Accepted debian-med 2.3 (source all) into unstable, unstable
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Hash: SHA256
Format: 1.8
Date: Mon, 12 Sep 2016 10:03:11 +0200
Source: debian-med
Binary: med-tasks med-config med-all med-bio med-bio-dev med-cloud med-data med-dental med-epi med-his med-imaging med-imaging-dev med-laboratory med-oncology med-pharmacy med-physics med-practice med-psychology med-rehabilitation med-statistics med-tools med-typesetting
Architecture: source all
Version: 2.3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
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 application
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 developmen
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
Closes: 732069
Changes:
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
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