[Blends-commit] [SCM] med branch, master, updated. 9307e7ae96234d8bd736e97a159d15427e2f4a23

[Andreas Tille]

The following commit has been merged in the master branch:
commit 9307e7ae96234d8bd736e97a159d15427e2f4a23
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 10 20:08:44 2016 +0100

    Recreate control using blends-dev 0.6.95 which is able to properly parse dependencies without '\' at EOL

diff --git a/debian-med-tasks.desc b/debian-med-tasks.desc
index 6689025..6108c40 100644
--- a/debian-med-tasks.desc
+++ b/debian-med-tasks.desc
@@ -10,7 +10,6 @@ Section: debian-med
 Description: Debian Med bioinformatics packages
  This metapackage will install Debian packages for use in molecular biology,
  structural biology and other biological sciences.
-Enhances: t-coffee
 Test-new-install: mark show
 Key: 
  med-bio
diff --git a/debian/control b/debian/control
index 143737d..47ed31a 100644
--- a/debian/control
+++ b/debian/control
@@ -84,11 +84,11 @@ Section: metapackages
 Architecture: all
 Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
 Recommends: abacas,
+ abyss,
  acedb-other,
  acedb-other-belvu,
  acedb-other-dotter,
  adapterremoval,
- adun-core,
  aegean,
  aevol,
  alien-hunter,
@@ -97,7 +97,9 @@ Recommends: abacas,
  amap-align,
  ampliconnoise,
  andi,
+ anfo,
  aragorn,
+ arden,
  ariba,
  art-nextgen-simulation-tools,
  artemis,
@@ -115,8 +117,8 @@ Recommends: abacas,
  beast2-mcmc,
  bedtools,
  berkeley-express,
+ bio-eagle,
  bio-rainbow,
- biomaj,
  blasr,
  blast2,
  bowtie,
@@ -141,6 +143,7 @@ Recommends: abacas,
  conservation-code,
  cutadapt,
  daligner,
+ dascrubber,
  dawg,
  dazzdb,
  dialign,
@@ -182,6 +185,7 @@ Recommends: abacas,
  gamgi,
  garli,
  garlic,
+ gasic,
  gbrowse,
  gdpc,
  genometools,
@@ -222,6 +226,7 @@ Recommends: abacas,
  kmc,
  kmer,
  kraken,
+ lambda-align,
  last-align,
  leaff,
  lefse,
@@ -234,6 +239,7 @@ Recommends: abacas,
  maffilter,
  mafft,
  mapdamage,
+ mapsembler2,
  maq,
  maqview,
  mash,
@@ -241,6 +247,7 @@ Recommends: abacas,
  mauve-aligner,
  melting,
  meryl,
+ metaphlan2,
  metastudent,
  mhap,
  microbegps,
@@ -272,6 +279,7 @@ Recommends: abacas,
  norsp,
  paraclu,
  parsinsert,
+ parsnp,
  pbalign,
  pbbarcode,
  pbdagcon,
@@ -357,9 +365,9 @@ Recommends: abacas,
  r-cran-pscbs,
  r-cran-qtl,
  r-cran-seqinr,
- r-cran-treescape,
  r-cran-vegan,
  r-other-mott-happy.hbrem,
+ rapmap,
  rasmol,
  raster3d,
  rate4site,
@@ -386,8 +394,10 @@ Recommends: abacas,
  scythe,
  seaview,
  seer,
+ seqan-apps,
  seqprep,
  seqtk,
+ sga,
  sibsim4,
  sickle,
  sigma-align,
@@ -409,8 +419,10 @@ Recommends: abacas,
  sprai,
  spread-phy,
  squizz,
+ sra-toolkit,
  srst2,
  ssake,
+ sspace,
  ssw-align,
  stacks,
  staden,
@@ -447,16 +459,14 @@ Recommends: abacas,
  wigeon,
  wise,
  zalign
-Suggests: abyss,
- acacia,
+Suggests: acacia,
+ adun-core,
  adun.app,
  amos-assembler,
  amoscmp,
- anfo,
  apollo,
  arachne,
  arb,
- arden,
  asap,
  autodocktools,
  axparafit,
@@ -468,11 +478,13 @@ Suggests: abyss,
  biceps,
  big-blast,
  bigsdb,
+ biomaj,
  biomaj-watcher,
  bitseq,
  blat,
  blimps-utils,
  blixem,
+ blobology,
  btk-core,
  cactus,
  caftools,
@@ -487,6 +499,7 @@ Suggests: abyss,
  coalesce,
  compclust,
  condetri,
+ contrafold,
  contralign,
  coot,
  copycat,
@@ -498,6 +511,7 @@ Suggests: abyss,
  das-proserver,
  dazzle,
  decipher,
+ deepnano,
  e-hive,
  ecell,
  elph,
@@ -522,7 +536,6 @@ Suggests: abyss,
  forge,
  freebayes,
  galaxy,
- gasic,
  gassst,
  gatk,
  gbioseq,
@@ -553,14 +566,13 @@ Suggests: abyss,
  kronatools,
  lagan,
  lamarc,
- lambda-align,
  lofreq,
  logomat-m,
  lucy,
  mach-haplotyper,
  mage2tab,
  maker2,
- mapsembler2,
+ malt,
  martj,
  maude,
  maxd,
@@ -568,7 +580,6 @@ Suggests: abyss,
  meme,
  mesquite,
  metabit,
- metaphlan2,
  metarep,
  metastudent-data,
  metastudent-data-2,
@@ -591,6 +602,7 @@ Suggests: abyss,
  mugsy,
  mummergpu,
  mview,
+ nanocall,
  ncbi-entrez-direct,
  ngila,
  ngsqctoolkit,
@@ -604,7 +616,6 @@ Suggests: abyss,
  operondb,
  pal2nal,
  paml,
- parsnp,
  partigene,
  partitionfinder,
  patman,
@@ -641,11 +652,11 @@ Suggests: abyss,
  r-cran-boolnet,
  r-cran-metamix,
  r-cran-pheatmap,
+ r-cran-treescape,
  r-other-apmswapp,
  r-other-valdar-bagphenotype.library,
  raccoon,
  rambo-k,
- rapmap,
  rbs-finder,
  recombine,
  repeatmasker,
@@ -659,18 +670,14 @@ Suggests: abyss,
  science-workflow,
  segemehl,
  seq-gen,
- seqan-apps,
  sequenceconverter.app,
- sga,
  sift,
  situs,
  snpeff,
  sparta,
  spice,
  splitstree,
- sra-toolkit,
  ssaha,
- sspace,
  strap,
  strap-base,
  tacg,
@@ -786,10 +793,12 @@ Recommends: bioperl,
  libzerg0-dev,
  mcl,
  pyfai,
+ python-biom-format,
  python-cobra,
  python-cogent,
  python-corepywrap,
  python-freecontact,
+ python-htseq,
  python-kineticstools,
  python-pbcommand,
  python-pbcore,
@@ -800,7 +809,6 @@ Recommends: bioperl,
  python3-csb | python-csb,
  python3-cutadapt | python-cutadapt,
  python3-dendropy | python-dendropy,
- python3-hyphy | python-hyphy,
  python3-ngs | python-ngs,
  python3-pbconsensuscore | python-pbconsensuscore,
  python3-pyfaidx | python-pyfaidx,
@@ -814,13 +822,15 @@ Recommends: bioperl,
  r-cran-rncl,
  r-cran-rnexml,
  ruby-bio,
- sbmltoolbox
+ sbmltoolbox,
+ seqan-dev
 Suggests: bioclipse,
  libbam-dev,
  libdisorder-dev,
  libforester-java,
  libfreecontact-doc,
  libgff-perl,
+ libgkarrays-dev,
  libgtextutils-dev,
  libopenms-dev,
  libqcpp-dev,
@@ -834,10 +844,9 @@ Suggests: bioclipse,
  mgltools-vision,
  octace-bioinfo,
  octave-bioinfo,
- python-biom-format,
  python-biopython-doc,
  python-consensuscore2,
- python-htseq,
+ python-hyphy,
  python-intervaltree-bio,
  python-miso,
  python-mmtk,
@@ -846,13 +855,34 @@ Suggests: bioclipse,
  python-skbio,
  python3-biopython-sql | python-biopython-sql,
  python3-consensuscore2,
+ python3-hyphy,
  python3-intervaltree-bio,
  python3-pyfasta,
  python3-skbio,
  r-bioc-affy,
+ r-bioc-affyio,
+ r-bioc-altcdfenvs,
+ r-bioc-annotationdbi,
+ r-bioc-biocgenerics,
+ r-bioc-biomart,
+ r-bioc-biovizbase,
+ r-bioc-bsgenome,
+ r-bioc-genomeinfodb,
+ r-bioc-genomicalignments,
+ r-bioc-genomicfeatures,
+ r-bioc-genomicranges,
+ r-bioc-graph,
+ r-bioc-hypergraph,
+ r-bioc-iranges,
+ r-bioc-makecdfenv,
+ r-bioc-preprocesscore,
+ r-bioc-rsamtools,
+ r-bioc-shortread,
+ r-bioc-snpstats,
+ r-bioc-variantannotation,
+ r-bioc-xvector,
  r-cran-rocr,
- ruby-crb-blast,
- seqan-dev
+ ruby-crb-blast
 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.
@@ -861,13 +891,16 @@ Package: med-cloud
 Section: metapackages
 Architecture: all
 Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: acedb-other,
+Recommends: abyss,
+ acedb-other,
  aevol,
  alien-hunter,
  altree,
  amap-align,
  ampliconnoise,
+ anfo,
  aragorn,
+ arden,
  autodock,
  autodock-vina,
  autogrid,
@@ -889,12 +922,22 @@ Recommends: acedb-other,
  circos,
  clearcut,
  clonalframe,
+ clustalo,
+ clustalw,
  concavity,
+ conservation-code,
  datamash,
+ dialign,
+ dialign-tx,
  discosnp,
  disulfinder,
  dnaclust,
  dssp,
+ embassy-domainatrix,
+ embassy-domalign,
+ embassy-domsearch,
+ emboss,
+ exonerate,
  fastdnaml,
  fastlink,
  fastqc,
@@ -904,46 +947,100 @@ Recommends: acedb-other,
  fitgcp,
  flexbar,
  freecontact,
+ gasic,
  genometools,
+ gff2aplot,
+ gff2ps,
  giira,
+ glam2,
  grinder,
+ gromacs,
+ hhsuite,
+ hmmer,
  idba,
  infernal,
+ jellyfish,
+ kalign,
  kissplice,
  last-align,
  loki,
  macs,
+ mafft,
+ mapsembler2,
  maq,
  melting,
  minia,
  mipe,
  mira-assembler,
+ mlv-smile,
  mothur,
+ mrbayes,
+ mummer,
+ muscle,
+ mustang,
  ncbi-epcr,
  ncbi-tools-bin,
  ncoils,
+ neobio,
+ paraclu,
  parsinsert,
+ pdb2pqr,
  perm,
  phyml,
  phyutility,
  picard-tools,
  plink,
+ poa,
+ prank,
+ prime-phylo,
  primer3,
+ probabel,
+ probcons,
+ proda,
+ prodigal,
+ pynast,
+ python-biopython,
  python-cogent,
+ python3-biopython,
+ r-bioc-edger,
+ r-bioc-hilbertvis,
+ r-cran-pvclust,
+ r-cran-qtl,
+ r-cran-vegan,
+ r-other-mott-happy.hbrem,
+ raster3d,
+ readseq,
  rnahybrid,
  rtax,
  samtools,
+ seqan-apps,
+ sibsim4,
+ sigma-align,
+ sim4,
  smalt,
+ snap,
+ soapdenovo,
+ soapdenovo2,
+ squizz,
+ sra-toolkit,
  ssake,
+ staden-io-lib-utils,
+ t-coffee,
+ tabix,
+ theseus,
+ tigr-glimmer,
  tophat,
- velvet
-Suggests: abyss,
- anfo,
- arden,
- bagpipe,
+ tree-puzzle | tree-ppuzzle,
+ vcftools,
+ velvet,
+ wise,
+ zalign
+Suggests: bagpipe,
  cufflinks,
- gasic,
- mapsembler2
+ 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,
  structural biology and bioinformatics for use in life sciences, that do not
@@ -1045,7 +1142,6 @@ Recommends: aeskulap,
  ginkgocadx,
  gwyddion,
  imagej,
- imagevis3d,
  ismrmrd-tools,
  itksnap,
  king,
@@ -1067,6 +1163,7 @@ Recommends: aeskulap,
  python-nipy,
  python-nipype,
  python-nitime,
+ python-surfer,
  python-tifffile,
  teem-apps,
  voxbo,
@@ -1107,6 +1204,7 @@ Suggests: afni,
  gofigure2,
  hid,
  imagemagick,
+ imagevis3d,
  imview,
  incf-nidash-oneclick-clients,
  insightapplications,
@@ -1146,9 +1244,7 @@ Suggests: afni,
  piano,
  pngquant,
  pymeg,
- python-dipy,
  python-pyxid,
- python-surfer,
  science-workflow,
  sigviewer,
  slicer,
@@ -1178,11 +1274,12 @@ Package: med-imaging-dev
 Section: metapackages
 Architecture: all
 Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: ctn-dev,
+Recommends: cimg-dev,
+ ctn-dev,
  gmic,
  libbart-dev,
  libbiosig-dev,
- libcamitk4-dev,
+ libcamitk-dev,
  libcv-dev,
  libedf-dev,
  libgdcm2-dev,
@@ -1213,9 +1310,7 @@ Recommends: ctn-dev,
  python-casmoothing,
  python-cfflib,
  python-dicom,
- python-gdcm,
  python-mia | python3-mia,
- python-mne,
  python-mvpa2,
  python-nibabel,
  python-nipy,
@@ -1225,11 +1320,11 @@ Recommends: ctn-dev,
  python-pyxnat,
  python-vigra,
  r-cran-rniftilib
-Suggests: cimg-dev,
- emokit,
+Suggests: emokit,
  igstk-examples,
  libbio-formats-java,
  libcamp0.7-dev,
+ libcifti-dev,
  libctk-dev,
  libeegdev-dev,
  libfreeimage-dev,
@@ -1251,6 +1346,7 @@ Suggests: cimg-dev,
  python-dipy,
  python-imageio,
  python-libavg,
+ python-mne,
  python-tifffile,
  python-vmtk
 Description: Debian Med image processing and visualization packages development
@@ -1413,7 +1509,7 @@ Recommends: cronometer,
  galileo,
  hunspell-de-med,
  hunspell-en-med,
- nut-nutrition,
+ nutsqlite,
  pcalendar,
  pondus,
  python-clips,
@@ -1427,6 +1523,7 @@ Suggests: cycle,
  goldencheetah,
  mencal,
  mssstest,
+ nut-nutrition,
  sleepyhead
 Description: Debian Med several tools
  This metapackage will install tools for several purposes in health care.

-- 
Debian Med metapackages