Publishing details

• Published on 2017-10-24
• Copied from ubuntu artful in Primary Archive for Ubuntu

Changelog

debian-med (3.0.1ubuntu1) artful; urgency=medium

  * Merge from Debian unstable.  Remaining changes:
    - Regenerate control file for artful.

debian-med (3.0.1) unstable; urgency=medium

  * Re-render before Stretch release

debian-med (3.0) unstable; urgency=medium

  * Bump version for Stretch release

  * start of automatic changelog entry *

  * Changes in metapackage dependencies
   -med-tools
    added:
      Depends:  r-cran-fitcoach, pesco
   -med-typesetting
    added:
      Suggests:  r-cran-qqman
   -med-bio
    added:
      Depends:  euler2, nextsv, r-bioc-metagenomeseq, diamond-aligner,
                bedops, ccs, euler-sr, r-bioc-mergeomics, baitfisher,
                libvcflib-tools, r-bioc-phyloseq, r-cran-rotl, tvc
      Suggests: r-cran-qqman, r-bioc-savr, r-cran-rentrez
    removed:
      Depends:  fermi-lite
   -med-imaging
    added:
      Depends:  bart-view, dcm2niix
   -med-bio-dev
    added:
      Depends:  python3-gffutils, libjloda-java, libbio-eutilities-perl,
                libvcflib-dev, python3-pybedtools, python3-fast5 | python-fast5,
                python3-misopy | python-misopy, libbio-coordinate-perl,
                python3-skbio, python3-bx | python-bx, libswiss-perl,
                python3-bd2k | python-bd2k
      Suggests: r-bioc-biomformat, r-bioc-rbgl, ruby-rgfa, r-cran-rentrez,
                libpbcopper-dev
    removed:
      Depends:  libbiojava3-java, libvcflib, python3-skbio | python-skbio,
                python-miso, unanimity

debian-med (2.4) unstable; urgency=medium

  * rebuild using blends-dev 0.6.96

  * start of automatic changelog entry *

  * Changes in metapackage dependencies
   -med-tools
    added:
      Depends:  nutsqlite
   -med-bio
    added:
      Depends:  dascrubber, manta, blobology, bio-eagle, malt, atac, qtltools, deepnano, contrafold, nanocall, falcon
      Suggests:  biomaj
    removed:
      Depends:  falconkit, biomaj
   -med-imaging-dev
    added:
      Depends:  libcifti-dev, libcamitk-dev
    removed:
      Depends:  libcamitk4-dev
   -med-bio-dev
    added:
      Depends:  libgkarrays-dev, unanimity

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

debian-med (2.2) unstable; urgency=medium

  * Moved to Git

  * start of automatic changelog entry *

  * Changes in metapackage dependencies
   -med-tools
    removed:
      Depends:  python3-fitbitscraper
   -med-bio
    added:
      Depends:  sortmerna, r-bioc-limma, r-cran-metamix, iqtree,
                relion-bin+gui | relion-bin+mpi+gui, berkeley-express,
                daligner, mhap, sumatra, hyphy-mpi | hyphy-pt,
                python-pbalign, bio-rainbow, python-kineticstools,
                ea-utils, suitename, wgsim, r-bioc-annotate, r-bioc-edger,
                adun-core, r-bioc-genefilter, hyphygui, sumtrees, blasr,
                repeatmasker-recon, pbdagcon, relion-bin | relion-bin+mpi,
                axe-demultiplexer, tantan
      Suggests:  adun.app
    removed:
      Depends:  relion-bin | relion-bin-mpi, express, relion-gui, hyphy,
                adun.app
   -med-imaging-dev
    added:
      Depends:  libvtk-dicom-java, libmaxflow-dev, libvtk-dicom0.5-dev
      Suggests:  liblimereg-dev
    removed:
      Depends:  libvtk-dicom0.4-dev
      Suggests:  limereg-dev
   -med-bio-dev
    added:
      Depends:  libdivsufsort-dev, python3-cutadapt | python-cutadapt,
                python3-skbio | python-skbio, python3-dendropy |
                python-dendropy, python3-ruffus | python-ruffus,
                python3-hyphy | python-hyphy
    removed:
      Depends:  librdp-readseq-java, librdp-alignment-java

 -- Bhavani Shankar <email address hidden>  Wed, 24 May 2017 17:31:34 +0530

Builds

Built packages

• med-all Default selection of tasks for Debian Med

• med-bio Debian Med bioinformatics packages

• med-bio-dev Debian Med packages for development of bioinformatics applications

• med-cloud Debian Med bioinformatics applications usable in cloud computing

• med-config Debian Med general config package

• med-data Debian Med drug databases

• med-dental Debian Med packages related to dental practice

• med-epi Debian Med epidemiology related packages

• med-his Debian Med suggestions for Hospital Information Systems

• med-imaging Debian Med image processing and visualization packages

• med-imaging-dev Debian Med image processing and visualization packages development

• med-laboratory Debian Med suggestions for medical laboratories

• med-oncology Debian Med packages for oncology

• med-pharmacy Debian Med packages for pharmaceutical research

• med-physics Debian Med packages for medical physicists

• med-practice Debian Med packages for practice management

• med-psychology Debian Med packages for psychology

• med-rehabilitation Debian Med packages for rehabilitation technologies

• med-statistics Debian Med statistics

• med-tasks Debian Med tasks for tasksel

• med-tools Debian Med several tools

• med-typesetting Debian Med support for typesetting and publishing

Package files

• debian-med_3.0.1ubuntu1.dsc (2.5 KiB)
• debian-med_3.0.1ubuntu1.tar.xz (104.5 KiB)
• med-all_3.0.1ubuntu1_all.deb (4.8 KiB)
• med-bio-dev_3.0.1ubuntu1_all.deb (4.8 KiB)
• med-bio_3.0.1ubuntu1_all.deb (7.2 KiB)
• med-cloud_3.0.1ubuntu1_all.deb (4.1 KiB)
• med-config_3.0.1ubuntu1_all.deb (9.2 KiB)
• med-data_3.0.1ubuntu1_all.deb (3.2 KiB)
• med-dental_3.0.1ubuntu1_all.deb (3.2 KiB)
• med-epi_3.0.1ubuntu1_all.deb (3.6 KiB)
• med-his_3.0.1ubuntu1_all.deb (3.4 KiB)
• med-imaging-dev_3.0.1ubuntu1_all.deb (3.9 KiB)
• med-imaging_3.0.1ubuntu1_all.deb (4.5 KiB)
• med-laboratory_3.0.1ubuntu1_all.deb (3.2 KiB)
• med-oncology_3.0.1ubuntu1_all.deb (3.2 KiB)
• med-pharmacy_3.0.1ubuntu1_all.deb (3.2 KiB)
• med-physics_3.0.1ubuntu1_all.deb (3.5 KiB)
• med-practice_3.0.1ubuntu1_all.deb (3.4 KiB)
• med-psychology_3.0.1ubuntu1_all.deb (3.2 KiB)
• med-rehabilitation_3.0.1ubuntu1_all.deb (3.2 KiB)
• med-statistics_3.0.1ubuntu1_all.deb (3.2 KiB)
• med-tasks_3.0.1ubuntu1_all.deb (6.4 KiB)
• med-tools_3.0.1ubuntu1_all.deb (3.3 KiB)
• med-typesetting_3.0.1ubuntu1_all.deb (3.2 KiB)