debian-med-tasks.desc

@@ -171,6 +171,15 @@ Description: Debian Med packages for rehabilitation technologies
 Key:
  med-rehabilitation
 
+Task: med-research
+Parent: debian-med
+Section: debian-med
+Description: Debian Med packages for medical research
+ This metapackage will install tools that are useful for
+ medical research.
+Key:
+ med-research
+
 Task: med-statistics
 Parent: debian-med
 Section: debian-med

debian/control

-# This file is autogenerated via make -f debian/rules dist.  Do not edit!
+# This file is autogenerated. Do not edit!
 Source: debian-med
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille@debian.org>
@@ -56,6 +56,7 @@ Description: Debian Med general config package
 Package: med-all
 Section: metapackages
 Architecture: all
+Depends: ${misc:Depends}
 Recommends: med-bio,
             med-bio-dev,
             med-statistics
@@ -73,6 +74,7 @@ Suggests: med-cloud,
           med-practice,
           med-psychology,
           med-rehabilitation,
+          med-research,
           med-tools,
           med-typesetting
 Description: Default selection of tasks for Debian Med
@@ -82,7 +84,9 @@ Description: Default selection of tasks for Debian Med
 Package: med-bio
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: abacas,
             abyss,
             acedb-other,
@@ -112,6 +116,7 @@ Recommends: abacas,
             avogadro,
             axe-demultiplexer,
             baitfisher,
+            bali-phy,
             ballview,
             bamtools,
             barrnap,
@@ -197,6 +202,7 @@ Recommends: abacas,
             fastx-toolkit,
             ffindex,
             figtree,
+            filo,
             fitgcp,
             flexbar,
             fml-asm,
@@ -269,7 +275,6 @@ Recommends: abacas,
             maq,
             maqview,
             mash,
- massxpert,
             mauve-aligner,
             melting,
             meryl,
@@ -287,6 +292,7 @@ Recommends: abacas,
             mothur,
             mptp,
             mrbayes,
+            msxpertsuite,
             mummer,
             murasaki,
             muscle,
@@ -400,6 +406,7 @@ Recommends: abacas,
             r-bioc-limma,
             r-bioc-mergeomics,
             r-bioc-metagenomeseq,
+            r-bioc-pcamethods,
             r-bioc-phyloseq,
             r-bioc-rtracklayer,
             r-cran-adegenet,
@@ -538,6 +545,7 @@ Suggests: acacia,
           biceps,
           big-blast,
           bigsdb,
+          biosyntax-gedit,
           blat,
           blimps-utils,
           blobology,
@@ -549,6 +557,7 @@ Suggests: acacia,
           ccs,
           cdna-db,
           cellprofiler,
+          chromhmm,
           cinema,
           cluster3,
           cmap,
@@ -587,7 +596,6 @@ Suggests: acacia,
           fasta3,
           ffp,
           figaro,
- filo,
           finex,
           forester,
           forge,
@@ -694,6 +702,7 @@ Suggests: acacia,
           qualimap,
           r-bioc-annotationhub,
           r-bioc-aroma.light,
+          r-bioc-bitseq,
           r-bioc-ensembldb,
           r-bioc-go.db,
           r-bioc-savr,
@@ -702,6 +711,7 @@ Suggests: acacia,
           r-cran-pheatmap,
           r-cran-qqman,
           r-cran-rentrez,
+          r-cran-samr,
           r-other-apmswapp,
           raccoon,
           raxml-ng,
@@ -766,7 +776,9 @@ Description: Debian Med bioinformatics packages
 Package: med-bio-dev
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: bio-tradis,
             bioperl,
             bioperl-run,
@@ -880,11 +892,9 @@ Recommends: bio-tradis,
             python3-dendropy | python-dendropy,
             python3-fast5 | python-fast5,
             python3-gfapy,
- python3-gffutils,
             python3-intervaltree-bio | python-intervaltree-bio,
             python3-ngs | python-ngs,
             python3-pbconsensuscore | python-pbconsensuscore,
- python3-pybedtools,
             python3-pyfaidx | python-pyfaidx,
             python3-pymummer,
             python3-pyvcf | python-pyvcf,
@@ -897,7 +907,6 @@ Recommends: bio-tradis,
             r-cran-rncl,
             r-cran-rnexml,
             ruby-bio,
- ruby-crb-blast,
             sbmltoolbox,
             seqan-dev
 Suggests: bioclipse,
@@ -922,24 +931,20 @@ Suggests: bioclipse,
           octave-bioinfo,
           python-biomaj3,
           python-biopython-doc,
- python-bx,
- python-consensuscore2,
- python-ete3,
- python-hyphy,
- python-misopy,
           python-mmtk,
- python-pyfasta,
           python-pyflow,
           python-roadrunner,
           python-screed,
           python3-bd2k,
           python3-biopython-sql | python-biopython-sql,
- python3-bx,
- python3-consensuscore2,
- python3-ete3,
- python3-hyphy,
- python3-misopy,
- python3-pyfasta,
+          python3-bx | python-bx,
+          python3-consensuscore2 | python-consensuscore2,
+          python3-ete3 | python-ete3,
+          python3-gffutils,
+          python3-hyphy | python-hyphy,
+          python3-misopy | python-misopy,
+          python3-pybedtools,
+          python3-pyfasta | python-pyfasta,
           r-bioc-affy,
           r-bioc-affyio,
           r-bioc-altcdfenvs,
@@ -967,6 +972,7 @@ Suggests: bioclipse,
           r-cran-natserv,
           r-cran-rentrez,
           r-cran-rocr,
+          ruby-crb-blast,
           ruby-rgfa
 Description: Debian Med packages for development of bioinformatics applications
  This metapackage will install Debian packages which might be helpful
@@ -975,7 +981,9 @@ Description: Debian Med packages for development of bioinformatics applications
 Package: med-cloud
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: abyss,
             acedb-other,
             aevol,
@@ -1027,6 +1035,7 @@ Recommends: abyss,
             fastqc,
             fasttree,
             fastx-toolkit,
+            filo,
             fitgcp,
             flexbar,
             freecontact,
@@ -1122,7 +1131,6 @@ Recommends: abyss,
 Suggests: bagpipe,
           cufflinks,
           embassy-phylip,
- filo,
           gmap
 Description: Debian Med bioinformatics applications usable in cloud computing
  This metapackage will install Debian packages related to molecular biology,
@@ -1133,7 +1141,9 @@ Description: Debian Med bioinformatics applications usable in cloud computing
 Package: med-data
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: freediams,
             freemedforms-freedata,
             python-hl7
@@ -1147,7 +1157,9 @@ Description: Debian Med drug databases
 Package: med-dental
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: entangle,
             imagetooth,
             openmolar
@@ -1158,7 +1170,9 @@ Description: Debian Med packages related to dental practice
 Package: med-epi
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: epigrass,
             python-treetime,
             r-cran-diagnosismed,
@@ -1187,7 +1201,9 @@ Description: Debian Med epidemiology related packages
 Package: med-his
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: fis-gtm,
             orthanc-wsi
 Suggests: care2x,
@@ -1212,7 +1228,9 @@ Description: Debian Med suggestions for Hospital Information Systems
 Package: med-imaging
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: aeskulap,
             amide,
             ants,
@@ -1254,6 +1272,7 @@ Recommends: aeskulap,
             pixelmed-apps,
             plastimatch,
             python-dicom,
+            python-dipy,
             python-mvpa2,
             python-nibabel,
             python-nipy,
@@ -1361,7 +1380,9 @@ Description: Debian Med image processing and visualization packages
 Package: med-imaging-dev
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: cimg-dev,
             ctn-dev,
             gmic,
@@ -1382,6 +1403,7 @@ Recommends: cimg-dev,
             libmiaviewit-dev,
             libminc-dev,
             libnifti-dev,
+            libodil0-dev,
             libopenigtlink-dev,
             libopenslide-dev,
             libopensurgsim-dev,
@@ -1423,7 +1445,6 @@ Suggests: emokit,
           liblimereg-dev,
           libmni-perllib-perl,
           libnifti-doc,
- libodil0-dev,
           libopenmeeg-dev,
           libopenslide-java,
           libvia-dev,
@@ -1441,7 +1462,9 @@ Description: Debian Med image processing and visualization packages development
 Package: med-laboratory
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: opencfu,
             orthanc-wsi
 Suggests: catissuesuite,
@@ -1454,7 +1477,9 @@ Description: Debian Med suggestions for medical laboratories
 Package: med-oncology
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: dicompyler,
             orthanc-wsi
 Suggests: planunc,
@@ -1466,7 +1491,9 @@ Description: Debian Med packages for oncology
 Package: med-pharmacy
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: chemtool,
             r-cran-dosefinding
 Suggests: raccoon
@@ -1478,7 +1505,9 @@ Description: Debian Med packages for pharmaceutical research
 Package: med-physics
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: biosig-tools,
             gdf-tools,
             octave,
@@ -1501,7 +1530,9 @@ Description: Debian Med packages for medical physicists
 Package: med-practice
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: entangle,
             freediams,
             freemedforms-emr,
@@ -1540,7 +1571,9 @@ Description: Debian Med packages for practice management
 Package: med-psychology
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: praat,
             psignifit,
             psychopy,
@@ -1562,24 +1595,43 @@ Description: Debian Med packages for psychology
 Package: med-rehabilitation
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: sitplus
 Suggests: aghermann
 Description: Debian Med packages for rehabilitation technologies
  This metapackage will install tools that are useful for
  rehabilitation and therapy.
 
+Package: med-research
+Section: metapackages
+Architecture: all
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
+Suggests: openclinica
+Description: Debian Med packages for medical research
+ This metapackage will install tools that are useful for
+ medical research.
+
 Package: med-statistics
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: r-bioc-limma,
             r-bioc-multtest,
             r-bioc-qvalue,
             r-cran-ade4,
             r-cran-beeswarm,
             r-cran-pvclust,
- r-cran-randomforest
+            r-cran-randomforest,
+            r-cran-rwave,
+            r-cran-snowfall,
+            r-cran-waveslim,
+            r-cran-wavethresh
 Suggests: rstudio,
           science-statistics
 Description: Debian Med statistics
@@ -1589,7 +1641,9 @@ Description: Debian Med statistics
 Package: med-tools
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: cronometer,
             edfbrowser,
             galileo,
@@ -1620,7 +1674,9 @@ Description: Debian Med several tools
 Package: med-typesetting
 Section: metapackages
 Architecture: all
-Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
+Depends: ${misc:Depends},
+         med-config (= ${source:Version}),
+         med-tasks (= ${source:Version})
 Recommends: king,
             texlive-latex-extra,
             texlive-science