
  mni-colin27-nifti,
  mni-icbm152-nlin-2009,
  mni-n3,
- mricron,
  mrisim,
  omero,
  opendicom.net,
  openelectrophy,
- openmeeg-tools,
  opensourcepacs,
  openwalnut-qt4,
  orthanc-dicomweb,
@@ -1090,12 +1148,9 @@ Suggests: afni,
  piano,
  pngquant,
  pymeg,
- python-nipy,
- python-nipype,
  python-pyxid,
  science-workflow,
  slicer,
- sofa-apps,
  stabilitycalc,
  stir,
  tempo,
@@ -1136,12 +1191,12 @@ Recommends: cimg-dev,
  libismrmrd-dev,
  libmaxflow-dev,
  libmdc2-dev,
- libmia-2.2-dev,
  libmialm-dev,
  libmiaviewit-dev,
  libminc-dev,
  libnifti-dev,
  libodil0-dev,
+ libopenmeeg-dev,
  libopenslide-dev,
  libopensurgsim-dev,
  libpapyrus3-dev,
@@ -1163,6 +1218,8 @@ Recommends: cimg-dev,
  python-mne,
  python-mvpa2,
  python-nibabel,
+ python-nipy,
+ python-nipype,
  python-nitime,
  python-openslide,
  python-pyxnat,
@@ -1170,7 +1227,6 @@ Recommends: cimg-dev,
  r-cran-rniftilib
 Suggests: emokit,
  igstk-examples,
- libactiviz.net-cil,
  libbio-formats-java,
  libcamitk3-dev,
  libcamp0.7-dev,
@@ -1180,10 +1236,10 @@ Suggests: emokit,
  libics-dev,
  libigstk4-dev,
  liblimereg-dev,
+ libmia-2.2-dev,
  libmni-perllib-perl,
  libnifti-doc,
  libopenigtlink1-dev,
- libopenmeeg-dev,
  libopenslide-java,
  libvia-dev,
  libvmtk-dev,
@@ -1194,8 +1250,6 @@ Suggests: emokit,
  octave-dicom,
  python-imageio,
  python-libavg,
- python-nipy,
- python-nipype,
  python-tifffile,
  python-vmtk
 Description: Debian Med image processing and visualization packages development
@@ -1355,6 +1409,7 @@ Architecture: all
 Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
 Recommends: cronometer,
  edfbrowser,
+ galileo,
  hunspell-de-med,
  hunspell-en-med,
  nut-nutrition,

-- 
Debian Med metapackages