diff -Nru debian-med-3.1/debian/changelog debian-med-3.2/debian/changelog --- debian-med-3.1/debian/changelog 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/debian/changelog 2019-01-24 14:07:55.000000000 +0000 @@ -1,3 +1,104 @@ +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 diff -Nru debian-med-3.1/debian/compat debian-med-3.2/debian/compat --- debian-med-3.1/debian/compat 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/debian/compat 2019-01-24 14:07:55.000000000 +0000 @@ -1 +1 @@ -9 +12 diff -Nru debian-med-3.1/debian/control debian-med-3.2/debian/control --- debian-med-3.1/debian/control 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/debian/control 2019-01-24 14:07:55.000000000 +0000 @@ -4,19 +4,20 @@ Uploaders: Andreas Tille Section: misc Priority: optional -Build-Depends-Indep: blends-dev (>= 0.7~) -Standards-Version: 4.1.4 +Build-Depends-Indep: blends-dev (>= 0.7.2~), + debhelper (>= 12~) +Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/blends-team/med Vcs-Git: https://salsa.debian.org/blends-team/med.git Package: med-tasks Architecture: all -Depends: tasksel +Depends: tasksel, ${misc:Depends} Description: Debian Med tasks for tasksel This package provides Debian Med tasks in tasksel. . These tasks are described in detail at - http://debian-med.alioth.debian.org/tasks/ + https://blends.debian.org/med/tasks/ Package: med-config Architecture: all @@ -73,6 +74,8 @@ med-physics, med-practice, med-psychology, + med-rehabilitation, + med-research, med-tools, med-typesetting Description: Default selection of tasks for Debian Med @@ -103,6 +106,7 @@ arden, ariba, art-nextgen-simulation-tools, + artemis, artfastqgenerator, assemblytics, atac, @@ -114,12 +118,16 @@ axe-demultiplexer, baitfisher, bali-phy, + ballview, bamtools, + bandage, barrnap, + bcbio, bcftools, beads, beagle, beast-mcmc, + beast2-mcmc, bedops, bedtools, belvu, @@ -127,7 +135,7 @@ bio-eagle, bio-rainbow, bio-tradis, - biosyntax-gedit, + biosyntax, bitseq, blasr, blixem, @@ -141,10 +149,12 @@ bwa, canu, cassiopee, + cct, cd-hit, cdbfasta, centrifuge, cgview, + changeo, chimeraslayer, chromhmm, chromimpute, @@ -157,6 +167,7 @@ clustalo, clustalw, clustalx, + cnvkit, codonw, concavity, conservation-code, @@ -168,6 +179,7 @@ dawg, dazzdb, deepnano, + delly, dialign, dialign-tx, diamond-aligner, @@ -183,10 +195,12 @@ ecopcr, edtsurf, eigensoft, + elph, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, + estscan, examl, exonerate, falcon, @@ -195,6 +209,7 @@ fastdnaml, fastlink, fastml, + fastp, fastqc, fastqtl, fasttree, @@ -212,14 +227,17 @@ garli, garlic, gasic, + gatb-core, gbrowse, gdpc, gemma, + genometester, genometools, gentle, gff2aplot, gff2ps, ghemical, + ghmm, giira, glam2, grabix, @@ -236,7 +254,6 @@ hmmer, hmmer2, hyphy-mpi | hyphy-pt, - hyphygui, idba, indelible, infernal, @@ -244,7 +261,9 @@ iqtree, iva, jaligner, + jalview, jellyfish, + jellyfish1, jmodeltest, jmol, kalign, @@ -255,8 +274,10 @@ kmc, kmer, kraken, + lagan, lamarc, lambda-align, + lambda-align2, last-align, leaff, lefse, @@ -265,6 +286,7 @@ logol, loki, ltrsift, + lucy, macs, macsyfinder, maffilter, @@ -284,7 +306,9 @@ microbiomeutil, minia, miniasm, + minimac4, minimap, + minimap2, mipe, mira-assembler, mlv-smile, @@ -293,7 +317,7 @@ mrbayes, msxpertsuite, mummer, - murasaki, + murasaki | murasaki-mpi, muscle, mustang, nanook, @@ -312,6 +336,8 @@ njplot, norsnet, norsp, + obitools, + openms, pal2nal, paleomix, paml, @@ -339,17 +365,21 @@ phyml, physamp, phyutility, + phyx, picard-tools, piler, + pilon, pirs, placnet, plasmidomics, + plasmidseeker, plast, plink, plink1.9, plip, poa, populations, + porechop, poretools, prank, predictnls, @@ -387,14 +417,20 @@ pynast, pyscanfcs, python-cogent, - python-treetime, - python3-biomaj3, + python3-biomaj3-daemon, + python3-gffutils, + python3-presto, + python3-pybedtools, + pyvcf, qcumber, + qiime, qtltools, quorum, + qutemol, r-bioc-annotate, r-bioc-biostrings, r-bioc-bitseq, + r-bioc-cner, r-bioc-cummerbund, r-bioc-deseq2, r-bioc-dnacopy, @@ -410,25 +446,36 @@ r-bioc-pcamethods, r-bioc-phyloseq, r-bioc-rtracklayer, + r-bioc-tfbstools, r-cran-adegenet, r-cran-adephylo, + r-cran-alakazam, r-cran-ape, r-cran-bio3d, r-cran-distory, r-cran-genabel, + r-cran-metamix, r-cran-phangorn, r-cran-phytools, r-cran-pscbs, r-cran-qtl, r-cran-rotl, + r-cran-samr, + r-cran-sdmtools, r-cran-seqinr, + r-cran-shazam, + r-cran-tcr, + r-cran-tigger, r-cran-treescape, r-cran-vegan, r-other-hms-dbmi-spp, r-other-mott-happy.hbrem, + racon, radiant, rambo-k, + rampler, rapmap, + rasmol, raster3d, rate4site, raxml, @@ -438,6 +485,8 @@ rdp-readseq, readseq, reapr, + relion-bin | relion-bin+mpi, + relion-bin+gui | relion-bin+mpi+gui, repeatmasker-recon, reprof, rna-star, @@ -450,11 +499,13 @@ saint, salmon, sambamba, + samblaster, samtools, scrm, scythe, seaview, seer, + segemehl, seqan-apps, seqmagick, seqprep, @@ -482,6 +533,7 @@ sortmerna, spaced, spades, + spoa, sprai, spread-phy, squizz, @@ -500,6 +552,7 @@ sumtrees, surankco, swarm, + sweed, t-coffee, tabix, tantan, @@ -507,8 +560,12 @@ tigr-glimmer, tm-align, tnseq-transit, + toil, tophat, + topp, toppred, + trace2dbest, + tracetuner, transdecoder, transrate-tools, transtermhp, @@ -517,14 +574,19 @@ treeviewx, trimmomatic, trinityrnaseq, + tvc, uc-echo, + unanimity, + unicycler, varna, vcftools, velvet | velvet-long, velvetoptimiser, + viewmol, vsearch, wigeon, wise, + yaha, zalign Suggests: acacia, adun.app, @@ -534,17 +596,13 @@ apollo, arachne, arb, - artemis, asap, autodocktools, axparafit, axpcoords, bagpipe, - ballview, bambus, - bandage, - bcbio, - beast2-mcmc, + bax2bam, biceps, big-blast, bigsdb, @@ -562,7 +620,6 @@ cinema, cluster3, cmap, - cnvkit, compclust, condetri, contrafold, @@ -573,21 +630,17 @@ crux-toolkit, cufflinks, cytoscape, - das-proserver, dascrubber, dazzle, - decipher, + deepbinner, e-hive, ecell, - elph, embassy-phylip, emboss-explorer, emmax, emperor, ensembl, - est-db, estferret, - estscan, euler-sr, euler2, exabayes, @@ -596,41 +649,33 @@ fasta3, ffp, figaro, - finex, forester, forge, galaxy, gassst, - gatb-core, gatk, - gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, - genometester, getdata, - ghmm, glimmerhmm, gmap, gmv, + gramalign, haploview, hawkeye, - hexamer, - hilbertvisgui, htqc, + igdiscover, + igor, igv, inspect, - jalview, jbrowse, jigsaw, - jstreeview, kempbasu, - lagan, lofreq, - lucy, mach-haplotyper, mage2tab, maker2, @@ -653,6 +698,7 @@ migrate, minimus, mirbase, + mirtop, mobyle, mobyle-programs, mobyle-tutorials, @@ -666,17 +712,17 @@ mummergpu, mview, nanocall, + ncbi-igblast, nextsv, ngila, ngsqctoolkit, nw-align, oases, - obitools, obo-edit, oligoarrayaux, omegamap, - openms, operondb, + paipline, partigene, partitionfinder, patristic, @@ -688,20 +734,19 @@ phylophlan, phyloviz-core, phylowin, - phyx, - pilon, pipasic, plato, - porechop, profit, prokka, prot4est, psipred, pssh2, + pybel, pyrophosphate-tools, python-orange, python-reaper, - qiime, + python-treetime, + python3-sqt, qtlcart, qualimap, r-bioc-annotationhub, @@ -709,44 +754,34 @@ r-bioc-ensembldb, r-bioc-go.db, r-bioc-savr, - r-bioc-tfbstools, r-cran-boolnet, - r-cran-metamix, r-cran-pheatmap, r-cran-qqman, r-cran-rentrez, - r-cran-samr, r-other-apmswapp, raccoon, - racon, - rampler, - rasmol, raxml-ng, rbs-finder, - relion-bin | relion-bin+mpi, - relion-bin+gui | relion-bin+mpi+gui, repeatmasker, rmblast, roadtrips, roche454ace2caf, rose, - rosetta, rsat, sap, science-workflow, scoary, - segemehl, seq-gen, + seq-seq-pan, sequenceconverter.app, sift, sistr, situs, snpeff, solvate, + sourmash, sparta, - spice, splitstree, - spoa, ssaha, strap, strap-base, @@ -758,23 +793,18 @@ tide, tigr-glimmer-mg, tn-seqexplorer, - toil, - topp, - trace2dbest, - tracetuner, treebuilder3d, treetime, tripal, trnascan-se, - tvc, twain, ugene, umap, unc-fish, - unicycler, uniprime, varmatch, varscan, + vdjtools, vienna-rna, vmd, x-tandem-pipeline, @@ -809,6 +839,7 @@ libbiod-dev, libbiojava-java, libbiojava4-java, + libbioparser-dev, libblasr-dev, libbpp-core-dev, libbpp-phyl-dev, @@ -821,13 +852,15 @@ libchado-perl, libconsensuscore-dev, libdivsufsort-dev, + libedlib-dev, libfast5-dev, libfastahack-dev, libffindex0-dev, libfml-dev, libfreecontact-dev, libfreecontact-perl, - libgenome-1.3-dev, + libgatbcore-dev, + libgenome-dev, libgenome-model-tools-music-perl, libgenome-perl, libgenometools0-dev, @@ -840,23 +873,26 @@ libjebl2-java, libjloda-java, libkmer-dev, - libmems-1.6-dev, + libmems-dev, libminimap-dev, - libmuscle-3.7-dev, + libmuscle-dev, libncbi-vdb-dev, libncbi6-dev, libncl-dev, libngs-java, libngs-sdk-dev, libnhgri-blastall-perl, + libopenms-dev, libpal-java, libpbbam-dev, libpbdata-dev, libpbihdf-dev, libpbseq-dev, + libpll-dev, libqes-dev, librcsb-core-wrapper0-dev, librdp-taxonomy-tree-java, + librelion-dev, librg-blast-parser-perl, librg-reprof-bundle-perl, librostlab-blast0-dev, @@ -866,23 +902,24 @@ libsmithwaterman-dev, libsnp-sites1-dev, libsort-key-top-perl, + libspoa-dev, libsrf-dev, libssm-dev, libssw-dev, libssw-java, libstaden-read-dev, + libstatgen-dev, libswiss-perl, libtabixpp-dev, libtfbs-perl, + libthread-pool-dev, libvcflib-dev, libvibrant6-dev, libzerg-perl, libzerg0-dev, mcl, pyfai, - python-bd2k, python-biom-format, - python-cobra, python-cogent, python-corepywrap, python-freecontact, @@ -891,73 +928,81 @@ python-pbcommand, python-pbcore, python-pbh5tools, - python-pysam, + python-rdkit, + python3-airr, + python3-bcbio, python3-biomaj3, - python3-biopython | python-biopython, - python3-biotools | python-biotools, - python3-csb | python-csb, - python3-cutadapt | python-cutadapt, - python3-dendropy | python-dendropy, - python3-fast5 | python-fast5, + python3-biopython, + python3-biotools, + python3-bx, + python3-cobra, + python3-csb, + python3-cutadapt, + python3-cyvcf2, + python3-dendropy, + python3-fast5, python3-gfapy, - python3-intervaltree-bio | python-intervaltree-bio, - python3-ngs | python-ngs, - python3-pbconsensuscore | python-pbconsensuscore, - python3-pyfaidx | python-pyfaidx, + python3-gffutils, + python3-intervaltree-bio, + python3-ngs, + python3-pbconsensuscore, + python3-presto, + python3-pybedtools, + python3-pyfaidx, python3-pymummer, - python3-pyvcf | python-pyvcf, - python3-ruffus | python-ruffus, + python3-pysam, + python3-pyvcf, + python3-ruffus, + python3-screed, python3-skbio, + python3-treetime, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, r-cran-phylobase, r-cran-rncl, r-cran-rnexml, + ruby-bio, + ruby-crb-blast, sbmltoolbox, - seqan-dev + seqan-dev, + snakemake, + toil Suggests: bioclipse, + ctdconverter, + galaxy-lib, libbam-dev, - libbioparser-dev, libdisorder-dev, - libedlib-dev, libforester-java, libfreecontact-doc, - libgatbcore-dev, - libgff-perl, libgoby-java, libgtextutils-dev, - libopenms-dev, + libmilib-java, + libmodhmm-dev, libpbcopper-dev, libqcpp-dev, - librelion-dev, libroadrunner-dev, librostlab-blast-doc, librostlab-doc, - libspoa-dev, + libsvmloc-dev, libswarm2-dev, - libthread-pool-dev, mgltools-networkeditor, mgltools-pybabel, mgltools-vision, octace-bioinfo, - octave-bioinfo, - python-biomaj3, python-biopython-doc, python-mmtk, python-pyflow, - python-rdkit, python-roadrunner, python-screed, - python3-biopython-sql | python-biopython-sql, - python3-bx | python-bx, - python3-consensuscore2 | python-consensuscore2, - python3-ete3 | python-ete3, - python3-gffutils, - python3-hyphy | python-hyphy, - python3-misopy | python-misopy, - python3-pybedtools, - python3-pyfasta | python-pyfasta, + python3-biopython-sql, + python3-consensuscore2, + python3-ctdopts, + python3-ete3, + python3-hyphy, + python3-misopy, + python3-seqcluster, + python3-sqt, r-bioc-affy, r-bioc-affyio, r-bioc-altcdfenvs, @@ -985,9 +1030,8 @@ r-cran-natserv, r-cran-rentrez, r-cran-rocr, - ruby-bio, - ruby-crb-blast, - ruby-rgfa + ruby-rgfa, + vdjtools Description: Debian Med packages for development of bioinformatics applications This metapackage will install Debian packages which might be helpful for development of applications for biological research. @@ -1108,6 +1152,7 @@ python-cogent, python3-biomaj3-cli, python3-biopython, + qiime, r-bioc-hilbertvis, r-cran-pvclust, r-cran-qtl, @@ -1143,8 +1188,7 @@ Suggests: bagpipe, cufflinks, embassy-phylip, - gmap, - qiime + gmap Description: Debian Med bioinformatics applications usable in cloud computing This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not @@ -1174,8 +1218,8 @@ med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: entangle, - imagetooth, - openmolar + imagetooth +Suggests: openmolar Description: Debian Med packages related to dental practice This metapackage contains dependencies for a collection of software which might be helpful for dentists to manage their practice. @@ -1186,7 +1230,7 @@ Depends: ${misc:Depends}, med-config (= ${source:Version}), med-tasks (= ${source:Version}) -Recommends: python-treetime, +Recommends: epigrass, r-cran-diagnosismed, r-cran-epi, r-cran-epibasix, @@ -1195,14 +1239,15 @@ r-cran-epitools, r-cran-lexrankr, r-cran-seroincidence, + r-cran-sf, + r-cran-sjplot, r-cran-surveillance -Suggests: epigrass, +Suggests: epifire, netepi-analysis, netepi-collection, + python-treetime, r-cran-cmprsk, r-cran-msm, - r-cran-sf, - r-cran-sjplot, repast, shiny-server, ushahidi @@ -1248,6 +1293,7 @@ med-tasks (= ${source:Version}) Recommends: aeskulap, amide, + ants, bart, bart-view, biosig-tools, @@ -1259,6 +1305,7 @@ dicom3tools, dicomnifti, dicomscope, + fw4spl, gdf-tools, ginkgocadx, gwyddion, @@ -1277,23 +1324,30 @@ mriconvert, mricron, mrtrix, + mrtrix3, nifti-bin, + odil, + odin, openslide-tools, orthanc, orthanc-wsi, + pixelmed-apps, plastimatch, python-dicom, + python-dipy, + python-mvpa2, python-nibabel, python-nipy, python-nipype, python-nitime, - python-tifffile, + python-surfer, sigviewer, sofa-apps, + teem-apps, + voxbo, vtk-dicom-tools, xmedcon Suggests: afni, - ants, bioimagesuite, bioimagexd, blox, @@ -1323,7 +1377,6 @@ freesurfer, fsl, fslview, - fw4spl, gimias, hid, imagemagick, @@ -1348,7 +1401,6 @@ mni-icbm152-nlin-2009, mni-n3, mrisim, - odin, omero, opendicom.net, openelectrophy, @@ -1357,28 +1409,25 @@ openwalnut-qt4, orthanc-dicomweb, orthanc-imagej, + orthanc-mysql, orthanc-postgresql, orthanc-webviewer, paraview, piano, - pixelmed-apps, pngquant, pymeg, - python-dipy, - python-mvpa2, python-pyxid, - python-surfer, + python-tifffile, science-workflow, slicer, stabilitycalc, stir, - teem-apps, tempo, + tifffile, trimage, via-bin, visit, vmtk, - voxbo, xnat Description: Debian Med image processing and visualization packages This metapackage will install Debian packages which might be useful in @@ -1418,21 +1467,30 @@ libmiaviewit-dev, libminc-dev, libnifti-dev, - libodil0-dev, + libodil-dev, libopenigtlink-dev, libopenslide-dev, + libopensurgsim-dev, libpapyrus3-dev, + libsimpleitk1-dev, + libteem-dev, libvigraimpex-dev, libvistaio-dev, libvolpack1-dev, libvtk-dicom-dev, libvtk6-dev, + libxdf-dev, octave-bart, + octave-dicom, octave-gdf, + odin, + python-cfflib, python-dicom, - python-gdcm, + python-dipy, python-imageio, python-mia | python3-mia, + python-mne, + python-mvpa2, python-nibabel, python-nipy, python-nipype, @@ -1440,6 +1498,8 @@ python-openslide, python-pyxnat, python-vigra, + python3-biosig, + python3-simpleitk, r-cran-rniftilib Suggests: emokit, libbio-formats-java, @@ -1454,18 +1514,11 @@ libnifti-doc, libopenmeeg-dev, libopenslide-java, - libopensurgsim-dev, - libteem-dev, libvia-dev, libvmtk-dev, libxdffileio-dev, - octave-dicom, - odin, - python-cfflib, - python-dipy, + python-gdcm, python-libavg, - python-mne, - python-mvpa2, python-tifffile, python-vmtk Description: Debian Med image processing and visualization packages development @@ -1509,7 +1562,8 @@ med-config (= ${source:Version}), med-tasks (= ${source:Version}) Recommends: chemtool, - r-cran-dosefinding + r-cran-dosefinding, + r-cran-rpact Suggests: raccoon Description: Debian Med packages for pharmaceutical research This metapackage contains dependencies for a @@ -1533,8 +1587,8 @@ octave-biosig, openvibe, paw-demos, - python-biosig, - python-multipletau + python-multipletau, + python3-biosig Description: Debian Med packages for medical physicists This metapackage contains dependencies for a collection of software and documentation which is useful for @@ -1590,15 +1644,15 @@ med-tasks (= ${source:Version}) Recommends: praat, psignifit, + psychopy, + python-pyepl, r-cran-foreign, r-cran-psy Suggests: miscpsycho, psych, psychometric, - psychopy, psychotree, psyphy, - python-pyepl, python-pypsignifit, python-visionegg, science-psychophysics @@ -1606,6 +1660,30 @@ This metapackage contains dependencies for a collection of software which might be helpful for psychological research. +Package: med-rehabilitation +Section: metapackages +Architecture: all +Depends: ${misc:Depends}, + med-config (= ${source:Version}), + med-tasks (= ${source:Version}) +Recommends: sitplus +Suggests: aghermann +Description: Debian Med packages for rehabilitation technologies + This metapackage will install tools that are useful for + rehabilitation and therapy. + +Package: med-research +Section: metapackages +Architecture: all +Depends: ${misc:Depends}, + med-config (= ${source:Version}), + med-tasks (= ${source:Version}) +Recommends: r-cran-rpact +Suggests: openclinica +Description: Debian Med packages for medical research + This metapackage will install tools that are useful for + medical research. + Package: med-statistics Section: metapackages Architecture: all @@ -1675,8 +1753,7 @@ bibus, jabref-plugin-oo, kbibtex, - r-cran-qqman, - referencer + r-cran-qqman Description: Debian Med support for typesetting and publishing This metapackage will install Debian packages that might be helpful for typesetting and publishing in medical care and structural diff -Nru debian-med-3.1/debian/control.stub debian-med-3.2/debian/control.stub --- debian-med-3.1/debian/control.stub 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/debian/control.stub 2019-01-24 14:07:55.000000000 +0000 @@ -3,17 +3,18 @@ Uploaders: Andreas Tille Section: misc Priority: optional -Build-Depends-Indep: blends-dev (>= 0.7~) -Standards-Version: 4.1.4 +Build-Depends-Indep: blends-dev (>= 0.7.2~), + debhelper (>= 12~) +Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/blends-team/med Vcs-Git: https://salsa.debian.org/blends-team/med.git Package: med-tasks Architecture: all -Depends: tasksel +Depends: tasksel, ${misc:Depends} Description: Debian Med tasks for tasksel This package provides Debian Med tasks in tasksel. . These tasks are described in detail at - http://debian-med.alioth.debian.org/tasks/ + https://blends.debian.org/med/tasks/ diff -Nru debian-med-3.1/debian/med-tasks.lintian-overrides debian-med-3.2/debian/med-tasks.lintian-overrides --- debian-med-3.1/debian/med-tasks.lintian-overrides 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/debian/med-tasks.lintian-overrides 2019-01-24 14:07:55.000000000 +0000 @@ -1,3 +1,3 @@ # The link inside the description is no homepage replacement but rather a reference # for more detailed information about the topic -med-tasks: description-possibly-contains-homepage http://debian-med.alioth.debian.org/tasks/ +med-tasks: description-possibly-contains-homepage https://blends.debian.org/med/tasks/ diff -Nru debian-med-3.1/debian-med-tasks.desc debian-med-3.2/debian-med-tasks.desc --- debian-med-3.1/debian-med-tasks.desc 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/debian-med-tasks.desc 2019-01-24 14:07:55.000000000 +0000 @@ -162,6 +162,24 @@ Key: med-psychology +Task: med-rehabilitation +Parent: debian-med +Section: debian-med +Description: Debian Med packages for rehabilitation technologies + This metapackage will install tools that are useful for + rehabilitation and therapy. +Key: + med-rehabilitation + +Task: med-research +Parent: debian-med +Section: debian-med +Description: Debian Med packages for medical research + This metapackage will install tools that are useful for + medical research. +Key: + med-research + Task: med-statistics Parent: debian-med Section: debian-med diff -Nru debian-med-3.1/dependency_data/debian-med_3.2.json debian-med-3.2/dependency_data/debian-med_3.2.json --- debian-med-3.1/dependency_data/debian-med_3.2.json 1970-01-01 00:00:00.000000000 +0000 +++ debian-med-3.2/dependency_data/debian-med_3.2.json 2019-01-24 14:07:55.000000000 +0000 @@ -0,0 +1 @@ +{"cms": {"depends": [], "suggests": ["zope-zms", "xnat", "hid"], "recommends": [], "ignore": [], "avoid": []}, "bio": {"depends": [], "suggests": ["dascrubber", "emboss-explorer", "adun.app", "melting-gui", "cain", "science-workflow", "getdata", "metastudent-data", "metastudent-data-2", "metastudent-data-3", "mrs", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-ensembldb", "r-bioc-go.db", "r-bioc-savr", "r-cran-qqman", "r-cran-rentrez", "r-cran-boolnet", "r-cran-pheatmap", "mobyle", "mobyle-programs", "mobyle-tutorials", "maude"], "recommends": ["altree", "beast-mcmc", "beast2-mcmc", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle", "probalign", "treeviewx", "figtree", "hyphy-mpi | hyphy-pt", "spread-phy", "omegamap", "sweed", "phylip", "fastlink", "loki", "plink", "plink1.9", "r-cran-qtl", "r-cran-genabel", "gemma", "bolt-lmm", "amap-align", "boxshade", "fastx-toolkit", "gff2aplot", "muscle", "sim4", "sibsim4", "tabix", "tophat", "wise", "maqview", "blasr", "daligner", "mhap", "bwa", "mummer", "e-mem", "ncbi-blast+-legacy", "plast", "ncbi-blast+", "mafft", "sra-toolkit", "t-coffee", "kalign", "ghmm", "hmmer", "gramalign", "exonerate", "elph", "dialign", "dialign-tx", "poa", "probcons", "proda", "seaview", "sigma-align", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "arb", "clustalx", "clustalo", "clustalw", "mothur", "bowtie", "bowtie2", "transtermhp", "last-align", "maq", "ssake", "velvet | velvet-long", "qiime", "scoary", "umap", "infernal", "rnahybrid", "adun-core", "avogadro", "garlic", "gamgi", "gdpc", "ghemical", "jmol", "pymol", "r-cran-bio3d", "msxpertsuite", "gromacs", "rasmol", "viewmol", "qutemol", "modeller", "plasmidomics", "gff2ps", "ncbi-epcr", "ncbi-tools-bin", "ncbi-tools-x11", "perlprimer", "readseq", "tigr-glimmer", "melting", "mipe", "primer3", "artemis", "gbrowse", "python3-biomaj3-daemon", "glam2", "raster3d", "phyml", "autodock", "autogrid", "autodock-vina", "autodocktools", "mgltools-pmv", "mgltools-vision", "mgltools-cadd", "mustang", "probabel", "theseus", "staden-io-lib-utils", "samtools", "bedtools", "datamash", "gassst", "hinge", "r-bioc-hilbertvis", "r-other-mott-happy.hbrem", "seq-gen", "snp-sites", "mira-assembler", "alien-hunter", "seqan-apps", "ncoils", "gentle", "gmap", "igv", "picard-tools", "acedb-other", "blixem", "dotter", "belvu", "python-cogent", "paml", "velvetoptimiser", "ensembl", "mrbayes", "pdb2pqr", "squizz", "clonalframe", "clonalframeml", "dssp", "jellyfish", "jellyfish1", "ballview", "pynast", "raxml", "mlv-smile", "cd-hit", "cufflinks", "r-bioc-cummerbund", "eigensoft", "grinder", "jalview", "reprof", "tm-align", "norsnet", "norsp", "predictnls", "prime-phylo", "proftmb", "profbval", "profisis", "hhsuite", "ffindex", "flexbar", "blimps-utils", "sift", "neobio", "ray", "ugene", "logol", "soapdenovo", "soapdenovo2", "soapsnp", "soapaligner", "microbiomeutil", "chimeraslayer", "nast-ier", "wigeon", "minia", "trimmomatic", "saint", "rtax", "rate4site", "rna-star", "topp", "openms", "scythe", "sickle", "smalr", "kmc", "king-probe", "ncl-tools", "tvc", "libvcflib-tools", "bppsuite", "bppphyview", "acacia", "adapterremoval", "aegean", "andi", "arden", "artfastqgenerator", "art-nextgen-simulation-tools", "assemblytics", "augustus", "baitfisher", "bandage", "beagle", "bedops", "biceps", "cnvkit", "csb", "diamond-aligner", "emperor", "euler2", "euler-sr", "fitgcp", "gasic", "giira", "ipig", "aevol", "alter-sequence-alignment", "amos-assembler", "hawkeye", "anfo", "apollo", "aragorn", "ariba", "atac", "axe-demultiplexer", "axparafit", "axpcoords", "bali-phy", "barrnap", "bamtools", "bagpipe", "bax2bam", "bcbio", "bcftools", "bigsdb", "bio-eagle", "bio-tradis", "biosyntax", "bitseq", "blat", "blobology", "bio-rainbow", "card-rgi", "cassiopee", "ccs", "cdbfasta", "centrifuge", "cellprofiler", "chromhmm", "cgview", "brig", "cct", "cinema", "circlator", "clearcut", "clonalorigin", "cluster3", "chromimpute", "codonw", "condetri", "contrafold", "crac", "crossbow", "crux-toolkit", "cutadapt", "cytoscape", "dawg", "dazzdb", "dazzle", "deepbinner", "delly", "deepnano", "dindel", "dwgsim", "ea-utils", "ecell", "ecopcr", "edtsurf", "emmax", "examl", "raxml-ng", "exabayes", "berkeley-express", "falcon", "fasta3", "fasttree", "fastahack", "fastaq", "fastml", "fastp", "fastqc", "fastqtl", "ffp", "unc-fish", "fml-asm", "forester", "freecontact", "freebayes", "fsa", "fsm-lite", "garli", "gatb-core", "gatk", "genometester", "genometools", "grabix", "graphlan", "gwama", "gubbins", "haploview", "harvest-tools", "hilive", "hisat2", "hmmer2", "htqc", "idba", "igdiscover", "indelible", "iqtree", "iva", "jaligner", "jbrowse", "jmodeltest", "kempbasu", "kineticstools", "kissplice", "kraken", "lagan", "lambda-align", "lambda-align2", "leaff", "ltrsift", "lofreq", "khmer", "kmer", "radiant", "lefse", "mach-haplotyper", "macs", "macsyfinder", "maffilter", "mage2tab", "tab2mage", "malt", "manta", "mapdamage", "martj", "mash", "progressivemauve", "mauve-aligner", "meme", "meryl", "metabit", "metaphlan2", "metastudent", "microbegps", "miniasm", "minimac4", "minimap", "minimap2", "mirtop", "molekel", "mosaik-aligner", "mpsqed", "mptp", "mugsy", "murasaki | murasaki-mpi", "mview", "nanocall", "nanook", "nanopolish", "ncbi-entrez-direct", "ncbi-seg", "nextsv", "ngila", "ngsqctoolkit", "nw-align", "oases", "obitools", "paipline", "pal2nal", "paleomix", "paraclu", "parsinsert", "parsnp", "partitionfinder", "patman", "patristic", "pbalign", "pbbarcode", "pbdagcon", "pbsuite", "pbgenomicconsensus", "pbjelly", "pbhoney", "pbh5tools", "pbsim", "pcma", "perm", "pftools", "phast", "phipack", "phybin", "phylophlan", "phyloviz-core", "phyutility", "phyx", "physamp", "piler", "pilon", "pipasic", "inspect", "tide", "pirs", "placnet", "plasmidseeker", "plato", "plip", "poretools", "porechop", "prank", "predictprotein", "proalign", "prodigal", "prokka", "proteinortho", "prottest", "psortb", "pscan-tfbs", "pscan-chip", "psipred", "pssh2", "pybel", "pycorrfit", "pyscanfcs", "python3-gffutils", "python3-pybedtools", "python3-sqt", "python-reaper", "python-treetime", "qcumber", "qtltools", "qualimap", "quorum", "rambo-k", "rapmap", "r-bioc-rtracklayer", "r-bioc-gviz", "r-bioc-biostrings", "r-bioc-annotate", "r-bioc-genefilter", "r-bioc-deseq2", "r-bioc-dnacopy", "r-bioc-geneplotter", "r-bioc-impute", "r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-phyloseq", "r-bioc-ebseq", "r-bioc-limma", "r-bioc-bitseq", "r-bioc-pcamethods", "r-cran-samr", "r-bioc-tfbstools", "r-bioc-cner", "r-cran-metamix", "r-cran-rotl", "r-cran-adegenet", "r-cran-adephylo", "r-cran-distory", "r-cran-metamix", "r-cran-phangorn", "r-cran-pscbs", "r-cran-seqinr", "r-cran-vegan", "r-other-hms-dbmi-spp", "r-other-apmswapp", "relion-bin+gui | relion-bin+mpi+gui", "relion-bin | relion-bin+mpi", "rdp-alignment", "rdp-readseq", "rdp-classifier", "reapr", "repeatmasker-recon", "repeatmasker", "roadtrips", "roary", "roguenarok", "rsat", "rsem", "sambamba", "samblaster", "salmon", "sap", "scrm", "sga", "seer", "segemehl", "seq-seq-pan", "seqmagick", "seqprep", "seqsero", "seqtk", "sequenceconverter.app", "sistr", "situs", "sim4db", "smalt", "smithwaterman", "ssw-align", "smrtanalysis", "snpeff", "snpomatic", "solvate", "sortmerna", "snap-aligner", "sniffles", "sourmash", "spaced", "spades", "sparta", "sprai", "srst2", "ssaha", "sspace", "staden", "stacks", "strap", "strap-base", "subread", "suitename", "sumatra", "sumaclust", "sumtrees", "surankco", "swarm", "tacg", "tantan", "toppred", "transdecoder", "tnseq-transit", "tn-seqexplorer", "toil", "tracetuner", "transrate-tools", "treeview", "trinityrnaseq", "uc-echo", "unanimity", "unicycler", "varna", "varmatch", "varscan", "vdjtools", "vienna-rna", "vmd", "vsearch", "yaha", "canu", "zalign", "zodiac-zeden", "discosnp", "mapsembler2", "dnaclust", "r-cran-tcr", "r-cran-tigger", "r-cran-alakazam", "r-cran-shazam", "igor", "r-cran-sdmtools", "python3-presto", "changeo", "ncbi-igblast", "copycat", "btk-core", "asap", "cactus", "contralign", "concavity", "conservation-code", "galaxy", "genographer", "phylographer", "phylowin", "phpphylotree", "twain", "rose", "glimmerhmm", "genezilla", "exalt", "jigsaw", "genesplicer", "mummergpu", "amoscmp", "minimus", "bambus", "gmv", "pyrophosphate-tools", "figaro", "mirbase", "uniprime", "genetrack", "operondb", "trnascan-se", "cdna-db", "coot", "r-cran-ape", "r-cran-phytools", "r-cran-treescape", "caftools", "roche454ace2caf", "big-blast", "estferret", "lamarc", "lucy", "maxd", "mesquite", "migrate", "msatfinder", "oligoarrayaux", "partigene", "pfaat", "prot4est", "qtlcart", "rbs-finder", "splitstree", "taverna", "taxinspector", "tetra", "trace2dbest", "estscan", "profit", "obo-edit", "phagefinder", "compclust", "treebuilder3d", "excavator", "treetime", "abacas", "profnet-bval", "profnet-chop", "profnet-con", "profnet-isis", "profnet-md", "profnet-norsnet", "profnet-prof", "profnet-snapfun", "profphd-net", "profphd-utils", "profphd", "abyss", "ampliconnoise", "disulfinder", "circos", "runcircos-gui", "populations", "raccoon", "racon", "spoa", "rampler", "librg-utils-perl", "snap", "pyvcf", "vcftools", "beads", "x-tandem-pipeline", "forge", "metarep", "arachne", "maker2", "rmblast", "e-hive", "cmap", "gbrowse-syn", "tripal", "genemark", "annovar", "python-orange", "tigr-glimmer-mg"], "ignore": ["mozilla-biofox", "riso", "catissuecore", "trapss"], "avoid": []}, "research": {"depends": [], "suggests": [], "recommends": ["r-cran-rpact", "openclinica"], "ignore": [], "avoid": []}, "data": {"depends": [], "suggests": ["sleepyhead"], "recommends": ["freediams", "freemedforms-freedata", "python-hl7", "drugref.org"], "ignore": [], "avoid": []}, "epi": {"depends": [], "suggests": ["r-cran-msm", "r-cran-cmprsk", "shiny-server", "repast"], "recommends": ["epigrass", "r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi", "r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "r-cran-seroincidence", "ushahidi", "r-cran-lexrankr", "r-cran-sf", "r-cran-sjplot", "python-treetime", "netepi-analysis", "netepi-collection", "epifire"], "ignore": [], "avoid": []}, "bio-ngs": {"depends": [], "suggests": [], "recommends": ["bedtools", "bwa", "bowtie", "blasr", "daligner", "mhap", "fastx-toolkit", "last-align", "maq", "picard-tools", "r-bioc-hilbertvis", "rna-star", "samtools", "sra-toolkit", "ssake", "tabix", "tophat", "bcftools", "vcftools", "velvet", "libvcflib-tools", "mothur", "qiime", "microbiomeutil", "r-bioc-metagenomeseq", "rtax", "sortmerna", "srst2", "stacks", "subread", "sumatra", "sumaclust", "vsearch", "wigeon", "anfo", "arden", "bowtie", "bowtie2", "artfastqgenerator", "art-nextgen-simulation-tools", "last-align", "maq", "ssake", "velvet | velvet-long", "bamtools", "bcbio", "bcftools", "berkeley-express", "bio-rainbow", "canu", "crac", "cufflinks", "cutadapt", "deepnano", "dindel", "discosnp", "dnaclust", "dwgsim", "ea-utils", "fastaq", "fastp", "fastqc", "fastx-toolkit", "flexbar", "fml-asm", "fsm-lite", "grinder", "giira", "hinge", "hilive", "hisat2", "idba", "igdiscover", "igv", "iva", "khmer", "kissplice", "kraken", "macs", "mapdamage", "maqview", "mira-assembler", "mapsembler2", "nanopolish", "paleomix", "pbsuite", "pbh5tools", "pbjelly", "pbhoney", "pirs", "placnet", "poretools", "python3-gffutils", "python3-pybedtools", "python3-sqt", "qcumber", "quorum", "r-bioc-deseq2", "salmon", "sambamba", "samblaster", "scythe", "seqprep", "seqtk", "sga", "sickle", "smalt", "smrtanalysis", "snap-aligner", "sniffles", "snp-sites", "snpomatic", "soapdenovo", "soapdenovo2", "spades", "sprai", "sra-toolkit", "tophat", "transrate-tools", "trimmomatic", "trinityrnaseq", "uc-echo", "velvetoptimiser", "kissplice", "scoary", "umap", "dindel", "mosaik-aligner", "r-cran-tcr", "r-cran-tigger", "r-cran-alakazam", "r-cran-shazam", "igor", "python3-airr", "python3-presto", "changeo", "vdjtools", "forge", "uc-echo", "annovar"], "ignore": [], "avoid": []}, "his": {"depends": [], "suggests": [], "recommends": ["care2x", "fis-gtm", "vista-foia", "ewd-920", "orthanc-wsi", "tryton-modules-health", "openmaxims", "world-vista", "ipath", "patientos", "openmrs", "hkma-cms", "oscar-mcmaster", "openeyes"], "ignore": [], "avoid": []}, "pharmacy": {"depends": [], "suggests": [], "recommends": ["chemtool", "raccoon", "r-cran-dosefinding", "r-cran-rpact"], "ignore": [], "avoid": []}, "practice": {"depends": [], "suggests": ["libctapimkt1", "openpms", "resmedicinae", "sqlclinic", "openrep"], "recommends": ["gnumed-client", "gnumed-server", "libchipcard-tools", "ginkgocadx", "freediams", "freemedforms-emr", "r-cran-medadherence", "entangle", "sleepyhead", "orthanc", "orthanc-wsi", "medintux", "mirth", "tinyheb", "mirrormed", "elexis", "freeb", "freemed", "elementalclinic", "openemr", "clearhealth", "proteus", "thera-pi", "freeshim", "remitt", "qrisk2"], "ignore": ["clearhealth"], "avoid": []}, "laboratory": {"depends": [], "suggests": [], "recommends": ["opencfu", "orthanc-wsi", "openelis", "openfreezer", "catissuesuite"], "ignore": [], "avoid": []}, "cloud": {"depends": [], "suggests": [], "recommends": ["altree", "clearcut", "fastdnaml", "fasttree", "parsinsert", "phyml", "phyutility", "prime-phylo", "mrbayes", "tree-puzzle | tree-ppuzzle", "alien-hunter", "bagpipe", "fastlink", "loki", "gasic", "genometools", "plink", "probabel", "r-cran-qtl", "r-other-mott-happy.hbrem", "amap-align", "blast2", "biosquid", "boxshade", "cassiopee", "cdbfasta", "cd-hit", "clustalo", "clustalw", "conservation-code", "dialign", "dialign-tx", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "exonerate", "gff2aplot", "gff2ps", "glam2", "gmap", "hmmer", "jellyfish", "kalign", "mafft", "mlv-smile", "mummer", "muscle", "neobio", "poa", "prank", "probcons", "proda", "pynast", "sibsim4", "sigma-align", "sim4", "snap", "squizz", "t-coffee", "wise", "zalign", "bamtools", "bedtools", "fastx-toolkit", "flexbar", "picard-tools", "samtools", "tabix", "vcftools", "anfo", "cufflinks", "bowtie", "bowtie2", "bwa", "last-align", "maq", "perm", "tophat", "smalt", "soapdenovo", "soapdenovo2", "abyss", "mapsembler2", "idba", "minia", "mira-assembler", "ssake", "velvet", "ampliconnoise", "arden", "fastqc", "discosnp", "dnaclust", "fitgcp", "giira", "grinder", "kissplice", "macs", "mothur", "paraclu", "r-bioc-hilbertvis", "sra-toolkit", "aragorn", "infernal", "rnahybrid", "rtax", "autodock", "autodock-vina", "autogrid", "concavity", "dssp", "freecontact", "gromacs", "hhsuite", "mustang", "pdb2pqr", "raster3d", "theseus", "melting", "mipe", "ncbi-epcr", "primer3", "acedb-other", "disulfinder", "ncbi-tools-bin", "ncoils", "python-cogent", "readseq", "tigr-glimmer", "seqan-apps", "staden-io-lib-utils", "aevol", "python3-biomaj3-cli", "bioperl", "bioperl-run", "cain", "clonalframe", "circos", "datamash", "prodigal", "python-biopython", "python3-biopython", "qiime", "r-cran-pvclust", "r-cran-vegan"], "ignore": [], "avoid": []}, "imaging": {"depends": [], "suggests": ["imagemagick", "pngquant", "imview", "trimage", "conquest-dbase", "conquest-mysql", "conquest-postgres", "conquest-sqlite", "paraview", "orthanc-webviewer", "orthanc-dicomweb", "orthanc-imagej", "orthanc-postgresql", "orthanc-mysql", "visit", "mrisim", "connectomeviewer", "eeglab", "elastix", "python-pyxid", "dtitk", "openwalnut-qt4", "miview", "cmtk", "freesurfer", "xnat", "isis", "pymeg", "stabilitycalc", "hid", "incf-nidash-oneclick-clients", "science-workflow", "tifffile"], "recommends": ["amide", "ctsim", "ctn", "dicomnifti", "imagej", "minc-tools", "medcon", "python-nibabel", "python-dicom", "xmedcon", "dcmtk", "nifti-bin", "aeskulap", "fsl", "fslview", "via-bin", "gwyddion", "sofa-apps", "python-mvpa2", "python-nipy", "python-nipype", "python-nitime", "caret", "libgdcm-tools", "slicer", "lipsia", "dicom3tools", "imagevis3d", "odin", "dicomscope", "pixelmed-apps", "vmtk", "ginkgocadx", "openslide-tools", "conquest-common", "camitk-imp", "crea", "orthanc", "teem-apps", "bioimagesuite", "drjekyll", "libdcm4che-java", "dcm4chee", "piano", "mesa-test-tools", "devide", "dicom4j", "opendicom.net", "afni", "blox", "ecg2png", "kradview", "opensourcepacs", "mni-autoreg", "mni-n3", "brainvisa", "maris", "micromanager", "fiji", "cdmedicpacs", "stir", "openelectrophy", "invesalius", "mricron", "voxbo", "mrtrix", "mrtrix3", "ants", "itksnap", "mriconvert", "mia-tools", "mialmpick", "mia-viewit", "ismrmrd-tools", "sigviewer", "python-tifffile", "mni-icbm152-nlin-2009", "mni-colin27-nifti", "mipav", "jist", "openmeeg-tools", "jemris", "insightapplications", "tempo", "dti-query", "python-dipy", "plastimatch", "medisnap", "gimias", "mayam", "biosig-tools", "python-surfer", "dicoogle", "cellprofiler", "bioimagexd", "omero", "king", "vtk-dicom-tools", "gdf-tools", "fw4spl", "bart", "bart-view", "dcm2niix", "orthanc-wsi", "odil"], "ignore": [], "avoid": []}, "typesetting": {"depends": [], "suggests": ["kbibtex", "biber", "bibus", "jabref-plugin-oo", "r-cran-qqman"], "recommends": ["texlive-science", "texlive-latex-extra", "king"], "ignore": [], "avoid": []}, "bio-phylogeny": {"depends": [], "suggests": ["python3-treetime"], "recommends": ["altree", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle", "probalign", "treeviewx", "phylip", "muscle", "t-coffee", "kalign", "hmmer", "exonerate", "dialign", "dialign-tx", "poa", "probcons", "proda", "seaview", "sigma-align", "gmap", "clustalx", "clustalw", "mustang", "phyml", "beast-mcmc", "tm-align", "mrbayes", "figtree", "populations", "proalign", "prottest", "treeview", "phylowin", "gbioseq", "phpphylotree", "jstreeview", "treetime", "jmodeltest", "forester", "patristic", "spread-phy", "iqtree"], "ignore": [], "avoid": []}, "physics": {"depends": [], "suggests": ["paw-demos", "libbiosig-dev", "python3-biosig", "octave-biosig", "openvibe", "python-multipletau"], "recommends": ["paw++", "paw", "octave", "r-base", "biosig-tools", "gdf-tools", "gate"], "ignore": [], "avoid": []}, "dental": {"depends": [], "suggests": [], "recommends": ["openmolar", "imagetooth", "entangle"], "ignore": [], "avoid": []}, "psychology": {"depends": [], "suggests": ["science-psychophysics", "python-visionegg"], "recommends": ["python-pyepl", "praat", "r-cran-foreign", "psignifit", "python-pypsignifit", "r-cran-psy", "psychopy", "miscpsycho", "psych", "psychometric", "psychotree", "psyphy"], "ignore": [], "avoid": []}, "rehabilitation": {"depends": [], "suggests": ["aghermann"], "recommends": ["sitplus"], "ignore": [], "avoid": []}, "oncology": {"depends": [], "suggests": [], "recommends": ["uw-prism", "orthanc-wsi", "planunc", "dicompyler"], "ignore": [], "avoid": []}, "bio-dev": {"depends": [], "suggests": ["python3-biopython-sql", "python-biopython-doc", "libfreecontact-doc", "r-cran-rocr", "r-bioc-affy", "r-bioc-affyio", "r-bioc-altcdfenvs", "r-bioc-annotationdbi", "r-bioc-biocgenerics", "r-bioc-biomart", "r-bioc-biomformat", "r-bioc-biovizbase", "r-bioc-bsgenome", "r-bioc-genomeinfodb", "r-bioc-genomicalignments", "r-bioc-genomicfeatures", "r-bioc-genomicranges", "r-bioc-graph", "r-bioc-hypergraph", "r-bioc-iranges", "r-bioc-makecdfenv", "r-bioc-preprocesscore", "r-bioc-rbgl", "r-bioc-rsamtools", "r-bioc-shortread", "r-bioc-snpstats", "r-bioc-variantannotation", "r-bioc-xvector", "r-cran-rentrez", "ruby-rgfa", "librostlab-doc", "librostlab-blast-doc", "libswarm2-dev", "libgtextutils-dev", "libbam-dev", "libpbcopper-dev", "libdisorder-dev", "python-pyflow", "r-cran-natserv", "libmilib-java", "vdjtools", "python3-ctdopts", "ctdconverter", "libmodhmm-dev", "libsvmloc-dev"], "recommends": ["bioperl", "bioperl-run", "libncbi6-dev", "mcl", "biosquid", "cwltool", "snakemake", "libvibrant6-dev", "python3-biopython", "python-cogent", "python-screed", "python3-cutadapt", "ruby-bio", "libbiojava-java", "libbiojava4-java", "libgenome-dev", "libmuscle-dev", "libmems-dev", "libhtsjdk-java", "libai-fann-perl", "libbio-mage-perl", "libnhgri-blastall-perl", "libtfbs-perl", "libfreecontact-dev", "libfreecontact-perl", "libgo-perl", "r-cran-genetics", "r-cran-haplo.stats", "r-cran-phylobase", "r-cran-rncl", "r-cran-rnexml", "libbio-graphics-perl", "libbio-coordinate-perl", "libbio-primerdesigner-perl", "libace-perl", "libbiococoa-dev", "libstaden-read-dev", "libsrf-dev", "libzerg0-dev", "libzerg-perl", "librg-reprof-bundle-perl", "python-corepywrap", "librcsb-core-wrapper0-dev", "libsbml5-dev", "sbmltoolbox", "seqan-dev", "libbio-mage-utils-perl", "libchado-perl", "libpal-java", "libbioparser-dev", "libspoa-dev", "libedlib-dev", "libthread-pool-dev", "libjebl2-java", "r-bioc-biobase", "libffindex0-dev", "librostlab3-dev", "librostlab-blast0-dev", "librg-blast-parser-perl", "libsort-key-top-perl", "libhmsbeagle-dev", "libforester-java", "libbambamc-dev", "libbamtools-dev", "libpbbam-dev", "libbio-das-lite-perl", "python-mmtk", "libopenms-dev", "libgenometools0-dev", "librdp-taxonomy-tree-java", "python-biom-format", "python-rdkit", "libgenome-perl", "libgenome-model-tools-music-perl", "pyfai", "libhts-dev", "python-htseq", "python3-intervaltree-bio", "python3-csb", "python3-misopy", "python-freecontact", "python3-pymummer", "libkmer-dev", "libsnp-sites1-dev", "libssm-dev", "librelion-dev", "libdivsufsort-dev", "bioclipse", "libgff-dev", "python3-pysam", "python-pbcore", "python-pbh5tools", "python3-cobra", "libtabixpp-dev", "python3-ruffus", "python3-hyphy", "python3-dendropy", "python3-skbio", "python3-pbconsensuscore", "python3-consensuscore2", "libconsensuscore-dev", "python-pbcommand", "python3-pyvcf", "python3-pyfaidx", "python3-sqt", "python-kineticstools", "libqes-dev", "libfast5-dev", "python3-fast5", "libpbseq-dev", "libpbdata-dev", "libpbihdf-dev", "libblasr-dev", "libminimap-dev", "libncl-dev", "libngs-sdk-dev", "libngs-java", "python3-ngs", "libncbi-vdb-dev", "libqcpp-dev", "libbpp-core-dev", "libbpp-phyl-dev", "libbpp-phyl-omics-dev", "libbpp-popgen-dev", "libbpp-qt-dev", "libbpp-raa-dev", "libbpp-seq-dev", "libbpp-seq-omics-dev", "octace-bioinfo", "ruby-crb-blast", "libsmithwaterman-dev", "libfastahack-dev", "mgltools-networkeditor", "mgltools-vision", "mgltools-pybabel", "libssw-dev", "libssw-java", "libfml-dev", "libgkarrays-dev", "libjloda-java", "libvcflib-dev", "libswiss-perl", "python3-pybedtools", "python3-gffutils", "python3-bx", "toil", "galaxy-lib", "libbio-eutilities-perl", "libseqlib-dev", "libroadrunner-dev", "python-roadrunner", "python3-biotools", "bio-tradis", "python3-biomaj3", "libbiod-dev", "python3-ete3", "python3-gfapy", "libgoby-java", "python3-gffutils", "python3-pybedtools", "python3-seqcluster", "python3-cyvcf2", "libgatbcore-dev", "python3-airr", "python3-presto", "python3-bcbio", "libpll-dev", "libstatgen-dev", "python3-screed", "python3-treetime"], "ignore": [], "avoid": []}, "statistics": {"depends": [], "suggests": ["science-statistics"], "recommends": ["r-bioc-limma", "r-bioc-qvalue", "r-cran-randomforest", "r-cran-beeswarm", "r-cran-pvclust", "rstudio", "r-bioc-multtest", "r-cran-ade4", "r-cran-rwave", "r-cran-snowfall", "r-cran-wavethresh", "r-cran-waveslim"], "ignore": [], "avoid": []}, "tools": {"depends": [], "suggests": ["cycle", "mencal", "entangle", "goldencheetah", "sleepyhead"], "recommends": ["pcalendar", "pondus", "mssstest", "wgerman-medical", "hunspell-de-med", "quitcount", "workrave", "edfbrowser", "hunspell-en-med", "python-clips", "cronometer", "python-fitbit", "r-cran-fitcoach", "r-cran-fitbitscraper", "galileo", "nut-nutrition", "nutsqlite", "pesco"], "ignore": [], "avoid": []}, "imaging-dev": {"depends": [], "suggests": ["libnifti-doc", "libfreeimage-dev", "libics-dev", "liblimereg-dev", "python-libavg", "emokit", "libeegdev-dev", "libxdffileio-dev", "python-tifffile", "libcamp-dev"], "recommends": ["ctn-dev", "cimg-dev", "libminc-dev", "libmdc2-dev", "libvtk6-dev", "libnifti-dev", "libinsighttoolkit4-dev", "libvolpack1-dev", "libgdcm2-dev", "python-gdcm", "libopensurgsim-dev", "libmaxflow-dev", "python-mvpa2", "python-nipy", "python-nipype", "python-nitime", "libvia-dev", "odin", "libcv-dev", "libteem-dev", "gmic", "libgiftiio-dev", "libvistaio-dev", "libmia-2.4-dev", "libmiaviewit-dev", "libmialm-dev", "python-mia | python3-mia", "libopenigtlink-dev", "r-cran-rniftilib", "libmni-perllib-perl", "python-dicom", "libopenmeeg-dev", "python-nibabel", "libgdf-dev", "octave-gdf", "python-pyxnat", "python-dipy", "libbiosig-dev", "python3-biosig", "libctk-dev", "python-cfflib", "libopenslide-dev", "python-openslide", "libopenslide-java", "libbio-formats-java", "octave-dicom", "libcamitk-dev", "libpapyrus3-dev", "python-mne", "python-vmtk", "libvmtk-dev", "libvigraimpex-dev", "python-vigra", "libvtk-dicom-dev", "libedf-dev", "python-imageio", "libismrmrd-dev", "libodil-dev", "libbart-dev", "octave-bart", "libcifti-dev", "libxdf-dev", "libsimpleitk1-dev", "python3-simpleitk"], "ignore": [], "avoid": []}} \ No newline at end of file diff -Nru debian-med-3.1/tasks/bio debian-med-3.2/tasks/bio --- debian-med-3.1/tasks/bio 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/bio 2019-01-24 14:07:55.000000000 +0000 @@ -18,10 +18,15 @@ Recommends: figtree -Recommends: hyphygui, hyphy-mpi | hyphy-pt +Recommends: hyphy-mpi | hyphy-pt Recommends: spread-phy +Recommends: omegamap +Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html + +Recommends: sweed + X-End-Category: Phylogenetic analysis Recommends: phylip @@ -71,8 +76,12 @@ Recommends: ghmm, hmmer +Recommends: gramalign + Recommends: exonerate +Recommends: elph + Recommends: dialign Recommends: dialign-tx @@ -137,7 +146,7 @@ Recommends: gromacs -Recommends: rasmol +Recommends: rasmol, viewmol, qutemol Recommends: modeller Pkg-URL: http://salilab.org/modeller/release.html#deb @@ -182,7 +191,7 @@ X-End-Category: Genome Browser -Recommends: python3-biomaj3 +Recommends: python3-biomaj3-daemon Ignore: mozilla-biofox Remark: biofox was removed from Debian (see #727689) @@ -221,7 +230,7 @@ Recommends: hinge Recommends: r-bioc-hilbertvis -Remark: It would be interesting to package HilbertVisGUI (see below) as well. +Remark: It would be interesting to package HilbertVisGUI as well. Recommends: r-other-mott-happy.hbrem @@ -271,7 +280,7 @@ Recommends: dssp -Recommends: jellyfish +Recommends: jellyfish, jellyfish1 Recommends: ballview @@ -449,6 +458,8 @@ Recommends: bagpipe +Recommends: bax2bam + Recommends: bcbio Recommends: bcftools @@ -459,8 +470,7 @@ Recommends: bio-tradis -Recommends: biosyntax-gedit -Remark: Plugins for vim (biosyntax-vim) and less (biosyntax-less) are also available. +Recommends: biosyntax Recommends: bitseq @@ -484,7 +494,7 @@ Recommends: chromhmm -Recommends: cgview, brig +Recommends: cgview, brig, cct Recommends: cinema Language: Java @@ -522,6 +532,10 @@ Recommends: dazzle +Recommends: deepbinner + +Recommends: delly + Recommends: deepnano Remark: There is no intend to keep continue the existing packaging since the program nanocall seems to serve the intended purpose better @@ -558,6 +572,8 @@ Recommends: fastml +Recommends: fastp + Recommends: fastqc Recommends: fastqtl @@ -626,6 +642,8 @@ Recommends: idba +Recommends: igdiscover + Recommends: indelible Recommends: iqtree @@ -649,7 +667,7 @@ Recommends: lagan X-Category: Comparative genomics -Recommends: lambda-align +Recommends: lambda-align, lambda-align2 Recommends: leaff @@ -708,7 +726,11 @@ Recommends: miniasm -Recommends: minimap +Recommends: minimac4 + +Recommends: minimap, minimap2 + +Recommends: mirtop Recommends: molekel @@ -723,7 +745,9 @@ Recommends: mugsy -Recommends: murasaki +Recommends: murasaki | murasaki-mpi + +Recommends: mview Recommends: nanocall @@ -747,9 +771,7 @@ Recommends: obitools -Recommends: porechop - -Recommends: r-other-apmswapp +Recommends: paipline Recommends: pal2nal @@ -810,24 +832,28 @@ Recommends: phyx +Recommends: physamp + Recommends: piler Recommends: pilon Recommends: pipasic, inspect, tide -Recommends: physamp - Recommends: pirs Recommends: placnet +Recommends: plasmidseeker + Recommends: plato Recommends: plip Recommends: poretools +Recommends: porechop + Recommends: prank Recommends: predictprotein @@ -850,10 +876,18 @@ Recommends: pssh2 +Recommends: pybel + Recommends: pycorrfit Recommends: pyscanfcs +Recommends: python3-gffutils + +Recommends: python3-pybedtools + +Recommends: python3-sqt + Recommends: python-reaper Recommends: python-treetime @@ -890,7 +924,7 @@ Suggests: r-bioc-savr -Recommends: r-bioc-tfbstools +Recommends: r-bioc-tfbstools, r-bioc-cner Recommends: r-cran-metamix @@ -920,6 +954,8 @@ Recommends: r-other-hms-dbmi-spp +Recommends: r-other-apmswapp + Recommends: relion-bin+gui | relion-bin+mpi+gui, relion-bin | relion-bin+mpi Recommends: rdp-alignment, rdp-readseq, rdp-classifier @@ -936,14 +972,14 @@ Recommends: roguenarok -Recommends: rosetta - Recommends: rsat Recommends: rsem Recommends: sambamba +Recommends: samblaster + Recommends: salmon Recommends: sap @@ -958,6 +994,9 @@ Recommends: segemehl +Recommends: seq-seq-pan +Remark: Needs blat which is not re-distributable + Recommends: seqmagick Recommends: seqprep @@ -1007,6 +1046,8 @@ Recommends: sniffles +Recommends: sourmash + Recommends: spaced Recommends: spades @@ -1059,6 +1100,8 @@ Recommends: toil +Recommends: tracetuner + Recommends: transrate-tools Recommends: treeview @@ -1073,6 +1116,8 @@ Recommends: uc-echo X-Category: NGS +Recommends: unanimity + Recommends: unicycler Recommends: varna @@ -1081,6 +1126,8 @@ Recommends: varscan +Recommends: vdjtools + Recommends: vienna-rna X-Category: Secondary structure of nucleic acids @@ -1088,6 +1135,8 @@ Recommends: vsearch +Recommends: yaha + Recommends: canu Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/) @@ -1100,6 +1149,10 @@ Recommends: dnaclust +Recommends: r-cran-tcr, r-cran-tigger, r-cran-alakazam, r-cran-shazam, igor, r-cran-sdmtools, python3-presto, changeo + +Recommends: ncbi-igblast + X-Mark: The information below needs to be checked whether it can be obtained from Vcs or needs to stay here Recommends: copycat @@ -1193,7 +1246,7 @@ visualise modified annotation files as a custom track. Recommends: genographer -Homepage: http://hordeum.oscs.montana.edu/genographer/ +Homepage: https://sourceforge.net/projects/genographer/ License: GPL Pkg-Description: read data and reconstruct them into a gel image This program will read in data from an ABI 3700, 3100, 377 or 373, @@ -1250,14 +1303,6 @@ Probably it makes sense to remove this project from the prospective packages list. -Recommends: gbioseq -Homepage: http://www.bioinformatics.org/project/?group_id=94 -License: GPL -Pkg-Description: DNA sequence editor for Linux - gBioSeq is in an early stage of development, but it is already running. - The goal is to provide an easy to use software to edit DNA sequences under - Linux, Windows, MacOsX, using GTK C# (Mono). - Recommends: phpphylotree Homepage: http://www.bioinformatics.org/project/?group_id=372 License: GPL @@ -1265,35 +1310,6 @@ PhpPhylotree is a web application that is able to draw phylogenetic trees. It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files. -Recommends: tracetuner -Homepage: http://www.jcvi.org/cms/research/software/tracetuner/overview -License: GPL; but US Patent #6,681,186 -Pkg-Description: DNA sequencing and trace processing - TraceTuner is a DNA sequencing quality value, base calling and trace - processing software application originally developed by Paracel, - Inc. While providing a flexible interface and capability to adopt the - "pure" base calls produced by Phred, KB or any other "original" - caller, it offers competitive features not currently available in - other tools, such as customized calibration of quality values, - advanced heterozygote and mixed base calling and deconvolving the - "mixed" electropherograms resulting from the presence of indels into - a couple of "pure" electropherograms. Previous versions of TraceTuner - were used by Celera Genomics to process over 27 million reads from - both Drosophila and human genome projects and by Applied Biosystems, - as a component of its SNP detection and genotyping software product - SeqScape. TraceTuner implements an advanced peak processing - technology for resolving overlapping peaks of the same dye color into - individual, or "intrinsic" peaks. This technology was protected by US - Patent #6,681,186. Currently, TraceTuner is an open source software, - which has been used by J. Craig Venter Institute's DNA Sequencing and - Resequencing pipelines. - . - The TraceTuner Software (Copyright 1999-2003, Paracel, Inc. All - rights reserved.) (the "Software") is covered by US Patent #6,681,186 and is - being made available free of charge by Applera Corporation subject to the terms - and conditions of the GNU General Public License, version 2, as published by the - Free Software Foundation (the "GNU General Public License"). - Recommends: twain Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml License: Open Source @@ -1682,24 +1698,6 @@ It is possible that mirbase will not be a package from the main archive, but will be autogenerated as part of a larger data packaging effort. -Recommends: elph -Homepage: http://www.cbcb.umd.edu/software/ELPH/ -License: Artistic -Pkg-Description: motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites - ELPH (Estimated Locations of Pattern Hits) is a general-purpose Gibbs - sampler for finding motifs in a set of DNA or protein sequences. The - program takes as input a set containing anywhere from a few dozen to - thousands of sequences, and searches through them for the most common - motif, assuming that each sequence contains one copy of the motif. We - have used ELPH to find patterns such as ribosome binding sites (RBSs) - and exon splicing enhancers (ESEs). See below for instructions on - downloading the complete system, including source code. - . - An online tool that uses ELPH output for identifying exon splicing - enhancers can be found at - http://www.cbcb.umd.edu/software/SeeEse/index.html . -Remark: Other sequence analysis tools (http://www.cbcb.umd.edu/software/) - X-Recommends: repeatfinder X-Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/ X-License: Artistic @@ -1818,138 +1816,6 @@ dump cDNA clones sequences (such as those that passed the QC checking) from the cdna_db. -Recommends: das-proserver -Homepage: http://www.sanger.ac.uk/Software/analysis/proserver/ -License: Same as Perl -Pkg-Description: lightweight Distributed Annotation System (DAS) server - The Distributed Annotation System (DAS) is a data exchange protocol - for open sharing of biological information. - . - ProServer is a very lightweight DAS server written in Perl. It is - simple to install and configure and has existing adaptors for a wide - variety of data sources. It is also easily extensible allowing - adaptors to be written for other data sources. More information about - the DAS protocol and what it is useful for is available over at - http://biodas.org. - . - New large scale techniques in biology are producing a rapidly growing - amount of public available data. Centralized database resources are - confronted with the task how to scale their storage facilities, how - to manage frequent updates and how to exchange the data with the - community. - . - The Distributed Annotation System (DAS) addresses these issues. It is - frequently being used to openly exchange biological annotations - between distributed sites. Data distribution, performed by DAS - servers, is separated from visualization, which is done by DAS - clients. - . - DAS is a client-server system in which a client like Ensembl - integrates information from multiple servers. It allows a single - machine to gather up genome annotation information from multiple - distant web sites, collate the information, and display it to the - user in a single view. Little coordination is needed among the - various information providers. - . - DAS is heavily used in the genome bioinformatics community. Over the - last years we have also seen growing acceptance in the protein - sequence and structure communities. - -Recommends: spice -Homepage: http://www.efamily.org.uk/software/dasclients/spice/ -License: GPL -Pkg-Description: Distributed Annotation System (DAS) client - The Distributed Annotation System (DAS) is a data exchange protocol - for open sharing of biological information. - . - SPICE is a browser for protein sequences, structures and their - annotations. It can display annotations for PDB, UniProt and Ensembl - Peptides. All data is retrieved from different sites on the Internet, - that make their annotations available using the DAS protocol. It is - possible to add new annotations to SPICE, and to compare them with - the already available information. - -Recommends: decipher -Homepage: http://www.sanger.ac.uk/Software/analysis/decipher/ -License: To be clarified -Pkg-Description: tracks duplications and deletions of DNA in patients - DECIPHER tracks submicroscopic duplications and deletions of DNA in - patients together with phenotypes exhibited by those - patients. DECIPHER tallies these genetic abnormalities with genes and - other features of interest in the affected areas. The aim of DECIPHER - is to provide a research tool to aid clinical diagnosis and treatment - of these conditions. DECIPHER makes use of DAS technology to - integrate with Ensembl, the world's leading genome browser. - -Recommends: est-db -Homepage: http://www.sanger.ac.uk/Software/analysis/est_db/ -License: Artistic -Pkg-Description: Software suite for expressed sequence tag (EST) sequencing - The est_db package is a software suite and database system designed - to support expressed sequence tag (EST) sequencing projects, and to - provide comprehensive bioinformatic analysis of sequenced EST - libraries, for gene discovery and other purposes. The database can - hold and efficiently process hundreds of thousands of EST sequences, - track the cDNA libraries and clones to which they belong, and store - the results of their analysis. Should they be available, large - compute farms can be used for the analysis. - . - Extensive bioinformatic analysis can be carried out on the sequenced - EST libraries, including similarity (BLAST) searches, protein - sequence prediction, and the import of EST clustering and assembly - data from external sources. Results are searchable via a web page, - with graphic output of the various analyses, enabling one to retrieve - information pertaining to a particular cDNA clone, or EST read, as - well as view EST clustering results, or graphical representations of - BLAST results on the searched EST sequences. - . - The est_db package is likely to appeal not only to sequencing groups - directly employed in EST sequencing, but also to groups interested in - performing bespoke analysis of ESTs that may already be publically - available, in order to support their ongoing research aims. The - package is easily-extensible, via an API designed specifically to - handle ESTs and their analysis. It is open source and is made - available free of charge, and, where possible, similarly - open-licensed components have been used in its development. - -Recommends: finex -Homepage: http://www.sanger.ac.uk/Software/analysis/finex/ -License: To be clarified -Pkg-Description: sequence homology searching - The FINEX program allows sequence homology searching techniques to be - applied, where the sequence data is replaced with a fingerprint - abstracted from the intron/exon boundary phase and the exon length. - . - Please note FINEX is no longer supported but is available for - download. - -Recommends: hexamer -Homepage: http://www.sanger.ac.uk/Software/analysis/hexamer/ -License: GPL -Pkg-Description: scan DNA sequences to look for likely coding regions - Hexamer is a program to scan DNA sequences to look for likely coding - regions. The principle is to use 6mers, but to avoid deriving any - information from base composition. Therefore, the frequencies of each - 6mer are normalized by dividing by the total frequency of all 6mers - with the same base composition. - . - There are two programs involved in this process: - * hextable - hextable makes files of statistics that hexamer uses to scan for - likely coding regions. - The input of hextable is a fasta file of coding sequences in - frame. The -o file output is an ascii list of 4096 floating point - numbers giving log likelihood ratio scores in bits. The output on - stdout is a summary of the information content of the table, - indicating how disriminative it is likely to be. - * hexamer - Uses the .hex file from hextable to scan a DNA sequence for likely - coding regions. - The input is a fasta DNA file (n.b. that these programs assume all - 'a','c','g','t'. 'n's found in the sequence files will be - converted to 'c'. - The output of hexamer is in General Feature Format (GFF) format. - Recommends: coot Recommends: r-cran-ape @@ -1959,28 +1825,6 @@ Recommends: r-cran-treescape Recommends: caftools -Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml -License: Free for non-commercial purposes -Responsible: BioLinux - Bela Tiwari -Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ -Pkg-Description: Tools to maintain DNA sequence assemblies - This is V2 of the CAF (Common Assembly Format) C-tools. It comprises - a set of libraries and programs for manipulating DNA sequence - assemblies using CAF files. - . - The CAF specification can be found at: - http://www.sanger.ac.uk/Software/formats/CAF/ -Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html - maintains a package called bio-linux-assembly-conversion-tools which - contains caftools and roche2gap in one package with the following - description: - . - Conversion tools for handling 454 assemblies. - . - This package contains code from different authors that allow sequence - assemblies to be converted into formats such as CAF (Common Assembly - Format) or GAP4. This package includes tools to convert assemblies - from Newbler's ace format for loading into a gap4 assembly. Recommends: roche454ace2caf Homepage: http://genome.imb-jena.de/software/roche454ace2caf/ @@ -2068,11 +1912,14 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Recommends: lamarc +Homepage: http://evolution.genetics.washington.edu/lamarc/index.html Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ -Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html +Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html. + In 1/2018 upstream has apparently updated their tarball to help the + redistribution of their software. Someone please go for it. Recommends: lucy -Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html +Homepage: http://lucy.sourceforge.net/ License: GPL Responsible: BioLinux - Dan Swan Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ @@ -2154,22 +2001,6 @@ FASTA, EMBL and Swissprot formats are supported. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html -Recommends: mview -Homepage: http://bio-mview.sourceforge.net/ -License: GPL -Responsible: BioLinux - Stewart Houten -Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ -Pkg-Description: reformat results of a sequence database search or a multiple alignment - MView is a tool for converting the results of a sequence database - search (BLAST, FASTA, etc.) into the form of a coloured multiple - alignment of hits stacked against the query. Alternatively, an - existing multiple alignment (MSF, PIR, CLUSTAL, etc.) can be pr - ocessed. It reformats the results of a sequence database search or a - multiple alignment adding optional HTML markup to control colouring - and web page layout. MView is not a multiple alignment program, nor - is it a general purpose alignment editor. -Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html - Recommends: oligoarrayaux Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php License: non-free (fre academical use) @@ -2197,26 +2028,6 @@ this and so it might make soem sense to list it here - further investigation is needed. -Recommends: omegamap -Homepage: http://www.danielwilson.me.uk/software.html -License: to be clarified -Responsible: BioLinux - Stewart Houten -Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ -Pkg-Description: detecting natural selection and recombination in DNA or RNA sequences - OmegaMap is a program for detecting natural selection and - recombination in DNA or RNA sequences. It is based on a model of - population genetics and molecular evolution. The signature of natural - selection is detected using the dN/dS ratio (which measures the - relative excess of non-synonymous to synonymous polymorphism) and the - signature of recombination is detected from the patterns of linkage - disequilibrium. The model and the method of estimation are described - in - Wilson, D. J. and G. McVean (2006) - Estimating diversifying selection and functional constraint in the - presence of recombination. - Genetics doi:10.1534/genetics.105.044917. -Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html - Recommends: partigene Homepage: http://www.nematodes.org/bioinformatics/PartiGene/ License: GPL @@ -2398,21 +2209,6 @@ and part-of relations. Amongst the databases cureated by this tool is the GeneOntology. - -Recommends: jstreeview -Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml -License: MIT/X11 -Language: JavaScript -Pkg-Description: Editor for Phylogenetic Trees - A concise viewer/editor for phylogenetic trees in the Newick format. - The core functions are written in JavaScript, using the canvas tag - proposed by HTML 5. No server side support is needed for rendering the - picture and therefore you can grab this page together with knhx.js and - canvastext.js to locally view your trees in a supported web browser. - . - The source can be downloaded at - http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip - Recommends: phagefinder Homepage: http://phage-finder.sourceforge.net/ License: GPL @@ -2507,19 +2303,10 @@ Recommends: snap -Recommends: vcftools +Recommends: pyvcf, vcftools Suggests: mobyle, mobyle-programs, mobyle-tutorials -Recommends: hilbertvisgui -Homepage: http://www.bioconductor.org/help/bioc-views/2.7/bioc/html/HilbertVisGUI.html -License: GPL-3 -Pkg-Description: interactive tool to visualize long vectors of integer data by means of Hilbert curves - An interactive tool to visualize long vectors of integer data by means of Hilbert - curves. It provides a GUI for the Debian packaged r-bioc-hilbertvis and is thus - interesting for giving users some comfort. Until this software is not yet packaged - you can follow the hint at the homepage how to use it with R. - Recommends: beads Pkg-URL: https://launchpad.net/~olivier-langella/+archive/ppa/+packages @@ -2689,7 +2476,7 @@ Recommends: tripal -Homepage: http://www.genome.clemson.edu/software/tripal +Homepage: http://tripal.info/ License: GPL ( as Drupal a derivative ) Pkg-Description: collection of Drupal modules for genomic research Tripal is a collection of open-source freely available Drupal modules under diff -Nru debian-med-3.1/tasks/bio-dev debian-med-3.2/tasks/bio-dev --- debian-med-3.1/tasks/bio-dev 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/bio-dev 2019-01-24 14:07:55.000000000 +0000 @@ -12,25 +12,25 @@ Recommends: biosquid -Recommends: cwltool +Recommends: cwltool, snakemake Recommends: libvibrant6-dev -Recommends: python3-biopython | python-biopython +Recommends: python3-biopython -Suggests: python3-biopython-sql | python-biopython-sql, python-biopython-doc +Suggests: python3-biopython-sql, python-biopython-doc Recommends: python-cogent Recommends: python-screed -Recommends: python3-cutadapt | python-cutadapt +Recommends: python3-cutadapt Recommends: ruby-bio Recommends: libbiojava-java, libbiojava4-java -Recommends: libgenome-1.3-dev, libmuscle-3.7-dev, libmems-1.6-dev +Recommends: libgenome-dev, libmuscle-dev, libmems-dev Recommends: libhtsjdk-java @@ -53,23 +53,6 @@ Recommends: r-cran-rncl, r-cran-rnexml -Recommends: octave-bioinfo -Homepage: http://octave.sourceforge.net/bioinfo/ -Vcs-Git: git://git.debian.org/git/pkg-octave/octave-bioinfo.git -Vcs-Browser: http://git.debian.org/?p=pkg-octave/octave-bioinfo.git -License: GPL-3+ -Pkg-Description: bioinformatic functions for Octave - This package provides functions to do work in bioinformatics in - Octave, a numerical computation software. It contains functions to - convert amino acid characters into integers (aa2int), convert between - amino acid representations (aminolookup), cleave peptides (cleave), - convert integers into amino acid characters (int2aa) and reverse a - nucleotide sequence (seqreverse). - . - This Octave add-on package is part of the Octave-Forge project. -Remark: Not maintained upstream, see ROM: #620648 -Pkg-URL: http://snapshot.debian.org/archive/debian/20100201T042505Z/pool/main/o/octave-bioinfo/octave-bioinfo_0.1.2-2.dsc - Recommends: libbio-graphics-perl, libbio-coordinate-perl Recommends: libbio-primerdesigner-perl @@ -198,11 +181,11 @@ Recommends: python-htseq -Recommends: python3-intervaltree-bio | python-intervaltree-bio +Recommends: python3-intervaltree-bio -Recommends: python3-csb | python-csb +Recommends: python3-csb -Recommends: python3-misopy | python-misopy +Recommends: python3-misopy Recommends: python-freecontact @@ -243,57 +226,41 @@ Recommends: libgff-dev -Recommends: libgff-perl -Homepage: http://www.sanger.ac.uk/Software/formats/GFF/ -Responsible: David Paleino -License: GPL-1+ -WNPP: 468826 -Pkg-Description: Perl bindings for GFF Annotation Protocol - GFF (Gene Finding Feature) is a format for describing genes and other - features associated with DNA, RNA and Protein sequences. - . - This package provides a Perl module to use GFF objects. - -Recommends: python-pysam +Recommends: python3-pysam Recommends: python-pbcore, python-pbh5tools -Recommends: python-cobra +Recommends: python3-cobra Recommends: libtabixpp-dev -Recommends: python3-ruffus | python-ruffus +Recommends: python3-ruffus -Recommends: python3-hyphy | python-hyphy +Recommends: python3-hyphy -Recommends: python3-dendropy | python-dendropy +Recommends: python3-dendropy Recommends: python3-skbio -Recommends: python3-pbconsensuscore | python-pbconsensuscore +Recommends: python3-pbconsensuscore -Recommends: python3-consensuscore2 | python-consensuscore2, libconsensuscore-dev +Recommends: python3-consensuscore2, libconsensuscore-dev Recommends: python-pbcommand -Recommends: python3-pyvcf | python-pyvcf +Recommends: python3-pyvcf -Recommends: python3-pyfaidx | python-pyfaidx +Recommends: python3-pyfaidx -Recommends: python-kineticstools +Recommends: python3-sqt -Recommends: python3-pyfasta | python-pyfasta -Remark: Testsuite uncovers problems and code is not actively maintained - The upstream author of python-pyfasta confirmed that he stopped - the development and recommends python-pyfaidx instead. So the - packaging code for python-pyfasta in SVN works but there is no - intend to really upload the package. +Recommends: python-kineticstools Suggests: libbam-dev Recommends: libqes-dev -Recommends: libfast5-dev, python3-fast5 | python-fast5 +Recommends: libfast5-dev, python3-fast5 Recommends: libpbseq-dev, libpbdata-dev, libpbihdf-dev, libblasr-dev @@ -303,7 +270,7 @@ Recommends: libncl-dev -Recommends: libngs-sdk-dev, libngs-java, python3-ngs | python-ngs, libncbi-vdb-dev +Recommends: libngs-sdk-dev, libngs-java, python3-ngs, libncbi-vdb-dev Recommends: libqcpp-dev @@ -350,10 +317,9 @@ Recommends: python3-gffutils -Recommends: python3-bx | python-bx -WNPP: 851242 +Recommends: python3-bx -Recommends: python-bd2k +Recommends: toil, galaxy-lib Recommends: libbio-eutilities-perl @@ -361,11 +327,11 @@ Recommends: libroadrunner-dev, python-roadrunner -Recommends: python3-biotools | python-biotools +Recommends: python3-biotools Recommends: bio-tradis -Recommends: python3-biomaj3 | python-biomaj3 +Recommends: python3-biomaj3 Suggests: python-pyflow @@ -373,10 +339,34 @@ Recommends: libbiod-dev -Recommends: python3-ete3 | python-ete3 +Recommends: python3-ete3 Recommends: python3-gfapy Recommends: libgoby-java +Recommends: python3-gffutils, python3-pybedtools + +Recommends: python3-seqcluster + +Recommends: python3-cyvcf2 + Recommends: libgatbcore-dev + +Recommends: python3-airr, python3-presto + +Suggests: libmilib-java, vdjtools + +Recommends: python3-bcbio + +Suggests: python3-ctdopts, ctdconverter + +Recommends: libpll-dev + +Suggests: libmodhmm-dev, libsvmloc-dev + +Recommends: libstatgen-dev + +Recommends: python3-screed + +Recommends: python3-treetime diff -Nru debian-med-3.1/tasks/bio-ngs debian-med-3.2/tasks/bio-ngs --- debian-med-3.1/tasks/bio-ngs 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/bio-ngs 2019-01-24 14:07:55.000000000 +0000 @@ -70,6 +70,8 @@ Recommends: bamtools +Recommends: bcbio + Recommends: bcftools WNPP: 804007 @@ -100,6 +102,8 @@ Recommends: fastaq +Recommends: fastp + Recommends: fastqc Recommends: fastx-toolkit @@ -122,6 +126,8 @@ Recommends: idba +Recommends: igdiscover + Recommends: igv Recommends: iva @@ -159,6 +165,12 @@ Recommends: poretools +Recommends: python3-gffutils + +Recommends: python3-pybedtools + +Recommends: python3-sqt + Recommends: qcumber Recommends: quorum @@ -169,6 +181,8 @@ Recommends: sambamba +Recommends: samblaster + Recommends: scythe Recommends: seqprep @@ -230,6 +244,9 @@ Recommends: mosaik-aligner +Recommends: r-cran-tcr, r-cran-tigger, r-cran-alakazam, r-cran-shazam, igor, + python3-airr, python3-presto, changeo, vdjtools + Recommends: forge Homepage: http://combiol.org/forge/ License: Apache 2.0 diff -Nru debian-med-3.1/tasks/bio-phylogeny debian-med-3.2/tasks/bio-phylogeny --- debian-med-3.1/tasks/bio-phylogeny 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/bio-phylogeny 2019-01-24 14:07:55.000000000 +0000 @@ -160,3 +160,5 @@ Recommends: spread-phy Recommends: iqtree + +Suggests: python3-treetime diff -Nru debian-med-3.1/tasks/epi debian-med-3.2/tasks/epi --- debian-med-3.1/tasks/epi 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/epi 2019-01-24 14:07:55.000000000 +0000 @@ -44,6 +44,8 @@ Remark: See also: http://www.stockholmchallenge.se/data/2123 and http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf +Recommends: epifire + Suggests: repast Homepage: http://repast.sourceforge.net/ License: BSD diff -Nru debian-med-3.1/tasks/imaging debian-med-3.2/tasks/imaging --- debian-med-3.1/tasks/imaging 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/imaging 2019-01-24 14:07:55.000000000 +0000 @@ -101,7 +101,7 @@ Recommends: orthanc -Suggests: orthanc-webviewer, orthanc-dicomweb, orthanc-imagej, orthanc-postgresql +Suggests: orthanc-webviewer, orthanc-dicomweb, orthanc-imagej, orthanc-postgresql, orthanc-mysql Recommends: teem-apps @@ -500,13 +500,7 @@ Recommends: voxbo -Recommends: mrtrix -Published-Title: Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution -Published-Authors: J-Donald Tournier, Fernando Calamantea, Alan Connelly -Published-In: NeuroImage, 35: 1459-1472 -Published-Year: 2007 -Published-DOI: 10.1016/j.neuroimage.2007.02.016 - +Recommends: mrtrix, mrtrix3 Recommends: ants Published-Title: The optimal template effect in hippocampus studies of diseased populations @@ -885,3 +879,7 @@ Recommends: dcm2niix Recommends: orthanc-wsi + +Recommends: odil + +Suggests: tifffile diff -Nru debian-med-3.1/tasks/imaging-dev debian-med-3.2/tasks/imaging-dev --- debian-med-3.1/tasks/imaging-dev 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/imaging-dev 2019-01-24 14:07:55.000000000 +0000 @@ -98,7 +98,7 @@ Recommends: python-dipy -Recommends: libbiosig-dev +Recommends: libbiosig-dev, python3-biosig Recommends: libctk-dev @@ -119,10 +119,6 @@ Suggests: libxdffileio-dev Recommends: octave-dicom -Homepage: http://octave.sourceforge.net/dicom/ -License: GPL-v3+ -Pkg-Description: Dicom support in Octave - Digital communications in medicine (DICOM) file io. Depends on Grassroots DICOM (GDCM) Recommends: libcamitk-dev @@ -146,10 +142,14 @@ Recommends: libismrmrd-dev -Recommends: libodil0-dev +Recommends: libodil-dev Recommends: libbart-dev, octave-bart Suggests: libcamp-dev Recommends: libcifti-dev + +Recommends: libxdf-dev + +Recommends: libsimpleitk1-dev, python3-simpleitk diff -Nru debian-med-3.1/tasks/pharmacy debian-med-3.2/tasks/pharmacy --- debian-med-3.1/tasks/pharmacy 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/pharmacy 2019-01-24 14:07:55.000000000 +0000 @@ -10,6 +10,8 @@ Recommends: r-cran-dosefinding +Recommends: r-cran-rpact + Comment: Several related R packages are listed at CRAN: http://cran.r-project.org/web/views/Pharmacokinetics.html Specifically these might be of interest: diff -Nru debian-med-3.1/tasks/physics debian-med-3.2/tasks/physics --- debian-med-3.1/tasks/physics 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/physics 2019-01-24 14:07:55.000000000 +0000 @@ -24,7 +24,7 @@ Recommends: biosig-tools -Suggests: libbiosig-dev, python-biosig, octave-biosig +Suggests: libbiosig-dev, python3-biosig, octave-biosig Recommends: gdf-tools diff -Nru debian-med-3.1/tasks/research debian-med-3.2/tasks/research --- debian-med-3.1/tasks/research 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/research 2019-01-24 14:07:55.000000000 +0000 @@ -3,6 +3,8 @@ This metapackage will install tools that are useful for medical research. +Recommends: r-cran-rpact + Recommends: openclinica License: GPL Homepage: https://openclinica.com/ diff -Nru debian-med-3.1/tasks/typesetting debian-med-3.2/tasks/typesetting --- debian-med-3.1/tasks/typesetting 2018-04-26 20:33:08.000000000 +0000 +++ debian-med-3.2/tasks/typesetting 2019-01-24 14:07:55.000000000 +0000 @@ -28,7 +28,7 @@ Suggests: kbibtex, biber -Suggests: bibus, referencer, jabref-plugin-oo +Suggests: bibus, jabref-plugin-oo Remark: Desktop tools that help inserting references in LibreOffice, or help managing PDF collections. This list is probably incomplete.