debian-med-tasks.desc

@@ -162,15 +162,6 @@ 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

debian/changelog

-debian-med (3.3) UNRELEASED; urgency=medium
+debian-med (3.3) unstable; urgency=medium
 
-  * 
+  * Re-render tasks with Buster release state
+
+  * start of automatic changelog entry * 
+  
+  * Changes in metapackage dependencies
+   -med-bio
+    added:
+      Recommends: pilercr, mosdepth, quast, r-cran-webgestaltr, ragout,
+                  kraken2, gffread, filtlong, umis, sailfish, sibelia,
+                  atropos, braker, virulencefinder, vcfanno, biobambam2,
+                  python3-pybel, kmerresistance, optitype, spaln, kma,
+                  stringtie, oncofuse, optimir, kallisto, sina, dendroscope,
+                  multiqc, python3-geneimpacts, bismark
+      Suggests:   r-cran-forecast
+    removed:
+      Recommends: pybel
+      Suggests:   melting-gui
+   -med-bio-dev
+    added:
+      Recommends: libbio-samtools-perl, libbio-asn1-entrezgene-perl,
+                  libnexml-java, libbio-tools-run-alignment-clustalw-perl,
+                  libbigwig-dev, libbio-tools-phylo-paml-perl,
+                  libbio-chado-schema-perl, python3-cgecore, libbio-scf-perl,
+                  python3-mirtop, libbio-tools-run-alignment-tcoffee-perl,
+                  python3-pybel
+      Ignore:     golang-github-biogo-hts-dev
+   -med-bio-ngs
+    added:
+      Recommends: kraken2, stringtie
+   -med-cms
+    added:
+      Recommends: xnat
+    removed:
+      Suggests:   xnat
+   -med-imaging
+    added:
+      Recommends: xnat
+    removed:
+      Suggests:   xnat
+   -med-imaging-dev
+    added:
+      Recommends: libvtk7-dev
+      Suggests:   libvtk6-dev
+    removed:
+      Recommends:  libvtk6-dev
+   -med-psychology
+    added:
+      Recommends:  r-cran-psychometric, r-cran-psych, r-cran-psyphy,
+                   r-cran-psychotree
+    removed:
+      Recommends:  psychotree, psychometric, miscpsycho, psyphy, psych
 
  -- Andreas Tille <tille@debian.org>  Fri, 25 Jan 2019 14:49:50 +0100
 

debian/control

@@ -74,7 +74,6 @@ Suggests: med-cloud,
           med-physics,
           med-practice,
           med-psychology,
-          med-rehabilitation,
           med-research,
           med-tools,
           med-typesetting
@@ -203,7 +202,6 @@ Recommends: abacas,
             estscan,
             examl,
             exonerate,
-            falcon,
             fastahack,
             fastaq,
             fastdnaml,
@@ -255,13 +253,13 @@ Recommends: abacas,
             hmmer2,
             hyphy-mpi | hyphy-pt,
             idba,
+            igor,
             indelible,
             infernal,
             ipig,
             iqtree,
             iva,
             jaligner,
-            jalview,
             jellyfish,
             jellyfish1,
             jmodeltest,
@@ -315,7 +313,6 @@ Recommends: abacas,
             mothur,
             mptp,
             mrbayes,
-            msxpertsuite,
             mummer,
             murasaki | murasaki-mpi,
             muscle,
@@ -421,9 +418,10 @@ Recommends: abacas,
             python3-gffutils,
             python3-presto,
             python3-pybedtools,
+            python3-pybel,
+            python3-sqt,
             pyvcf,
             qcumber,
-            qiime,
             qtltools,
             quorum,
             qutemol,
@@ -498,9 +496,9 @@ Recommends: abacas,
             runcircos-gui,
             saint,
             salmon,
-            sambamba,
             samblaster,
             samtools,
+            scoary,
             scrm,
             scythe,
             seaview,
@@ -520,7 +518,6 @@ Recommends: abacas,
             smalr,
             smalt,
             smithwaterman,
-            smrtanalysis,
             snap,
             snap-aligner,
             sniffles,
@@ -597,6 +594,7 @@ Suggests: acacia,
           arachne,
           arb,
           asap,
+          atropos,
           autodocktools,
           axparafit,
           axpcoords,
@@ -606,9 +604,12 @@ Suggests: acacia,
           biceps,
           big-blast,
           bigsdb,
+          biobambam2,
+          bismark,
           blat,
           blimps-utils,
           blobology,
+          braker,
           btk-core,
           cactus,
           caftools,
@@ -633,6 +634,7 @@ Suggests: acacia,
           dascrubber,
           dazzle,
           deepbinner,
+          dendroscope,
           e-hive,
           ecell,
           embassy-phylip,
@@ -646,9 +648,11 @@ Suggests: acacia,
           exabayes,
           exalt,
           excavator,
+          falcon,
           fasta3,
           ffp,
           figaro,
+          filtlong,
           forester,
           forge,
           galaxy,
@@ -661,6 +665,7 @@ Suggests: acacia,
           genezilla,
           genographer,
           getdata,
+          gffread,
           glimmerhmm,
           gmap,
           gmv,
@@ -669,12 +674,16 @@ Suggests: acacia,
           hawkeye,
           htqc,
           igdiscover,
-          igor,
           igv,
           inspect,
+          jalview,
           jbrowse,
           jigsaw,
+          kallisto,
           kempbasu,
+          kma,
+          kmerresistance,
+          kraken2,
           lofreq,
           mach-haplotyper,
           mage2tab,
@@ -684,7 +693,6 @@ Suggests: acacia,
           martj,
           maude,
           maxd,
-          melting-gui,
           meme,
           mesquite,
           metabit,
@@ -705,10 +713,13 @@ Suggests: acacia,
           modeller,
           molekel,
           mosaik-aligner,
+          mosdepth,
           mpsqed,
           mrs,
           msatfinder,
+          msxpertsuite,
           mugsy,
+          multiqc,
           mummergpu,
           mview,
           nanocall,
@@ -721,7 +732,10 @@ Suggests: acacia,
           obo-edit,
           oligoarrayaux,
           omegamap,
+          oncofuse,
           operondb,
+          optimir,
+          optitype,
           paipline,
           partigene,
           partitionfinder,
@@ -734,6 +748,7 @@ Suggests: acacia,
           phylophlan,
           phyloviz-core,
           phylowin,
+          pilercr,
           pipasic,
           plato,
           profit,
@@ -741,25 +756,29 @@ Suggests: acacia,
           prot4est,
           psipred,
           pssh2,
-          pybel,
           pyrophosphate-tools,
           python-orange,
           python-reaper,
           python-treetime,
-          python3-sqt,
+          python3-geneimpacts,
+          qiime,
           qtlcart,
           qualimap,
+          quast,
           r-bioc-annotationhub,
           r-bioc-aroma.light,
           r-bioc-ensembldb,
           r-bioc-go.db,
           r-bioc-savr,
           r-cran-boolnet,
+          r-cran-forecast,
           r-cran-pheatmap,
           r-cran-qqman,
           r-cran-rentrez,
+          r-cran-webgestaltr,
           r-other-apmswapp,
           raccoon,
+          ragout,
           raxml-ng,
           rbs-finder,
           repeatmasker,
@@ -768,23 +787,29 @@ Suggests: acacia,
           roche454ace2caf,
           rose,
           rsat,
+          sailfish,
+          sambamba,
           sap,
           science-workflow,
-          scoary,
           seq-gen,
           seq-seq-pan,
           sequenceconverter.app,
+          sibelia,
           sift,
+          sina,
           sistr,
           situs,
+          smrtanalysis,
           snpeff,
           solvate,
           sourmash,
+          spaln,
           sparta,
           splitstree,
           ssaha,
           strap,
           strap-base,
+          stringtie,
           tab2mage,
           tacg,
           taverna,
@@ -800,12 +825,15 @@ Suggests: acacia,
           twain,
           ugene,
           umap,
+          umis,
           unc-fish,
           uniprime,
           varmatch,
           varscan,
+          vcfanno,
           vdjtools,
           vienna-rna,
+          virulencefinder,
           vmd,
           x-tandem-pipeline,
           zodiac-zeden
@@ -828,6 +856,8 @@ Recommends: bio-tradis,
             libai-fann-perl,
             libbambamc-dev,
             libbamtools-dev,
+            libbio-asn1-entrezgene-perl,
+            libbio-chado-schema-perl,
             libbio-coordinate-perl,
             libbio-das-lite-perl,
             libbio-eutilities-perl,
@@ -835,8 +865,12 @@ Recommends: bio-tradis,
             libbio-mage-perl,
             libbio-mage-utils-perl,
             libbio-primerdesigner-perl,
+            libbio-samtools-perl,
+            libbio-scf-perl,
+            libbio-tools-phylo-paml-perl,
+            libbio-tools-run-alignment-clustalw-perl,
+            libbio-tools-run-alignment-tcoffee-perl,
             libbiococoa-dev,
-            libbiod-dev,
             libbiojava-java,
             libbiojava4-java,
             libbioparser-dev,
@@ -948,13 +982,14 @@ Recommends: bio-tradis,
             python3-pbconsensuscore,
             python3-presto,
             python3-pybedtools,
+            python3-pybel,
             python3-pyfaidx,
             python3-pymummer,
             python3-pysam,
             python3-pyvcf,
             python3-ruffus,
             python3-screed,
-            python3-skbio,
+            python3-sqt,
             python3-treetime,
             r-bioc-biobase,
             r-cran-genetics,
@@ -972,6 +1007,8 @@ Suggests: bioclipse,
           ctdconverter,
           galaxy-lib,
           libbam-dev,
+          libbigwig-dev,
+          libbiod-dev,
           libdisorder-dev,
           libforester-java,
           libfreecontact-doc,
@@ -979,6 +1016,7 @@ Suggests: bioclipse,
           libgtextutils-dev,
           libmilib-java,
           libmodhmm-dev,
+          libnexml-java,
           libpbcopper-dev,
           libqcpp-dev,
           libroadrunner-dev,
@@ -996,13 +1034,15 @@ Suggests: bioclipse,
           python-roadrunner,
           python-screed,
           python3-biopython-sql,
+          python3-cgecore,
           python3-consensuscore2,
           python3-ctdopts,
           python3-ete3,
           python3-hyphy,
+          python3-mirtop,
           python3-misopy,
           python3-seqcluster,
-          python3-sqt,
+          python3-skbio,
           r-bioc-affy,
           r-bioc-affyio,
           r-bioc-altcdfenvs,
@@ -1152,7 +1192,6 @@ Recommends: abyss,
             python-cogent,
             python3-biomaj3-cli,
             python3-biopython,
-            qiime,
             r-bioc-hilbertvis,
             r-cran-pvclust,
             r-cran-qtl,
@@ -1188,7 +1227,8 @@ Recommends: abyss,
 Suggests: bagpipe,
           cufflinks,
           embassy-phylip,
-          gmap
+          gmap,
+          qiime
 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
@@ -1230,8 +1270,7 @@ Architecture: all
 Depends: ${misc:Depends},
          med-config (= ${source:Version}),
          med-tasks (= ${source:Version})
-Recommends: epigrass,
-            r-cran-diagnosismed,
+Recommends: r-cran-diagnosismed,
             r-cran-epi,
             r-cran-epibasix,
             r-cran-epicalc,
@@ -1243,6 +1282,7 @@ Recommends: epigrass,
             r-cran-sjplot,
             r-cran-surveillance
 Suggests: epifire,
+          epigrass,
           netepi-analysis,
           netepi-collection,
           python-treetime,
@@ -1293,7 +1333,6 @@ Depends: ${misc:Depends},
          med-tasks (= ${source:Version})
 Recommends: aeskulap,
             amide,
-            ants,
             bart,
             bart-view,
             biosig-tools,
@@ -1334,8 +1373,6 @@ Recommends: aeskulap,
             pixelmed-apps,
             plastimatch,
             python-dicom,
-            python-dipy,
-            python-mvpa2,
             python-nibabel,
             python-nipy,
             python-nipype,
@@ -1343,11 +1380,11 @@ Recommends: aeskulap,
             python-surfer,
             sigviewer,
             sofa-apps,
-            teem-apps,
             voxbo,
             vtk-dicom-tools,
             xmedcon
 Suggests: afni,
+          ants,
           bioimagesuite,
           bioimagexd,
           blox,
@@ -1416,12 +1453,15 @@ Suggests: afni,
           piano,
           pngquant,
           pymeg,
+          python-dipy,
+          python-mvpa2,
           python-pyxid,
           python-tifffile,
           science-workflow,
           slicer,
           stabilitycalc,
           stir,
+          teem-apps,
           tempo,
           tifffile,
           trimage,
@@ -1473,12 +1513,11 @@ Recommends: cimg-dev,
             libopensurgsim-dev,
             libpapyrus3-dev,
             libsimpleitk1-dev,
-            libteem-dev,
             libvigraimpex-dev,
             libvistaio-dev,
             libvolpack1-dev,
             libvtk-dicom-dev,
-            libvtk6-dev,
+            libvtk7-dev,
             libxdf-dev,
             octave-bart,
             octave-dicom,
@@ -1486,11 +1525,9 @@ Recommends: cimg-dev,
             odin,
             python-cfflib,
             python-dicom,
-            python-dipy,
             python-imageio,
             python-mia | python3-mia,
             python-mne,
-            python-mvpa2,
             python-nibabel,
             python-nipy,
             python-nipype,
@@ -1514,11 +1551,15 @@ Suggests: emokit,
           libnifti-doc,
           libopenmeeg-dev,
           libopenslide-java,
+          libteem-dev,
           libvia-dev,
           libvmtk-dev,
+          libvtk6-dev,
           libxdffileio-dev,
+          python-dipy,
           python-gdcm,
           python-libavg,
+          python-mvpa2,
           python-tifffile,
           python-vmtk
 Description: Debian Med image processing and visualization packages development
@@ -1644,34 +1685,21 @@ Depends: ${misc:Depends},
          med-tasks (= ${source:Version})
 Recommends: praat,
             psignifit,
-            psychopy,
             python-pyepl,
             r-cran-foreign,
-            r-cran-psy
-Suggests: miscpsycho,
-          psych,
-          psychometric,
-          psychotree,
-          psyphy,
+            r-cran-psy,
+            r-cran-psych
+Suggests: psychopy,
           python-pypsignifit,
           python-visionegg,
+          r-cran-psychometric,
+          r-cran-psychotree,
+          r-cran-psyphy,
           science-psychophysics
 Description: Debian Med packages for psychology
  This metapackage contains dependencies for a collection of software
  which might be helpful for psychological research.
 
-Package: med-rehabilitation
-Section: metapackages
-Architecture: all
-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