debian-med (3.8.2) unstable; urgency=medium * mriconvert removed from Debian * r-cran-treescape replaced by r-cran-treespace * aeskulap removed from Debian * miaviewit removed from Debian * Remove dicomnifti (see bug #1070243) * r-cran-rniftilib removed from Debian * Cleanup tasks from several removed packages * remove epigrass since we need to package dash first * squizz is removed from Debian * igdiscover will be removed from Debian * Standards-Version: 4.7.0 * Rules-Requires-Root: no * start of automatic changelog entry * * Changes in metapackage dependencies -med-bio added: Recommends: bifrost, deblur, r-cran-treespace, veryfasttree, python3-bioxtasraw, ctffind removed: Recommends: squizz, r-cran-treescape, logol, igdiscover, raccoon, r-cran-metamix Suggests: epigrass -med-bio-dev added: Suggests: cwltest, libbifrost-dev, libbiojava4-java removed: Recommends: libbiococoa-dev, r-cran-metamix, libbiojava4-java Suggests: r-bioc-deseq -med-bio-ngs removed: Recommends: igdiscover -med-bio-phylogeny added: Recommends: fasttree, veryfasttree -med-cloud added: Recommends: veryfasttree removed: Recommends: squizz -med-covid-19 removed: Recommends: conquest-common, pyomo, python3-typed-ast, epigrass, aeskulap -med-dental removed: Recommends: openmolar -med-epi removed: Recommends: epigrass -med-imaging added: Recommends: sightviewer, sightcalibrator removed: Recommends: dicomnifti, conquest-common, mriconvert, aeskulap Suggests: conquest-sqlite, conquest-postgres, conquest-dbase, conquest-mysql -med-imaging-dev removed: Recommends: libmiaviewit-dev, r-cran-rniftilib -med-pharmacy removed: Recommends: raccoon -med-psychology added: Suggests: python3-pynwb -- Andreas Tille Tue, 10 Dec 2024 18:53:30 +0100 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Thu, 26 Apr 2018 22:33:08 +0200 debian-med (3.0.1) unstable; urgency=medium * Re-render before Stretch release -- Andreas Tille 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 for the hint) * tasks/*: several updates of newly uploaded packages and prospective packages -- Andreas Tille 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 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 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 - XS-DM-Upload-Allowed: yes - Uploaders: Andreas Tille - 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 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 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 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 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 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 -- Andreas Tille 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 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 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 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 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 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 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 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 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 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 Mon, 22 Mar 2004 19:21:55 +0100