debian-med 2.3 source package in Debian

Changelog

debian-med (2.3) unstable; urgency=medium

  * blends-dev 0.6.93 does not add single packages to tasksel control file
    but only the metapackage itself
  * med-bio: Add mgltools-pmv, mgltools-vision, mgltools-cadd
    Closes: #732069

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-tools
    added:
      Depends:  galileo, r-cran-fitbitscraper
      Suggests:  sleepyhead
   -med-statistics
    added:
      Depends:  r-cran-ade4, rstudio, r-bioc-multtest
   -med-bio-ngs
    added:
      Depends:  sprai, rna-star, daligner, mhap, dindel, blasr, bcftools
   -med-bio
    added:
      Depends:  pbbarcode, spaced, varmatch, cgview, phipack, ffp,
                snap-aligner, plast, kineticstools, brig, harvest-tools,
                transrate-tools, meryl, metabit, parsnp, beagle, maffilter,
                pbhoney, jmodeltest, mgltools-cadd, roadtrips, roary,
                sim4db, alter-sequence-alignment, graphlan,
                ncbi-entrez-direct, falconkit, partitionfinder,
                art-nextgen-simulation-tools, sspace, phybin, fastahack,
                phylophlan, crux-toolkit, varna, dindel, smithwaterman,
                r-bioc-geneplotter, dawg, lefse, r-bioc-deseq2, fsm-lite,
                nanopolish, physamp, minimap, kmc, snpomatic, proteinortho,
                phast, prottest, qualimap, sprai, fml-asm, circlator, inspect,
                pipasic, hilive, mgltools-pmv, fastqtl, piler,
                r-cran-adephylo, r-cran-pscbs, hisat2, ssw-align, garli, pssh2,
                plink1.9, r-cran-adegenet, velvet | velvet-long, condetri,
                fastml, mapdamage, rsat, r-cran-distory, segemehl, andi,
                ncl-tools, sumaclust, sniffles, pbalign, scrm, miniasm,
                poretools, sparta, pbh5tools, r-cran-bio3d, kronatools,
                beast2-mcmc, clustalw, dwgsim, pirs, reapr, r-cran-treescape,
                leaff, seer, surankco, tide, placnet, canu, rambo-k, lofreq,
                artfastqgenerator, lambda-align, rapmap, metaphlan2,
                r-bioc-dnacopy, mgltools-vision, indelible, salmon, dazzdb,
                srst2, king-probe, cutadapt, pbgenomicconsensus, ariba,
                pbsuite, adapterremoval, kraken, pbjelly, mash, fermi-lite,
                pbsim, bcftools
      Suggests: science-workflow, r-bioc-aroma.light, r-cran-pheatmap, mrs,
                r-bioc-annotationhub, r-bioc-ensembldb, r-bioc-go.db
    removed:
      Depends:  python-kineticstools, r-other-bio3d, velvet, tigr-assembler,
                clustalw | clustalw-mpi, python-pbalign, wgsim, wgs-assembler,
                mrs, act, r8s, fastml2
   -med-his
    added:
      Depends:  openmaxims
   -med-practice
    added:
      Depends:  sleepyhead, orthanc
    removed:
      Depends:  clinica
   -med-imaging-dev
    added:
      Depends:  libinsighttoolkit4-dev, octave-bart, libvtk-dicom-dev,
                libbart-dev, libodil0-dev, libmia-2.4-dev, libcamitk4-dev,
                libopenigtlink-dev, libvtk6-dev
      Suggests: libcamp0.7-dev, libfreeimage-dev
    removed:
      Depends:  libopenigtlink1-dev, libactiviz.net-cil, libvtk5-dev,
                libinsighttoolkit3-dev | libinsighttoolkit4-dev,
                libvtk-dicom0.5-dev, libmia-2.2-dev, libcamitk3-dev
      Suggests: libvtk5.4, insighttoolkit3-examples
   -med-imaging
    added:
      Depends:  fw4spl, python-tifffile, bart
      Suggests: science-workflow, orthanc-postgresql, orthanc-imagej,
                orthanc-dicomweb
    removed:
      Depends:  tifffile
   -med-data
    added:
      Suggests: sleepyhead
   -med-bio-phylogeny
    added:
      Depends:  iqtree, clustalw
    removed:
      Depends:  clustalw | clustalw-mpi
   -med-bio-dev
    added:
      Depends:  python3-pyvcf | python-pyvcf, libsmithwaterman-dev,
                mgltools-vision, libbpp-phyl-omics-dev,
                python3-csb | python-csb, libqcpp-dev, libbio-das-lite-perl,
                libhtsjdk-java, libqes-dev,
                python3-biopython | python-biopython, python-kineticstools,
                libfreecontact-dev, libssw-dev, libminimap-dev, r-cran-rnexml,
                libssw-java, r-cran-rncl, python3-pymummer,
                python3-ngs | python-ngs, libpbdata-dev, libbpp-raa-dev,
                python3-pbconsensuscore | python-pbconsensuscore, libblasr-dev,
                libbpp-qt-dev,
                python3-intervaltree-bio | python-intervaltree-bio, libncl-dev,
                libngs-java, python3-pyfaidx | python-pyfaidx, libbpp-seq-dev,
                libfast5-dev, r-cran-phylobase, python-pbcommand,
                libncbi-vdb-dev, libbpp-core-dev, libpbbam-dev,
                libconsensuscore-dev, libpbihdf-dev, libtabixpp-dev,
                python3-pyfasta | python-pyfasta, libbpp-phyl-dev, libfml-dev,
                python3-consensuscore2 | python-consensuscore2,
                mgltools-networkeditor, libpbseq-dev, libgff-dev,
                libngs-sdk-dev, octave-bioinfo, libbpp-popgen-dev,
                mgltools-pybabel, libfastahack-dev, ruby-crb-blast,
                libbpp-seq-omics-dev
      Suggests: python3-biopython-sql | python-biopython-sql, libdisorder-dev,
                libbam-dev
    removed:
      Depends:  libgbfp-dev, python-biopython | python3-biopython, libtabixpp,
                libfreecontact0-dev, python-csb | python3-csb, libbio-das-perl
      Suggests: python-biopython-sql | python3-biopython-sql
   -med-epi
    added:
      Suggests:  r-cran-cmprsk

 -- Andreas Tille <email address hidden>  Mon, 12 Sep 2016 10:03:11 +0200

Upload details

Uploaded by:
Debian Med on 2016-09-13
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
all
Section:
misc
Urgency:
Medium Urgency

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debian-med_2.3.dsc 2.8 KiB e3c3bd7f85c855b3937138ad6ef3c67df3050b96d133c7cf6ff8fd7bdaee94a8
debian-med_2.3.tar.xz 103.0 KiB e6619cd6dc92ad279eb50c960c93f2e3b15dad270e9466493e308b491e14ae7b

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