debian-med-tasks.desc

@@ -162,6 +162,24 @@ Description: Debian Med packages for psychology
 Key:
  med-psychology
 
+Task: med-rehabilitation
+Parent: debian-med
+Section: debian-med
+Description: Debian Med packages for rehabilitation technologies
+ This metapackage will install tools that are useful for
+ rehabilitation and therapy.
+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/changelog

-debian-med (3.2) UNRELEASED; urgency=medium
+debian-med (3.2) unstable; urgency=medium
 
   * Fix broken reference to alioth
+  * Standards-Version: 4.3.0
+  * debhelper 12
+  * Versioned Build-Depends: blends-dev (>= 0.7.2~)
+  * Add missing ${misc:Depends}
 
- -- Andreas Tille <tille@debian.org>  Sun, 29 Jul 2018 02:22:44 +0200
+  * start of automatic changelog entry * 
+  
+  * Changes in metapackage dependencies
+   -med-bio
+    added:
+      Recommends:  r-cran-sdmtools, delly, python3-pybedtools, r-cran-tcr,
+                   qutemol, r-cran-tigger, bax2bam, python3-gffutils,
+                   vdjtools, r-cran-shazam, r-cran-alakazam, gramalign,
+                   igor, deepbinner, python3-sqt, minimap2, sourmash,
+                   samblaster, murasaki | murasaki-mpi, biosyntax, paipline,
+                   pyvcf, r-bioc-cner, igdiscover, fastp, ncbi-igblast,
+                   pybel, jellyfish1, minimac4, lambda-align2, sweed,
+                   viewmol, seq-seq-pan, yaha, python3-biomaj3-daemon,
+                   changeo, mirtop, python3-presto, cct, unanimity,
+                   plasmidseeker
+    removed:
+      Recommends:  hilbertvisgui, decipher, hyphygui, jstreeview,
+                   biosyntax-gedit, python3-biomaj3, spice, rosetta,
+                   hexamer, murasaki, gbioseq, finex, das-proserver, est-db
+   -med-bio-dev
+    added:
+      Recommends:  python3-screed, python3-misopy, python3-pyvcf,
+                   python3-biomaj3, python3-ngs, toil, python3-cutadapt,
+                   python3-ruffus, python3-biotools, python3-sqt,
+                   libmems-dev, python3-hyphy, libstatgen-dev, python3-cobra,
+                   python3-biopython, python3-pysam, python3-airr,
+                   python3-dendropy, libgenome-dev, python3-fast5,
+                   python3-cyvcf2, libpll-dev, python3-bx, libmuscle-dev,
+                   python3-treetime, python3-presto, python3-pbconsensuscore,
+                   python3-csb, python3-intervaltree-bio, python3-seqcluster,
+                   python3-ete3, python3-bcbio, python3-pyfaidx, galaxy-lib,
+                   python3-consensuscore2, snakemake
+      Suggests:    ctdconverter, libmodhmm-dev, libsvmloc-dev, vdjtools,
+                   python3-ctdopts, python3-biopython-sql, libmilib-java
+    removed:
+      Recommends:  python3-biotools | python-biotools, octave-bioinfo,
+                   python3-pyvcf | python-pyvcf,
+                   python3-biomaj3 | python-biomaj3,
+                   python3-pbconsensuscore | python-pbconsensuscore,
+                   libmuscle-3.7-dev, python3-pyfaidx | python-pyfaidx,
+                   python3-consensuscore2 | python-consensuscore2,
+                   python-bd2k, python3-bx | python-bx,
+                   python3-ete3 | python-ete3, python3-ruffus | python-ruffus,
+                   python3-fast5 | python-fast5,
+                   python3-dendropy | python-dendropy, python-pysam,
+                   python3-cutadapt | python-cutadapt, libgff-perl,
+                   python3-ngs | python-ngs, python3-pyfasta | python-pyfasta,
+                   python3-csb | python-csb, libgenome-1.3-dev,
+                   python3-biopython | python-biopython,
+                   python3-hyphy | python-hyphy, python-cobra,
+                   libmems-1.6-dev,
+                   python3-intervaltree-bio | python-intervaltree-bio,
+                   python3-misopy | python-misopy
+      Suggests:    python3-biopython-sql | python-biopython-sql
+   -med-bio-ngs
+    added:
+      Recommends:  python3-presto, changeo, bcbio, igor, python3-pybedtools,
+                   igdiscover, python3-airr, r-cran-tcr, r-cran-tigger,
+                   python3-sqt, python3-gffutils, fastp, vdjtools,
+                   samblaster, r-cran-shazam, r-cran-alakazam
+   -med-bio-phylogeny
+    added:
+      Suggests:    python3-treetime
+   -med-epi
+    added:
+      Recommends:  epifire
+   -med-imaging
+    added:
+      Recommends:  mrtrix3, odil
+      Suggests:    orthanc-mysql, tifffile
+   -med-imaging-dev
+    added:
+      Recommends:  libsimpleitk1-dev, python3-biosig, libodil-dev,
+                   python3-simpleitk, libxdf-dev
+    removed:
+      Recommends:  libodil0-dev
+   -med-pharmacy
+    added:
+      Recommends:  r-cran-rpact
+   -med-physics
+    added:
+      Suggests:    python3-biosig
+    removed:
+      Suggests:    python-biosig
+   -med-research
+    added:
+      Recommends:  r-cran-rpact
+   -med-typesetting
+    removed:
+      Suggests:    referencer
+
+ -- Andreas Tille <tille@debian.org>  Thu, 24 Jan 2019 15:07:55 +0100
 
 debian-med (3.1) unstable; urgency=medium
 

debian/compat

-9
+12

debian/control.stub

@@ -3,14 +3,15 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: misc
 Priority: optional
-Build-Depends-Indep: blends-dev (>= 0.7~)
-Standards-Version: 4.1.4
+Build-Depends-Indep: blends-dev (>= 0.7.2~),
+                     debhelper (>= 12~)
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/blends-team/med
 Vcs-Git: https://salsa.debian.org/blends-team/med.git
 
 Package: med-tasks
 Architecture: all
-Depends: tasksel
+Depends: tasksel, ${misc:Depends}
 Description: Debian Med tasks for tasksel
  This package provides Debian Med tasks in tasksel.
  .