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
