debian-med (3.5) unstable; urgency=medium
* Python2 packages only suggested
Closes: #945659
* Remove tophat since deprecated by upstream
* giira from Recommends to Suggests since it needs tophat
* lintian-override for field-too-long Recommends
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: idefix, resfinder, purple, pufferfish
Suggests: skewer, giira
removed:
Recommends: giira, tophat
Suggests: mobyle-programs, mobyle-tutorials, mobyle
-med-bio-dev
added:
Recommends: python3-dnaio, python3-pyani, biobambam2, libcdk-java
Suggests: r-bioc-dada2, python-pbcommand, python-pbh5tools,
r-cran-dt, r-cran-proc, python-kineticstools, libfast-perl,
python-corepywrap, libmaus2-dev, python-pbcore,
r-cran-pcapp, r-cran-dynamictreecut, python-cogent,
r-cran-kaos
removed:
Recommends: python-pbh5tools, python-pbcommand, python-kineticstools,
python-corepywrap, libmaus2-dev, python-pbcore,
r-cran-dynamictreecut, python-cogent
-med-bio-ngs
removed:
Recommends: tophat
-med-cloud
added:
Recommends: hisat2
Suggests: python-cogent
removed:
Recommends: python-cogent, tophat
-med-imaging
added:
Suggests: python-nipype, python-nitime, python-dipy, python-nipy
removed:
Recommends: python-nipype, python-nitime, python-dipy, python-nipy
Suggests: tifffile
-med-imaging-dev
added:
Suggests: python-vigra, python-nipype, python-cfflib, python-nitime,
python-pyxnat, python-nipy, python-vmtk, python-dipy
removed:
Recommends: python-vigra, python-nipype, python-cfflib, python-nitime,
python-pyxnat, python-nipy, python-vmtk, python-dipy
-med-psychology
added:
Suggests: python-pyepl
removed:
Recommends: python-pypsignifit, python-pyepl
-- Andreas Tille <email address hidden> Thu, 28 Nov 2019 09:25:44 +0100
debian-med (3.4) unstable; urgency=medium
* Standards-Version: 4.4.1
* Use debhelper-compat
* Re-render dependencies without Python2 packages
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: python3-deeptoolsintervals, skesa, python3-orange, vg,
mmseqs2, mindthegap, kaptive, r-cran-tsne,
python3-deeptools, r-cran-seurat, python3-cogent,
kleborate, python3-reaper, python3-treetime, pizzly,
trim-galore, pigx-scrnaseq, pigx-rnaseq,
r-bioc-multiassayexperiment, wham-align, r-other-wgcna,
r-bioc-mofa, seqcluster, r-cran-kaos, r-cran-drinsight
Suggests: r-bioc-tximport, r-bioc-qusage, python3-pyflow,
python3-alignlib, r-cran-corrplot, r-cran-fitdistrplus,
r-cran-dynamictreecut, python3-loompy, strelka,
r-cran-gprofiler, python3-py2bit, r-cran-sctransform
removed:
Recommends: python-orange, python-treetime, python-reaper, python-cogent
-med-bio-dev
added:
Recommends: python3-roadrunner, python3-deeptoolsintervals,
r-other-hms-dbmi-spp, python3-loompy, python3-py2bit,
r-cran-rotl, r-cran-seqinr, libseqan2-dev, r-cran-boolnet,
r-other-apmswapp, r-cran-vegan, r-cran-tsne, gffread,
python3-deeptools, r-cran-seurat, r-cran-corrplot,
r-cran-fitdistrplus, r-cran-qqman, r-cran-metamix,
r-cran-pscbs, r-cran-pheatmap, r-cran-sctransform,
r-cran-adephylo, r-cran-phangorn, r-cran-distory,
python3-htseq, libmaus2-dev, python3-rdkit, r-cran-samr,
r-cran-webgestaltr, python3-freecontact, libseqan3-dev,
r-cran-rentrez, r-cran-adegenet, r-cran-dynamictreecut,
r-cran-gprofiler, r-cran-forecast, libgclib,
python3-biom-format, r-cran-drinsight
Suggests: r-cran-rann, r-bioc-biostrings, r-bioc-deseq2,
r-bioc-mergeomics, r-cran-metap, r-bioc-qusage,
python3-pyflow, python3-pycosat, r-bioc-metagenomeseq,
r-bioc-annotate, r-bioc-cner, r-bioc-geneplotter,
r-bioc-ensembldb, r-bioc-rentrez, r-bioc-tximport,
r-bioc-rtracklayer, r-bioc-annotationhub, r-bioc-ebseq,
r-bioc-go.db, r-bioc-limma, r-cran-ica, r-bioc-pcamethods,
r-bioc-savr, r-cran-rsvd, python3-alignlib,
r-cran-future.batchtools, r-bioc-tfbstools, r-bioc-bitseq,
r-bioc-cummerbund, r-bioc-multiassayexperiment, r-bioc-gviz,
r-bioc-genefilter, r-bioc-phyloseq, r-bioc-impute,
r-bioc-aroma.light, r-cran-future.apply, r-bioc-mofa,
r-bioc-dnacopy
removed:
Recommends: python-htseq, python-mmtk, python-rdkit, python-screed,
python-biom-format, python-roadrunner, python-freecontact
Suggests: python-pyflow, r-cran-rentrez
-med-bio-ngs
added:
Recommends: wham-align
-med-cloud
removed:
Recommends: python-biopython
-med-data
added:
Recommends: python3-hl7
Suggests: oscar
removed:
Recommends: python-hl7
-med-epi
added:
Recommends: python3-treetime
removed:
Recommends: python-treetime
-med-imaging
added:
Recommends: python3-nibabel, python3-mvpa2, python3-dicom,
python3-surfer, tifffile
removed:
Recommends: python-surfer, python-mvpa2, python-dicom,
python-nibabel, python-tifffile
-med-imaging-dev
added:
Recommends: python3-mia, python3-mvpa2, python3-dicom,
python3-openslide, python3-gdcm, python3-imageio,
python3-mne, python3-nibabel
Suggests: tifffile
removed:
Recommends: python-mia | python3-mia, python-gdcm, python-mne,
python-mvpa2, python-dicom, python-nibabel,
python-imageio, python-openslide
Suggests: python-libavg, python-tifffile
-med-physics
added:
Suggests: python3-multipletau
removed:
Suggests: python-multipletau
-med-practice
added:
Recommends: oscar
-med-psychology
removed:
Suggests: python-visionegg
-med-tools
added:
Recommends: python3-fitbit
Suggests: oscar
removed:
Recommends: python-clips, python-fitbit
-- Andreas Tille <email address hidden> Sat, 05 Oct 2019 12:02:38 +0200
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 <email address hidden> Fri, 25 Jan 2019 14:49:50 +0100
