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|
debian-med (3.8.1) unstable; urgency=medium
* Standards-Version: 4.6.2
* Update dependencies to fit Bookworm release status
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio-dev
added:
Recommends: libwfa2-dev
-- Andreas Tille <tille@debian.org> Mon, 22 May 2023 14:04:33 +0200
debian-med (3.8) unstable; urgency=medium
* nifti2dicom, qnifti2dicom, libsimpleitk1-dev, python3-simpleitk removed
from Debian thus removed from tasks
* Suggests: libgatk-native-bindings-java
* Replace: msxpertsuite by massxpert, minexpert2 (see #1024780)
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: minexpert2, snippy, metaeuk, any2fasta, btllib-tools,
savvy-util, comet-ms, muscle3, pyfastx, seqan-needle,
seqan-raptor, massxpert
removed:
Recommends: sequenceconverter.app, msxpertsuite
-med-bio-dev
added:
Recommends: libbio-db-seqfeature-perl, python3-pyfastx,
libbiojava6-java, python3-bioframe
Suggests: libsavvy-dev, libgatk-native-bindings-java, libbtllib-dev,
python3-cgelib, python3-conda-package-streaming
removed:
Recommends: libbiojava5-java
-med-bio-phylogeny
added:
Recommends: muscle3
-med-cloud
added:
Recommends: muscle3
-med-covid-19
added:
Recommends: muscle3
-med-imaging
removed:
Recommends: qnifti2dicom, nifti2dicom
-med-imaging-dev
added:
Recommends: python3-bioxtasraw
removed:
Recommends: python3-simpleitk, libsimpleitk1-dev
-med-psychology
added:
Recommends: python3-bioxtasraw
-- Andreas Tille <tille@debian.org> Wed, 08 Feb 2023 11:04:38 +0100
debian-med (3.7.3) unstable; urgency=medium
* Build-Depends-Indep: blends-dev (>= 0.7.5~)
Closes: #1012341
* dicompyler removed from Debian thus from oncology task
* zalign removed from Debian
* Standards-Version: 4.6.1
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: ska, genomicsdb-tools, nxtrim, fastq-pair, unikmer,
xpore, abpoa, surpyvor, metaphlan, pullseq, pyensembl,
terraphast
removed:
Recommends: metaphlan2, zalign, falcon
-med-bio-dev
added:
Recommends: python3-pyabpoa, libbiojava5-java, ont-fast5-api,
python3-slow5, python3-gtfparse, libslow5-dev,
python3-propka, python3-pyspoa
Suggests: libgatk-fermilite-java, libgatk-fermilite-jni,
libvbz-hdf-plugin-dev, libterraces-dev,
libcapsule-maven-nextflow-java, libgatk-bwamem-java,
libicb-utils-java, libgatk-bwamem-jni, python3-bioblend,
libgenomicsdb-dev, libgenomicsdb-java, capsule-nextflow,
libbiosoup-dev
-med-cloud
removed:
Recommends: zalign
-med-imaging
added:
Recommends: heudiconv
Suggests: orthanc-neuro
-med-imaging-dev
added:
Recommends: python3-dcmstack
removed:
Suggests: libvtk7-dev
-med-oncology
removed:
Recommends: dicompyler
-med-psychology
added:
Recommends: orthanc-neuro
-med-tools
added:
Recommends: cycle
removed:
Suggests: cycle
-- Andreas Tille <tille@debian.org> Fri, 28 Oct 2022 10:12:35 +0200
debian-med (3.7.2) unstable; urgency=medium
* opensurgsim is removed from Debian
* substitute r-cran-gprofiler by r-cran-gprofiler2 (see #994212)
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: megan-ce, twopaco, lamassemble, ntcard, snpsift, mcaller,
dnarrange, megadepth, r-bioc-megadepth, provean,
libpwiz-tools, rockhopper, diann
Suggests: r-cran-gprofiler2
removed:
Suggests: mcaller, r-cran-gprofiler
-med-bio-dev
added:
Recommends: libpwiz-dev, python3-cogent3, r-cran-gprofiler2
removed:
Recommends: r-cran-gprofiler
Suggests: python3-cogent3, python3-mcaller
-med-covid-19
added:
Recommends: nf-core-artic
removed:
Recommends: artic
-med-epi
added:
Recommends: r-cran-prevalence
-med-imaging
removed:
Recommends: python3-mvpa2
-med-imaging-dev
added:
Recommends: libopencv-dev, python3-torchvision
removed:
Recommends: python3-mvpa2, pytorch-vision, libopensurgsim-dev, libcv-dev
-- Andreas Tille <tille@debian.org> Fri, 03 Jun 2022 12:04:09 +0200
debian-med (3.7.1) unstable; urgency=medium
* Remove libbiod-dev
* Remove r-cran-rsgcc (see #1002794)
* Remove r-other-hms-dbmi-spp since it is r-cran-spp
* Standards-Version: 4.6.0
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: r-bioc-mofa2, igblast, tipp, haploview, cutesv,
python3-cogent3
Suggests: r-bioc-isoformswitchanalyzer, catfishq, nano-snakemake,
tandem-genotypes, illustrate
removed:
Recommends: hinge, r-bioc-pcamethods, python3-cogent,
r-other-hms-dbmi-spp, haploview-cran-amap, compclust,
gassst, ccs, ncbi-igblast
Suggests: r-cran-rsgcc, r-bioc-org.ce.eg.db, r-bioc-org.rn.eg.db
-med-bio-dev
added:
Recommends: goby-java, python3-cigar, python3-pangolearn,
python3-compclust
removed:
Recommends: libgoby-java, r-other-hms-dbmi-spp, pangolearn, libbiod-dev,
python3-hyphy
Suggests: r-cran-rsgcc
-med-bio-ngs
added:
Recommends: q2cli
Suggests: r-bioc-mofa2, r-bioc-isoformswitchanalyzer
-med-covid-19
added:
Recommends: tipp, python3-idseq-dag, r-cran-kernelheaping
removed:
Recommends: idseq-dag
-med-epi
added:
Recommends: r-cran-kernelheaping
-med-imaging
added:
Suggests: illustrate
-med-imaging-dev
added:
Recommends: libvtk9-dev, libinsighttoolkit5-dev
Suggests: libvtk7-dev
removed:
Recommends: libvtk7-dev, libinsighttoolkit4-dev
Suggests: libvtk6-dev
-- Andreas Tille <tille@debian.org> Wed, 12 Jan 2022 20:44:28 +0100
debian-med (3.7) unstable; urgency=medium
* Re-render metapackages according the package pool in bullseye
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: bio-vcf, uncalled, covpipe, fastani, bioawk, bamclipper
Suggests: r-bioc-structuralvariantannotation
-med-bio-dev
added:
Recommends: libbio-db-ncbihelper-perl, libbio-variation-perl,
python3-scanpy, libbio-db-biofetch-perl, libbio-db-embl-perl,
python3-wdlparse, pangolearn, libpdb-redo-dev
Suggests: r-bioc-structuralvariantannotation
-med-covid-19
added:
Recommends: uncalled, covpipe, fastani, python3-scanpy, nthash,
bamclipper
-med-epi
added:
Suggests: python3-epimodels
-med-imaging
added:
Recommends: python3-nipype, bart-cuda
removed:
Suggests: python-nipype
-med-imaging-dev
added:
Recommends: python3-nipype, python3-brian, python3-vigra
removed:
Suggests: python-vigra, python-nipype
-- Andreas Tille <tille@debian.org> Mon, 03 May 2021 21:28:56 +0200
debian-med (3.6.2) unstable; urgency=medium
* DEP5 copyright
* Rename debian/NEWS.debian to debian/NEWS
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
removed:
Recommends: pbgenomicconsensus, unanimity, dindel
-med-bio-dev
added:
Suggests: libxxsds-dynamic-dev, r-bioc-affxparser,
r-bioc-oligoclasses, r-bioc-gseabase, r-bioc-arrayexpress,
r-bioc-oligo, r-bioc-gsva
removed:
Recommends: seqan-dev
Suggests: libdynamic-dev
-med-bio-ngs
removed:
Recommends: dindel
-- Andreas Tille <tille@debian.org> Mon, 01 Mar 2021 11:33:28 +0100
debian-med (3.6.1) unstable; urgency=medium
* Recommends: python3-dipy
Closes: #974765
* Migrate to udd-mirror.debian.net hostname
Closes: #976058
* Standards-Version: 4.5.1
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: ggd-utils, cif-tools, phylonium, relion, gsort,
relion-cuda, simkamin, plink2, pangolin,
relion-gui-cuda, simka, r-other-rajewsky-dropbead,
agat, r-bioc-scater, tortoize, shasta, survivor,
density-fitness, relion-gui, svim, r-other-fastbaps,
nanostat, pinfish, salmid
Suggests: r-bioc-genomicranges, r-cran-rcpphnsw, mcaller,
libhnswlib-dev, r-bioc-org.ce.eg.db, r-bioc-genomicalignments,
r-bioc-genomicfiles, nanocomp, r-bioc-biocsingular,
r-bioc-biocneighbors, r-bioc-singlecellexperiment,
r-bioc-beachmat, python3-nanoget, hts-nim-tools, resfinder-db,
r-bioc-org.hs.eg.db, r-bioc-org.mm.eg.db, seqcluster,
r-bioc-org.rn.eg.db
removed:
Recommends: relion-bin | relion-bin+mpi, predictprotein, relion-bin+gui |
relion-bin+mpi+gui, pynast
Suggests: r-bioc-biosingular
-med-bio-dev
added:
Recommends: nim-kexpr-dev, libbio-featureio-perl, python3-pybigwig,
libbio-cluster-perl, libbio-alignio-stockholm-perl,
python3-peptidebuilder, python3-shasta, nim-hts-dev,
nim-lapper-dev, libbio-db-hts-perl,
libbio-tools-run-remoteblast-perl, libcifpp-dev,
python3-bcbio-gff
Suggests: python3-mcaller, q2-cutadapt, q2-metadata, q2-alignment,
q2-deblur, libatomicqueue-dev, r-bioc-cager, q2cwl, q2lint,
r-bioc-titancna, libconcurrentqueue-dev, q2-shogun,
python3-joypy, q2-emperor, r-cran-rcpphnsw, libsuma-dev,
q2-phylogeny, libargs-dev, q2-gneiss, q2cli, q2-longitudinal,
q2-feature-classifier, q2-vsearch, q2-quality-control,
r-bioc-biocneighbors, q2-composition, r-bioc-purecn,
q2-sample-classifier, qiime, q2-quality-filter,
libdynamic-dev, q2templates, r-bioc-s4vectors, q2-diversity,
q2-dada2, q2-fragment-insertion, q2-feature-table, q2-taxa,
q2-types, cwlformat, q2-demux
-med-cloud
added:
Recommends: plink1.9, plink2
removed:
Recommends: pynast
-med-covid-19
added:
Recommends: r-other-fastbaps, pinfish, pangolin, plink2
-med-imaging
added:
Recommends: python3-dipy, nifti2dicom, qnifti2dicom
Suggests: orthanc-gdcm
removed:
Suggests: python-dipy
-med-imaging-dev
added:
Recommends: python3-dipy, libnifti2-dev
removed:
Recommends: libnifti-dev
Suggests: python-dipy
-med-oncology
added:
Recommends: simrisc
Suggests: python3-dicompylercore
-med-psychology
added:
Suggests: python3-bids-validator, python3-bmtk
-- Andreas Tille <tille@debian.org> Mon, 21 Dec 2020 18:45:13 +0100
debian-med (3.6) unstable; urgency=medium
* COVID-19 sprint release
* Drop autodocktools since it depends mgltools-pmv which is about to
be removed
* Drop all mgltools-* packages since these are unmaintained and there
is no Python3 port
* Remove cain from tasks since there is close to no chance to port it
to Python3
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Trim trailing whitespace.
-- Andreas Tille <tille@debian.org> Fri, 14 Aug 2020 22:37:10 +0200
debian-med (3.5.1) unstable; urgency=medium
* Drop fastx-toolkit and libgtextutils since unmaintained and
libgtextutils has issued with gcc9
* Drop mgltools-pmv which is constantly broken for several years
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: r-bioc-geoquery, r-cran-wgcna
removed:
Recommends: mgltools-pmv, r-other-wgcna, fastx-toolkit
-med-bio-dev
added:
Suggests: r-bioc-geoquery
removed:
Suggests: libgtextutils-dev
-med-bio-ngs
removed:
Recommends: fastx-toolkit
-med-cloud
removed:
Recommends: fastx-toolkit
-- Andreas Tille <tille@debian.org> Fri, 06 Dec 2019 18:24:39 +0100
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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> Fri, 25 Jan 2019 14:49:50 +0100
debian-med (3.2) unstable; urgency=medium
* Fix broken reference to alioth
* Standards-Version: 4.3.0
* debhelper 12
* Versioned Build-Depends: blends-dev (>= 0.7.2~)
* Add missing ${misc:Depends}
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-bio
added:
Recommends: r-cran-sdmtools, delly, python3-pybedtools, r-cran-tcr,
qutemol, r-cran-tigger, bax2bam, python3-gffutils,
vdjtools, r-cran-shazam, r-cran-alakazam, gramalign,
igor, deepbinner, python3-sqt, minimap2, sourmash,
samblaster, murasaki | murasaki-mpi, biosyntax, paipline,
pyvcf, r-bioc-cner, igdiscover, fastp, ncbi-igblast,
pybel, jellyfish1, minimac4, lambda-align2, sweed,
viewmol, seq-seq-pan, yaha, python3-biomaj3-daemon,
changeo, mirtop, python3-presto, cct, unanimity,
plasmidseeker
removed:
Recommends: hilbertvisgui, decipher, hyphygui, jstreeview,
biosyntax-gedit, python3-biomaj3, spice, rosetta,
hexamer, murasaki, gbioseq, finex, das-proserver, est-db
-med-bio-dev
added:
Recommends: python3-screed, python3-misopy, python3-pyvcf,
python3-biomaj3, python3-ngs, toil, python3-cutadapt,
python3-ruffus, python3-biotools, python3-sqt,
libmems-dev, python3-hyphy, libstatgen-dev, python3-cobra,
python3-biopython, python3-pysam, python3-airr,
python3-dendropy, libgenome-dev, python3-fast5,
python3-cyvcf2, libpll-dev, python3-bx, libmuscle-dev,
python3-treetime, python3-presto, python3-pbconsensuscore,
python3-csb, python3-intervaltree-bio, python3-seqcluster,
python3-ete3, python3-bcbio, python3-pyfaidx, galaxy-lib,
python3-consensuscore2, snakemake
Suggests: ctdconverter, libmodhmm-dev, libsvmloc-dev, vdjtools,
python3-ctdopts, python3-biopython-sql, libmilib-java
removed:
Recommends: python3-biotools | python-biotools, octave-bioinfo,
python3-pyvcf | python-pyvcf,
python3-biomaj3 | python-biomaj3,
python3-pbconsensuscore | python-pbconsensuscore,
libmuscle-3.7-dev, python3-pyfaidx | python-pyfaidx,
python3-consensuscore2 | python-consensuscore2,
python-bd2k, python3-bx | python-bx,
python3-ete3 | python-ete3, python3-ruffus | python-ruffus,
python3-fast5 | python-fast5,
python3-dendropy | python-dendropy, python-pysam,
python3-cutadapt | python-cutadapt, libgff-perl,
python3-ngs | python-ngs, python3-pyfasta | python-pyfasta,
python3-csb | python-csb, libgenome-1.3-dev,
python3-biopython | python-biopython,
python3-hyphy | python-hyphy, python-cobra,
libmems-1.6-dev,
python3-intervaltree-bio | python-intervaltree-bio,
python3-misopy | python-misopy
Suggests: python3-biopython-sql | python-biopython-sql
-med-bio-ngs
added:
Recommends: python3-presto, changeo, bcbio, igor, python3-pybedtools,
igdiscover, python3-airr, r-cran-tcr, r-cran-tigger,
python3-sqt, python3-gffutils, fastp, vdjtools,
samblaster, r-cran-shazam, r-cran-alakazam
-med-bio-phylogeny
added:
Suggests: python3-treetime
-med-epi
added:
Recommends: epifire
-med-imaging
added:
Recommends: mrtrix3, odil
Suggests: orthanc-mysql, tifffile
-med-imaging-dev
added:
Recommends: libsimpleitk1-dev, python3-biosig, libodil-dev,
python3-simpleitk, libxdf-dev
removed:
Recommends: libodil0-dev
-med-pharmacy
added:
Recommends: r-cran-rpact
-med-physics
added:
Suggests: python3-biosig
removed:
Suggests: python-biosig
-med-research
added:
Recommends: r-cran-rpact
-med-typesetting
removed:
Suggests: referencer
-- Andreas Tille <tille@debian.org> Thu, 24 Jan 2019 15:07:55 +0100
debian-med (3.1) unstable; urgency=medium
* Versioned Build-Depends bumped to 0.6.99 to enable Recommends in tasks
files
* s/Depends/Recommends/
(leave out list of changed metapackage dependencies which is messed up
due to this change)
* Moved to Salsa
* Standards-Version: 4.1.4
* Bumped versioned Build-Depends blends-dev to >= 0.7~
* Priotity: optional (as per policy 4.0.1.0 - see #759260)
-- Andreas Tille <tille@debian.org> Thu, 26 Apr 2018 22:33:08 +0200
debian-med (3.0.1) unstable; urgency=medium
* Re-render before Stretch release
-- Andreas Tille <tille@debian.org> Wed, 19 Apr 2017 15:29:37 +0200
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
-- Andreas Tille <tille@debian.org> Tue, 24 Jan 2017 10:51:13 +0100
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
-- Andreas Tille <tille@debian.org> Tue, 20 Dec 2016 11:27:35 +0100
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 <tille@debian.org> Mon, 12 Sep 2016 10:03:11 +0200
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
-- Andreas Tille <tille@debian.org> Tue, 01 Sep 2015 17:40:57 +0200
debian-med (2.1) unstable; urgency=medium
* Build-Depends: blends-dev (>= 0.6.92.3) to enable respecting user PATH
/usr/lib/debian-med/bin
* Fix bashism issue since fixed in blends-dev
Closes: #772308
* Rebuild in Jessie
* Updated descriptions for his and laboratory
* Introduce /usr/lib/debian-med/bin as PATH for Debian Med users
-- Andreas Tille <tille@debian.org> Thu, 02 Jul 2015 17:55:39 +0200
debian-med (2.0) unstable; urgency=medium
* Fixed syntax of med-cloud and rerender dependencies
* Versioned Build-Depends: blends-dev (>= 0.6.92.2) to ensure no packages
from non-free or unstable will be included by accident
* Since last metapackage creation (and before freeze) the following
packages made it into testing:
fastaq,
relion-bin + librelion-dev
These were adde to the list of Recommends
* After the freeze the package
psychopy
was removed from testing and thus it is removed from Recommends
-- Andreas Tille <tille@debian.org> Sun, 29 Mar 2015 13:47:07 +0200
debian-med (1.99) unstable; urgency=low
* debian/control.stub:
- Build-Depends: blends-dev (>= 0.6.92) to get Section: metapackage entries
- cme fix dpkg-control
- debhelper 9
* d/source/format: 3.0 (native)
* start of automatic changelog entry *
* Changes in metapackage dependencies
-med-pharmacy
added:
Depends: r-cran-dosefinding
-med-tools
added:
Depends: cronometer, python-fitbit, python3-fitbitscraper, nut-nutrition
Suggests: goldencheetah
removed:
Suggests: cl-pubmed
-med-cloud
added:
Depends: bagpipe, fitgcp, fastqc, biomaj, sibsim4, biosquid, pdb2pqr,
soapdenovo, clonalframe, kissplice, conservation-code, mummer,
gasic, datamash, t-coffee, ampliconnoise, cassiopee, snap,
tabix, flexbar, zalign, parsinsert, smalt, melting,
r-cran-vegan, autodock-vina, cufflinks, mafft, dialign, glam2,
freecontact, probabel, mustang, amap-align, gromacs, anfo,
sigma-align, giira, blast2, bowtie, phyutility, poa, dialign-tx,
arden, qiime, squizz, theseus, gmap, autogrid, r-bioc-edger,
cd-hit, dnaclust, idba, probcons, discosnp, prodigal, cain,
sra-toolkit, clearcut, gff2ps, genometools, neobio, mrbayes,
pynast, sim4, bioperl, prank, perm, prime-phylo,
mira-assembler, bowtie2, vcftools, mapsembler2, r-cran-pvclust,
hmmer, cdbfasta, clustalw, wise, kalign, soapdenovo2, boxshade,
clustalo, python3-biopython, proda, abyss, primer3, grinder,
fastx-toolkit, rtax, minia, mlv-smile, concavity,
r-other-mott-happy.hbrem, ncbi-epcr, gff2aplot, macs, mothur,
hhsuite, fasttree, mipe, bamtools, aragorn, bioperl-run,
exonerate, jellyfish, aevol, circos, paraclu, python-biopython,
muscle, dssp
removed:
Depends: clustalw | clustalw-mpi, r-other-mott-happy, bagphenotype
-med-psychology
added:
Depends: python-pypsignifit
Suggests: python-visionegg
removed:
Depends: psignifit3
Suggests: visionegg
-med-bio
added:
Depends: bagpipe, minia, emmax, clearcut, metastudent, cassiopee,
freebayes, relion-gui, r-cran-vegan, uc-echo, spades, pdb2pqr,
probabel, relion-bin | relion-bin-mpi, mrs, acacia, staden,
snp-sites, r-bioc-rtracklayer, kissplice, giira, aragorn, rtax,
gasic, fitgcp, chimeraslayer, perm, prime-phylo,
velvetoptimiser, saint, crac, grabix, phyutility, r-bioc-gviz,
ray, spread-phy, r-other-mott-happy.hbrem, pycorrfit,
rate4site, varscan, mapsembler2, flexbar, trimmomatic,
blimps-utils, nast-ier, blat, bitseq, mach-haplotyper,
ngsqctoolkit, discosnp, emperor, dnaclust, unc-fish, idba,
r-cran-ape, openms, topp, parsinsert, aevol, fsa, biceps,
ipig, kclust, circos, strap-base, freecontact, wigeon, fastaq,
soapdenovo2, r-bioc-biostrings, seqan-apps, eigensoft,
prodigal, modeller, arden, paraclu, situs, pyscanfcs
Suggests: biomaj-watcher, mobyle-tutorials, r-cran-boolnet,
mobyle-programs
Ignore: mozilla-biofox
removed:
Depends: r-ape, sra-sdk, ray-denovoassembler, phy-spread | spread-phy,
fas, vegan, dotur, r-other-mott-happy, bagphenotype
Suggests: circos, pdb2pqr, seqan-apps, eigensoft, blimps-utils,
python-rdkit, mozilla-biofox
-med-his
added:
Depends: vista-foia
removed:
Depends: vista
-med-bio-ngs
added:
Depends: kissplice
removed:
Depends: ssaha2
-med-practice
added:
Suggests: libctapimkt1
removed:
Depends: freeicd
Suggests: libctapimkt0
-med-imaging-dev
added:
Depends: libedf-dev, libpapyrus3-dev, libmialm-dev, r-cran-rniftilib,
libvmtk-dev, libvtk-dicom0.4-dev,
libinsighttoolkit3-dev | libinsighttoolkit4-dev,
python-mia | python3-mia, octave-gdf, python-vmtk,
python-mvpa2, libvigraimpex-dev, libteem-dev, python-vigra,
libmia-2.2-dev, libmiaviewit-dev, python-mne
Suggests: libics-dev, python-tifffile, libvtkedge-dev
removed:
Depends: libmia-2.0-dev, python-mvpa, libteem1-dev,
libinsighttoolkit3-dev
-med-imaging
added:
Depends: mia-viewit, vtk-dicom-tools, pixelmed-apps, conquest-common,
teem-apps, gdf-tools, python-surfer, python-mvpa2,
python-dicom, python-nibabel
Suggests: conquest-mysql, trimage, conquest-dbase, openwalnut-qt4,
conquest-sqlite, python-pyxid, conquest-postgres
removed:
Depends: conquest-dicom-server, python-mvpa, pixelmed-java, python-nifti
Suggests: pysurfer, pyxid, openwalnut
-med-bio-phylogeny
added:
Depends: spread-phy
removed:
Depends: phy-spread | spread-phy
-med-bio-dev
added:
Depends: python-rdkit, libbambamc-dev, libgenome-1.3-dev,
libfreecontact-perl, libhts-dev,
libgenome-model-tools-music-perl, python-corepywrap, pyfai,
libsnp-sites1-dev, libgenome-perl, libfreecontact0-dev,
libssm-dev, python-biopython | python3-biopython, sbmltoolbox,
python-csb | python3-csb, python-htseq, python-freecontact,
libopenms-dev, librelion-dev
Suggests: r-bioc-iranges, r-bioc-variantannotation, r-bioc-bsgenome,
r-bioc-preprocesscore, r-bioc-shortread, r-bioc-affy,
python-biopython-sql | python3-biopython-sql,
python-biopython-doc, r-bioc-makecdfenv, libfreecontact-doc,
libgtextutils-dev, r-bioc-affyio, librostlab-doc,
r-bioc-hypergraph, r-bioc-biovizbase, r-bioc-genomeinfodb,
librostlab-blast-doc, r-bioc-graph, r-bioc-xvector,
r-bioc-genomicfeatures, r-bioc-annotationdbi, r-bioc-snpstats,
r-bioc-rsamtools, r-bioc-altcdfenvs, r-bioc-genomicranges,
r-bioc-genomicalignments, r-bioc-biomart
removed:
Depends: libqsearch-dev, iranges, libopenmm4-dev, librostlab-blast-doc,
libgenome-1.3-0-dev, biostrings, librostlab-doc,
python-biopython, python-librcsb-core-wrapper, octave-bioinfo
-med-epi
added:
Depends: ushahidi
-med-physics
added:
Depends: gdf-tools, biosig-tools
Suggests: python-biosig, octave-biosig, python-multipletau, libbiosig-dev
removed:
Depends: biosig
-- Andreas Tille <tille@debian.org> Thu, 23 Oct 2014 23:42:18 +0200
debian-med (1.13.2) unstable; urgency=low
* Build-Depends: blends-dev (>= 0.6.16.2)
* Added dependency in imaging-dev: libopenigtlink1-dev
-- Andreas Tille <tille@debian.org> Thu, 20 Dec 2012 09:13:33 +0100
debian-med (1.13.1) unstable; urgency=low
* Revert name change from med-pharmacy -> med-pharma
Closes: #694424
-- Andreas Tille <tille@debian.org> Tue, 27 Nov 2012 17:37:26 +0100
debian-med (1.13) unstable; urgency=low
* med-rehabilitation: sitplus is back to testing - regenerate dependencies
* Some new prospective packages in tasks
-- Andreas Tille <tille@debian.org> Wed, 07 Nov 2012 11:39:29 +0100
debian-med (1.12) unstable; urgency=low
* debian/control:
Usual changes of dependency based on the resolving of new packages
in Debian as specified in the tasks files
* config/control: Enhanced readability and spelling of long description
* Added dependencies due to packages progressing to testing after last upload
Bio: r-cran-genabel, gentle, dssp, neobio, fasttree
Bio-dev: libbiojava3-java, libai-fann-perl, librg-blast-parser-perl,
libsort-key-top-perl, libhmsbeagle-dev
Imaging: ants, king
Practice: freediams, freemedforms-freedata, freemedforms-emr
* Removed dependencies due to packages removed from testing
Bio: gassst (removed in #689957)
Rehabilitation: sitplus (lacking build-depends in testing, see #680798)
* Renamed metapackages: med-pharmacy -> med-pharma
* Add debian/med-*.lintian-overrides to prevent false positives about
homepage links
-- Andreas Tille <tille@debian.org> Mon, 05 Nov 2012 15:52:59 +0100
debian-med (1.11) unstable; urgency=low
* debian/control(.stub):
Standards-Version: 3.9.3 (no changes needed)
* debian/control:
Usual changes of dependency based on the resolving of new packages
in Debian as specified in the tasks files
* tasks/physics: s/octave3.2/octave/
Closes: #667588
-- Andreas Tille <tille@debian.org> Thu, 05 Apr 2012 08:30:44 +0200
debian-med (1.10) unstable; urgency=low
* tasks/oncology: Fix typo
Closes: #647987
* tasks/dental: Fullfilled dependency imagetooth results in new
metapackage med-dental
-- Andreas Tille <tille@debian.org> Fri, 16 Dec 2011 13:25:18 +0100
debian-med (1.9) unstable; urgency=low
* Standards-Version: 3.9.2 (no changes needed)
* Do not create med-cms metapackage any more because the only
Dependency is dropped from testing / unstable
* New tasks bio-ngs + bio-phylogeny which are actual subsets
of med-bio created but not turned into metapackages for this
release
* New task oncology - packaging dependencies is in preparation
* Several new Dependencies created by Blends tools
* Fixed Vcs fields
-- Andreas Tille <tille@debian.org> Mon, 18 Jul 2011 10:32:39 +0200
debian-med (1.8) unstable; urgency=low
[Steffen Möller]
* Added task cloud: Cloud computing image for Debian Med
[Andreas Tille]
* config/control: Depends: blends-common (>= 0.6.15)
* debian/control.stub: Build-Depends-Indep: blends-dev (>= 0.6.15)
which provides postrm / preinst scripts for each metapackage to
enable handling failed-upgrade
Closes: ##603853
-- Andreas Tille <tille@debian.org> Thu, 18 Nov 2010 08:16:45 +0100
debian-med (1.7) unstable; urgency=low
* Rebuild against blends-dev >= 0.6.14 to prevent
accessint internet at package build time
* Standards-Version: 3.9.1 (no changes needed)
* tasks/imaging-dev: Revcent version of vtk to make
sure vtk migration will be not blocked by Debian Med
* config/control:
- Do not mention mention med-cms any more because the package
will not be created any more. The only dependency in Debian
zope-zms was removed.
- Add med-psychology and med-statistics
-- Andreas Tille <tille@debian.org> Wed, 04 Aug 2010 12:43:09 +0200
debian-med (1.6) unstable; urgency=low
* Rebuild against blends-dev >= 0.6.12. This results in
using a prerm script instead of postrm which ensures that
blends-common is installed while this script is running
* Standards-Version: 3.8.4 (no changes needed)
* debian/oldchangelogs: removed old stuff
-- Andreas Tille <tille@debian.org> Thu, 18 Mar 2010 10:07:26 +0100
debian-med (1.5) unstable; urgency=low
* Depend from blends-common >= 0.6.9 and explain in
NEWS.Debian that no attempt to take over any CDD
related configuration
Closes: #562553
-- Andreas Tille <tille@debian.org> Mon, 18 Jan 2010 22:22:05 +0100
debian-med (1.4) unstable; urgency=low
* Several new dependencies in Metapackages
* Depend from blends-common >= 0.6.8
Closes: #562553
* No need to Build-Depends from debhelper because blends-dev
does depend from it
* Several new package
-- Andreas Tille <tille@debian.org> Mon, 28 Dec 2009 08:58:27 +0100
debian-med (1.3) unstable; urgency=low
* tasks/physics: Enhanced information about biosig
* tasks/*: Several changes and additional information for a
lot of prospective packages; a certain amount of packages
is now available as official packages
* debian/control.stub:
- Fixed Vcs-Svn (missing svn/)
* Replaced some remaining "cdd" strings in the docs by "blends"
* Standards-Version: 3.8.3 (no changes needed)
* config/control: Depends: blends-common (>= 0.6.6)
Closes: #542656
-- Andreas Tille <tille@debian.org> Fri, 21 Aug 2009 14:09:18 +0200
debian-med (1.2) unstable; urgency=low
[ Andreas Tille ]
* Bumped policy to 3.8.1 and make use of the new feature that
debian/control allows comment lines starting with # with no
preceding whitespace. [Policy paragraph 5.2]
* debhelper (>=7)
* Added med-statistics
* tasks/bio: Replaced biococoa.app by sequenceconverter.app
* tasks/bio-dev: Added libbiococoa-dev
* Build-Depends: blends-dev (0.6.3) to make sure no useless
metapackages with no dependency available in Debian will be
created
* tasks.ctl: Added missing tasks; tasks data, his, laboratory
which do not yet feature an existing depenency in Debian
were set to priority-none.
[ Michael Hanke ]
* Added ODIN to imaging task.
* Added VIA to the imaging task.
* Updated LIPSIA item to ppoint to the packaging VCS and note ITP.
-- Andreas Tille <tille@debian.org> Mon, 30 Mar 2009 07:56:56 +0200
debian-med (1.1) experimental; urgency=low
* Make use of blends-dev instead of cdd-dev
* Versioned build depends from blends-dev >= 0.6.1 because this
also supports dist experimental
* Adapted Vcs fields to new location (cdd -> blends)
* tasks/practice: Depends: aeskulap
* Added link to tasks page in long description of med-tasks
(thanks to James Busser <jbusser@interchange.ubc.ca> for the
hint)
* tasks/*: several updates of newly uploaded packages and
prospective packages
-- Andreas Tille <tille@debian.org> Tue, 06 Jan 2009 10:01:49 +0100
debian-med (1.0) unstable; urgency=low
* tasks/bio-dev
- Added libgenome
- Added libmems as prospective package
- Moved bioconductor from bio to bio-dev
- Added prospective projects where Steffen Möller started some
packaging work
- libqsearch -> libqsearch-dev
* tasks/bio
- Added prospective projects where Steffen Möller started some
packaging work
- Suggests: texlive-latex-extra (because of TeXShade)
- Removed line breaks in Dependencies, because cdd-gen-control
is not compliant to RFC 822 and requires '\' at the end of
lines to continue parsing the tasks files. To simply circumvent
this problem the relevant lines were concatenated to not miss
the dependencies in the resulting control file
- Renamed dialign-t to dialign-tx
* tasks/tools
- Added mssstest
- Added wgerman-medical, hunspell-de-med (remark: these are not
really tools but we have no better section, typesetting might be
an option but does also fit not really good)
* tasks/imaging
- Added prospective packages from static page
* tasks/imaging-dev
- Removed libgtkimreg
- Added libvtk5
- Added prospective packages from static page
- libminc0-dev | libminc-dev -> libminc-dev
- insighttoolkit -> insighttoolkit3
* tasks/physics
- octave | octave2.1 -> octave3.0
* debian/control.stub: XS-DM-Upload-Allowed -> DM-Upload-Allowed
* Standards-Version: 3.8.0 (no changes needed)
* Fixed typing of Debian Med: sed -i 's/Debian-Med/Debian Med/' *
-- Andreas Tille <tille@debian.org> Mon, 30 Jun 2008 09:59:37 +0200
debian-med (0.17) unstable; urgency=low
* tasks/bio:
- Added emboss-kaptain as prospective package
- Added agdbnet as prospective package
- Added autodock, exonerate
- Suggests biococoa.app: Only suggests because status is
questionable
- Removed bugsx which is not really biology related
- Added gamgi as prospective package
- Moved unoffical and prospective packages from static
web pages to tasks file
* tasks/bio-dev:
- Added aceperl as prospective package
- Added libgff-perl as prospective package
- Added Recommends: libqsearch
* tasks/imaging
- Removed paul
- pngquant: Recommends -> Suggests
- Added gdmc as prospective package
- Added dicom4j as prospective package
* tasks/epi: New meta package: med-epi for epidemiology
research
* tasks/tools:
- Moved NetEpi prospective package to epi where it really
belongs to
- Added pondus
* Removed remark about recommended and suggested packages
from description or meta packages
* Build-Depends-Indep: cdd-dev (>= 0.5.0) which ensures that the
source tarball is builded properly and no network access is neede
to build the package
Closes: #470271
-- Andreas Tille <tille@debian.org> Wed, 20 Feb 2008 13:31:25 +0100
debian-med (0.16) unstable; urgency=low
* New upstream version
* Standards-Version: 3.7.3 (no changes needed)
* Added Vcs-Browser / Vcs-Svn tags
* tasks/imaging:
- Added Dr. Jekyll, libvista2 and dcm4che as prospective package
- Fixed minc and nifti library depends
- odin, gwyddion and many more as prospective package
- Removed libfslio1, libniftiio0 which are only available in Etch
- Suggests: Imview
* tasks/imaging-dev:
- libvista2-dev as prospective package
- Fixed minc-dev and nifti-dev library depends
- Removed libniftiio0-dev which is only available in Etch
* tasks/bio
- Added ballview and mustang as prospective packages
- dialign-t is now official package - removed long
description
- Added glam2 as prospective package
- textopo is now in texlilve-science, decreased this from Recommends
to Suggests to not spoil systems with whole texlive installation
* tasks/bio-dev: Added BioClipse as prospective package
Pkg-Description
* tasks/practice:
- Added Mirth as prospective package
- Fixed libchipcard depends
* Debian-Med packaging policy:
- Maintainer: Debian-Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
- XS-DM-Upload-Allowed: yes
- Uploaders: Andreas Tille <tille@debian.org>
- Vcs-Browser, Vcs-Svn
* Increased mozilla-biofox from Suggests to Recommends. Installation of
firefox as Dependency of this package should be no real problem.
* Increased bugsx from Suggests to Recommends. It is automatically decreased
to Suggests by cdd-gen-control so there is no need to decrease it in the
tasks file.
* Make tasks files compliant with rfc822 to be able to use python-debian
tools successfully. That means basically to have exactly one
Depends/Recommends/Suggest per paragraph so the fix was to insert some
newlines and remove '\' in end of lines
* tasks/tools: Fixed description
* tasks/practice: tinyheb as prospective package
* Increased Build-Dep version cdd-dev (>= 0.4.7) because
0.4.5 and 0.4.6 are broken
* config/control: med-config Depends cdd-common (>= 0.4.7)
-- Andreas Tille <tille@debian.org> Tue, 19 Feb 2008 17:07:36 +0100
debian-med (0.15) unstable; urgency=low
* med-imaging-dev: Added
Depends: libinsighttoolkit-dev
Suggests: insighttoolkit-examples
* med-imaging(-dev): Depend from libniftiio1(-dev) instead of
libniftiio0(-dev)
Closes: #448903
* Increased Build-Dep version cdd-dev (>= 0.4.4)
* Standards-Version: 3.7.3 (no changes needed)
* Added several prospective packages in tasks
-- Andreas Tille <tille@debian.org> Sun, 07 Oct 2007 18:25:56 +0200
debian-med (0.14) unstable; urgency=low
* Builded using new cdd-dev 0.4
- med-common is now renamed to med-config
- additional package med-tasks
* med-bio: added emboss
* med-imaging: amide, dicomnifti, imagej, python-nifti
decreased paul from Recommends to Suggests
* med-imaging-dev: cimg-dev
decreased libgtkimreg-dev from Recommends to Suggests
* med-practice: libchipcard3c1, libchipcard3d0
-- Andreas Tille <tille@debian.org> Sat, 11 Aug 2007 17:50:29 +0200
debian-med (0.13) unstable; urgency=low
* Removed entry for gnumed-client-debug because this package does
not exist any more. Removed gnumed-client menu as well because
this should be builded automatically from menu entry inside
gnumed-client package
Closes: #429217
* Added several packages to med-bio and reordering the task to
specific fields
* Imaging: Added dicomnifti
* Enhanced long description of med-common
* Remove header from po.stub/de.po because cdd-dev will add another
one
-- Andreas Tille <tille@debian.org> Thu, 28 Jun 2007 16:23:36 +0200
debian-med (0.12) unstable; urgency=low
* Changed med-practice menu
Closes: #385584
Use menu entry for gnumed-client-debug that regards #389932.
Note: gnumed-client-debug is not in the med-practice dependency
list but it is suggested by gnumed-client. So *if* the package
is installed at the box then an additional menu item occures correctly
in the Debian-Med menu. If it is not installed, only gnumed-client
is shown in the menu.
* med-bio: Added alternative to tree-puzzle as tree-ppuzzle
* Drop med-dent because odontolinux was removed from Debian
* med-bio: Added poa
Moved vrom Suggests to Depends: seaview (now really free)
Suggests: wise-doc
* med-imaging: Depends: libfslio0, libniftiio0, nifti-bin
Suggests:
* med-imaging-dev: Depends: libfslio0-dev, libniftiio0-dev
Suggests: libnifti-doc
-- Andreas Tille <tille@debian.org> Thu, 14 Sep 2006 15:28:51 +0200
debian-med (0.11) unstable; urgency=low
* bugsx to from Depends to Suggets because this package moved to non-free
Closes: #383265
* Standards-Version: 3.7.2
Build-Depends: debhelper
* med-bio:
Depends: gromacs, dialign, kalign, probcons, wise, amap-align, biosquid
Suggests: mozilla-biofox
* debian/compat: 5
* Uploaders: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-- Andreas Tille <tille@debian.org> Wed, 16 Aug 2006 10:07:41 +0200
debian-med (0.10.1) unstable; urgency=low
* Make med-common depend from ${misc:Depends}
Closes: #331797
* Now med-practice really depends from gnumed-client which is now
awailable at Debian mirror
-- Andreas Tille <tille@debian.org> Wed, 5 Oct 2005 07:55:13 +0200
debian-med (0.10) unstable; urgency=low
* Rebuilded with cdd-dev 0.3.11 (and increased versioned dependency
because 0.3.10 created broken *.dsc file)
Closes: #328428
* Standards-Version: 3.6.2 (no changes necessary)
* Added dependencies:
med-bio: mipe, sim4, perlprimer
med-bio-dev: libbio-ruby
* Addes meta package: med-practice
-- Andreas Tille <tille@debian.org> Sun, 25 Sep 2005 21:14:47 +0200
debian-med (0.9) unstable; urgency=low
* Removed gnutrion from tools because it was removed from Debian at all
* Rebuilded with cdd-dev 0.3.10 version
* med-bio:
Depends: muscle, gff2aplot, t-coffee, gff2ps, gdpc
Suggests: arb
* med-bio-dev
Recommends: libvibrant6-dev
Why: libmotif-dev conflicts lesstif-dev, so if someone wants to
install libmotif-dev it must be possible to deinstall
libvibrant6-dev without beeing forced to deinstall med-bio-dev
as well
Depends: python-biopython
* med-imaging:
paul now Recommends not Depends
Depends: dcmtk
Recommends: pngquant
* med-tools:
Depends: cycle
Suggests: cl-pubmed
Strong dependency would cost installing a large amount
of Common Lisp tools which in most cases is not worth
the effort
* Added user menu entries: bio/gff2aplot.txt, bio/gff2ps.txt,
bio/muscle.txt, bio/t-coffee.txt, bio/boxshade.txt,
bio-dev/python-biopython.txt, imaging/dcmtk.txt
* Added charset to debian/po.stub/de.po
-- Andreas Tille <tille@debian.org> Sun, 24 Oct 2004 20:59:03 +0200
debian-med (0.8.9) experimental; urgency=low
* New upstream version which now uses the features of cdd-dev 0.3.9
* Exclude .svn dirs in dist target of debian/rules
-- Andreas Tille <tille@debian.org> Fri, 16 Jul 2004 11:33:21 +0200
debian-med (0.8.3) unstable; urgency=high
* Rebuilded again against cdd-dev 0.3.4 which really closes the
mentioned bug.
* Urgency set to high because it *really* fixes a grave bug.
-- Andreas Tille <tille@debian.org> Thu, 15 Jul 2004 10:59:25 +0200
debian-med (0.8.2) unstable; urgency=high
* Rebuilded with cdd-dev 0.3.3 which closes a grave bug (which
was reassigned to cdd-dev and thus it is not closed in this
changelog).
* Please make sure that all ${HOME}/.menu/cdd-menu files or
${HOME}/.menu/med-* files are removed - they will not be
needed any more.
-- Andreas Tille <tille@debian.org> Wed, 14 Jul 2004 21:42:24 +0200
debian-med (0.8.1) unstable; urgency=low
* Adjust versioned dependency of med-common from cdd-common
Closes: #258373
-- Andreas Tille <tille@debian.org> Fri, 9 Jul 2004 09:18:49 +0200
debian-med (0.8) unstable; urgency=low
* Added med-physics, med-pharmacy, med-bio-dev
* Overworked menus of meta packages
-- Andreas Tille <tille@debian.org> Fri, 4 Jun 2004 14:44:36 +0200
debian-med (0.7) unstable; urgency=low
* Switched to new version of cdd package (0.3) which has many
enhancements (no really important changes to the Debian-Med stuff
except that the packages have to be rebuilded with cdd-dev).
* New cdd-dev package cares for versioned dependency on med-common
Closes: #244903
-- Andreas Tille <tille@debian.org> Tue, 20 Apr 2004 11:21:16 +0200
debian-med (0.6) unstable; urgency=medium
* Took over Debian-Edu method to build metapackages from one
common source.
The changelogs of the previous single meta package sources
can be found in the source package under debian/oldchangelogs.
-- Andreas Tille <tille@debian.org> Mon, 22 Mar 2004 19:21:55 +0100
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