[Debian-med-packaging] Bug#988040: unblock: debian-med/3.7
Andreas Tille
tille at debian.org
Tue May 4 07:55:03 BST 2021
Package: release.debian.org
Severity: normal
User: release.debian.org at packages.debian.org
Usertags: unblock
X-Debbugs-Cc: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Please unblock package debian-med
As in all release processes we need to update metapackages of Blends to
reflect the packaging pool (after late accepts before the freeze and
removals while the freeze) to make sure all Recommends are sensible and
can be fulfilled.
[ Reason ]
Removal of packages from testing that were recommended by the
metapackages.
[ Impact ]
Metapackages would list Recommends that are not released in Bullseye
if the unblock will not be accepted.
Please note: Nearly all changes (except the manual part of d/changelog)
is auto-generated by the Blends framework. That's the reason why the
attached debdiff looks a bit longish for this state of the release.
[ Tests ]
There are no tests.
[ Risks ]
I do not see any risks when this package is accepted.
[ Checklist ]
[x] all changes are documented in the d/changelog
[x] I reviewed all changes and I approve them
[x] attach debdiff against the package in testing
[ Other info ]
I just use the chance to say thank you to the release team. ;-)
unblock debian-med/3.7
-------------- next part --------------
diff -Nru debian-med-3.6.2/debian/changelog debian-med-3.7/debian/changelog
--- debian-med-3.6.2/debian/changelog 2021-03-01 11:33:28.000000000 +0100
+++ debian-med-3.7/debian/changelog 2021-05-03 21:28:56.000000000 +0200
@@ -1,3 +1,40 @@
+debian-med (3.7) unstable; urgency=medium
+
+ * Re-render metapackages according the package pool in bullseye
+
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-bio
+ added:
+ Recommends: bio-vcf, uncalled, covpipe, fastani, bioawk, bamclipper
+ Suggests: r-bioc-structuralvariantannotation
+ -med-bio-dev
+ added:
+ Recommends: libbio-db-ncbihelper-perl, libbio-variation-perl,
+ python3-scanpy, libbio-db-biofetch-perl, libbio-db-embl-perl,
+ python3-wdlparse, pangolearn, libpdb-redo-dev
+ Suggests: r-bioc-structuralvariantannotation
+ -med-covid-19
+ added:
+ Recommends: uncalled, covpipe, fastani, python3-scanpy, nthash,
+ bamclipper
+ -med-epi
+ added:
+ Suggests: python3-epimodels
+ -med-imaging
+ added:
+ Recommends: python3-nipype, bart-cuda
+ removed:
+ Suggests: python-nipype
+ -med-imaging-dev
+ added:
+ Recommends: python3-nipype, python3-brian, python3-vigra
+ removed:
+ Suggests: python-vigra, python-nipype
+
+ -- Andreas Tille <tille at debian.org> Mon, 03 May 2021 21:28:56 +0200
+
debian-med (3.6.2) unstable; urgency=medium
* DEP5 copyright
diff -Nru debian-med-3.6.2/debian/control debian-med-3.7/debian/control
--- debian-med-3.6.2/debian/control 2021-03-01 11:33:28.000000000 +0100
+++ debian-med-3.7/debian/control 2021-05-03 21:28:56.000000000 +0200
@@ -140,6 +140,7 @@
bio-eagle,
bio-rainbow,
bio-tradis,
+ bio-vcf,
biobambam2,
biosyntax,
bitseq,
@@ -676,6 +677,7 @@
uc-echo,
umap-learn,
umis,
+ uncalled,
unicycler,
varna,
vcfanno,
@@ -709,11 +711,13 @@
axpcoords,
bagpipe,
bambus,
+ bamclipper,
bax2bam,
bcbio,
biceps,
big-blast,
bigsdb,
+ bioawk,
bismark,
blat,
blimps-utils,
@@ -736,6 +740,7 @@
contralign,
coot,
copycat,
+ covpipe,
crossbow,
crux-toolkit,
cufflinks,
@@ -759,6 +764,7 @@
exalt,
excavator,
falcon,
+ fastani,
ffp,
fieldbioinformatics,
figaro,
@@ -940,6 +946,7 @@
r-bioc-qusage,
r-bioc-savr,
r-bioc-singlecellexperiment,
+ r-bioc-structuralvariantannotation,
r-bioc-tximport,
r-cran-amap,
r-cran-biwt,
@@ -1050,7 +1057,10 @@
libbio-cluster-perl,
libbio-coordinate-perl,
libbio-das-lite-perl,
+ libbio-db-biofetch-perl,
+ libbio-db-embl-perl,
libbio-db-hts-perl,
+ libbio-db-ncbihelper-perl,
libbio-eutilities-perl,
libbio-featureio-perl,
libbio-graphics-perl,
@@ -1063,6 +1073,7 @@
libbio-tools-run-alignment-clustalw-perl,
libbio-tools-run-alignment-tcoffee-perl,
libbio-tools-run-remoteblast-perl,
+ libbio-variation-perl,
libbiococoa-dev,
libbiod-dev,
libbiojava-java,
@@ -1122,6 +1133,7 @@
libpbdata-dev,
libpbihdf-dev,
libpbseq-dev,
+ libpdb-redo-dev,
libpll-dev,
libqes-dev,
librcsb-core-wrapper0-dev,
@@ -1212,6 +1224,7 @@
python3-tinyalign,
python3-torch,
python3-treetime,
+ python3-wdlparse,
r-bioc-biobase,
r-cran-boolnet,
r-cran-corrplot,
@@ -1279,6 +1292,7 @@
libtfbs-perl,
libxxsds-dynamic-dev,
octace-bioinfo,
+ pangolearn,
python-biopython-doc,
python3-alignlib,
python3-bcbio,
@@ -1300,6 +1314,7 @@
python3-pycosat,
python3-pyflow,
python3-roadrunner,
+ python3-scanpy,
python3-seqcluster,
python3-unifrac,
q2-alignment,
@@ -1397,6 +1412,7 @@
r-bioc-savr,
r-bioc-shortread,
r-bioc-snpstats,
+ r-bioc-structuralvariantannotation,
r-bioc-tfbstools,
r-bioc-titancna,
r-bioc-tximport,
@@ -1655,6 +1671,7 @@
epifire,
netepi-analysis,
netepi-collection,
+ python3-epimodels,
r-cran-cmprsk,
r-cran-covid19,
r-cran-msm,
@@ -1742,6 +1759,7 @@
plastimatch,
python3-dipy,
python3-nibabel,
+ python3-nipype,
python3-nitime,
python3-pydicom,
python3-pyxid,
@@ -1755,6 +1773,7 @@
xmedcon
Suggests: afni,
ants,
+ bart-cuda,
bioimagesuite,
bioimagexd,
blox,
@@ -1825,7 +1844,6 @@
piano,
pngquant,
pymeg,
- python-nipype,
python3-mvpa2,
python3-nipy,
science-workflow,
@@ -1895,16 +1913,19 @@
octave-gdf,
odin,
python3-biosig,
+ python3-brian,
python3-dipy,
python3-gdcm,
python3-imageio,
python3-mia,
python3-mne,
python3-nibabel,
+ python3-nipype,
python3-nitime,
python3-openslide,
python3-pydicom,
python3-pyxnat,
+ python3-vigra,
r-cran-rniftilib
Suggests: emokit,
libbio-formats-java,
@@ -1925,8 +1946,6 @@
libvmtk-dev,
libvtk6-dev,
libxdffileio-dev,
- python-nipype,
- python-vigra,
python-vmtk,
python3-mvpa2,
python3-nipy,
@@ -1959,10 +1978,10 @@
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: dicompyler,
- orthanc-wsi,
+Recommends: orthanc-wsi,
simrisc
-Suggests: planunc,
+Suggests: dicompyler,
+ planunc,
python3-dicompylercore,
uw-prism
Description: Debian Med packages for oncology
diff -Nru debian-med-3.6.2/dependency_data/debian-med_3.7.json debian-med-3.7/dependency_data/debian-med_3.7.json
--- debian-med-3.6.2/dependency_data/debian-med_3.7.json 1970-01-01 01:00:00.000000000 +0100
+++ debian-med-3.7/dependency_data/debian-med_3.7.json 2021-05-03 21:28:56.000000000 +0200
@@ -0,0 +1 @@
+{"bio-dev": {"depends": [], "suggests": ["conda-package-handling", "cwlformat", "python3-biopython-sql", "python-biopython-doc", "python3-cogent3", "python3-mcaller", "python3-joypy", "python3-ncls", "python3-pycosat", "libtfbs-perl", "libfreecontact-dev", "libfreecontact-perl", "libfreecontact-doc", "qiime", "q2-alignment", "q2-composition", "q2-cutadapt", "q2-dada2", "q2-deblur", "q2-demux", "q2-diversity", "q2-emperor", "q2-feature-classifier", "q2-feature-table", "q2-fragment-insertion", "q2-gneiss", "q2-longitudinal", "q2-metadata", "q2-phylogeny", "q2-quality-control", "q2-quality-filter", "q2-sample-classifier", "q2-shogun", "q2-taxa", "q2-types", "q2-vsearch", "q2cli", "q2cwl", "q2lint", "q2templates", "r-bioc-affxparser", "r-bioc-affy", "r-bioc-affyio", "r-bioc-altcdfenvs", "r-bioc-annotate", "r-bioc-annotationdbi", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-arrayexpress", "r-bioc-biocgenerics", "r-bioc-biocneighbors", "r-bioc-biomart", "r-bioc-biomformat", "r-bioc-biostrings", "r-bioc-biovizbase", "r-bioc-bitseq", "r-bioc-bridgedbr", "r-bioc-bsgenome", "r-bioc-cager", "r-bioc-cner", "r-bioc-complexheatmap", "r-bioc-cummerbund", "r-bioc-ctc", "r-bioc-dada2", "r-bioc-deseq", "r-bioc-deseq2", "r-bioc-dnacopy", "r-bioc-ebseq", "r-bioc-enrichedheatmap", "r-bioc-ensembldb", "r-bioc-genefilter", "r-bioc-geneplotter", "r-bioc-genomeinfodb", "r-bioc-genomicalignments", "r-bioc-genomicfeatures", "r-bioc-genomicranges", "r-bioc-geoquery", "r-bioc-go.db", "r-bioc-graph", "r-bioc-gseabase", "r-bioc-gsva", "r-bioc-gviz", "r-bioc-hypergraph", "r-bioc-impute", "r-bioc-iranges", "r-bioc-limma", "r-bioc-makecdfenv", "r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-mofa", "r-bioc-multiassayexperiment", "r-bioc-nanostringqcpro", "r-bioc-oligo", "r-bioc-oligoclasses", "r-bioc-org.hs.eg.db", "r-bioc-pcamethods", "r-bioc-phyloseq", "r-bioc-preprocesscore", "r-bioc-purecn", "r-bioc-qusage", "r-bioc-rbgl", "r-bioc-rsamtools", "r-bioc-rentrez", "r-bioc-rtracklayer", "r-bioc-s4vectors", "r-bioc-savr", "r-bioc-shortread", "r-bioc-snpstats", "r-bioc-structuralvariantannotation", "r-bioc-titancna", "r-bioc-tfbstools", "r-bioc-tximport", "r-bioc-variantannotation", "r-bioc-xvector", "r-cran-adegenet", "r-cran-adephylo", "r-cran-amap", "r-cran-biwt", "r-cran-dt", "r-cran-dynamictreecut", "r-cran-fastcluster", "r-cran-future.apply", "r-cran-future.batchtools", "r-cran-ica", "r-cran-itertools", "r-cran-kaos", "r-cran-metap", "r-cran-minerva", "r-cran-natserv", "r-cran-nmf", "r-cran-optimalcutpoints", "r-cran-parmigene", "r-cran-pcapp", "r-cran-proc", "r-cran-rann", "r-cran-rcpphnsw", "r-cran-rsgcc", "r-cran-robustrankaggreg", "r-cran-rocr", "r-cran-rook", "r-cran-rsvd", "r-cran-shazam", "r-cran-sitmo", "r-cran-venndiagram", "ruby-rgfa", "librostlab-doc", "librostlab-blast-doc", "libswarm2-dev", "python3-networkx", "libbam-dev", "libfast-perl", "libpbcopper-dev", "libminimap-dev", "libdisorder-dev", "cthreadpool-dev", "python3-pyflow", "libmilib-java", "vdjtools", "python3-alignlib", "python3-ctdopts", "ctdconverter", "libmodhmm-dev", "libsvmloc-dev", "python3-bel-resources", "libmaus2-dev", "libbbhash-dev", "python3-intake", "libconcurrentqueue-dev", "libxxsds-dynamic-dev", "libatomicqueue-dev", "libargs-dev", "libsuma-dev"], "recommends": ["bioperl", "bioperl-run", "libncbi6-dev", "mcl", "biosquid", "cwltool", "snakemake", "python3-wdlparse", "libvibrant6-dev", "python3-biopython", "python3-screed", "python3-cutadapt", "python3-dnaio", "python3-tinyalign", "ruby-bio", "libbiojava-java", "libbiojava4-java", "libgenome-dev", "libmuscle-dev", "libmems-dev", "libhtsjdk-java", "libai-fann-perl", "libbio-mage-perl", "libnhgri-blastall-perl", "libhdf5-dev", "libgo-perl", "libbio-graphics-perl", "libbio-coordinate-perl", "libbio-primerdesigner-perl", "libbio-alignio-stockholm-perl", "libbio-cluster-perl", "libbio-db-biofetch-perl", "libbio-db-embl-perl", "libbio-db-hts-perl", "libbio-db-ncbihelper-perl", "libbio-featureio-perl", "libbio-tools-run-remoteblast-perl", "libbio-variation-perl", "libace-perl", "libbiococoa-dev", "libcifpp-dev", "libstaden-read-dev", "libsrf-dev", "libzerg0-dev", "libzerg-perl", "librg-reprof-bundle-perl", "python3-corepywrap", "librcsb-core-wrapper0-dev", "libsbml5-dev", "sbmltoolbox", "libseqan2-dev", "libseqan3-dev", "libbio-mage-utils-perl", "libchado-perl", "libpal-java", "libpdb-redo-dev", "libbioparser-dev", "libspoa-dev", "libedlib-dev", "libthread-pool-dev", "libjebl2-java", "r-cran-boolnet", "r-cran-corrplot", "r-cran-distory", "r-cran-drinsight", "r-cran-forecast", "r-cran-fitdistrplus", "r-cran-genetics", "r-cran-gprofiler", "r-cran-haplo.stats", "r-cran-metamix", "r-cran-phangorn", "r-cran-pheatmap", "r-cran-phylobase", "r-cran-pscbs", "r-cran-qqman", "r-cran-rentrez", "r-cran-rncl", "r-cran-rnexml", "r-cran-rotl", "r-cran-samr", "r-cran-sctransform", "r-cran-seurat", "r-cran-seqinr", "r-cran-tsne", "r-cran-vegan", "r-cran-webgestaltr", "r-other-hms-dbmi-spp", "r-other-apmswapp", "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", "libbigwig-dev", "libbio-das-lite-perl", "libopenms-dev", "libgenometools0-dev", "librdp-taxonomy-tree-java", "python3-biom-format", "python3-rdkit", "libgenome-perl", "libgenome-model-tools-music-perl", "pyfai", "libhts-dev", "python3-htseq", "python3-intervaltree-bio", "python3-csb", "python3-misopy", "python3-freecontact", "python3-pymummer", "libkmer-dev", "libsnp-sites1-dev", "libssm-dev", "librelion-dev", "libdivsufsort-dev", "nim-hts-dev", "nim-kexpr-dev", "nim-lapper-dev", "bioclipse", "libgff-dev", "python3-pysam", "python3-pbcore", "python3-cobra", "python3-pybigwig", "python3-bcbio-gff", "libtabixpp-dev", "python3-ruffus", "python3-hyphy", "python3-dendropy", "python3-skbio", "libparasail-dev", "python3-parasail", "python3-pbconsensuscore", "python3-consensuscore2", "libconsensuscore-dev", "python3-pbcommand", "python3-pyvcf", "python3-pyfaidx", "python3-shasta", "python3-sqt", "python3-kineticstools", "libqes-dev", "libfast5-dev", "python3-fast5", "libpbseq-dev", "libpbdata-dev", "libpbihdf-dev", "libblasr-dev", "libminimap2-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", "libssw-dev", "libssw-java", "libfml-dev", "libgkarrays-dev", "libjloda-java", "libvcflib-dev", "libswiss-perl", "python3-pybedtools", "python3-gffutils", "python3-bx", "toil", "python3-galaxy-lib", "libbio-eutilities-perl", "libseqlib-dev", "libroadrunner-dev", "python3-roadrunner", "python3-biotools", "bio-tradis", "python3-biomaj3", "libbiod-dev", "python3-ete3", "python3-gfapy", "libgoby-java", "python3-seqcluster", "python3-cyvcf2", "libgatbcore-dev", "python3-airr", "python3-presto", "python3-bcbio", "libpll-dev", "libstatgen-dev", "python3-pyani", "python3-treetime", "libbio-tools-run-alignment-tcoffee-perl", "libbio-asn1-entrezgene-perl", "libbio-chado-schema-perl", "libbio-samtools-perl", "libbio-scf-perl", "libbio-tools-phylo-paml-perl", "libbio-tools-run-alignment-clustalw-perl", "python3-pybel", "python3-mirtop", "libnexml-java", "python3-cgecore", "python3-deeptools", "python3-deeptoolsintervals", "python3-py2bit", "python3-loompy", "gffread", "libgclib-dev", "biobambam2", "libcdk-java", "libhtscodecs-dev", "python3-torch", "python3-anndata", "python3-bx", "python3-cooler", "python3-pairix", "pangolearn", "python3-pyranges", "python3-streamz", "libssu-dev", "python3-unifrac", "python3-nanoget", "python3-peptidebuilder", "libopenmm-dev", "libmmblib-dev", "python3-scanpy"], "ignore": ["golang-github-biogo-hts-dev"], "avoid": []}, "oncology": {"depends": [], "suggests": ["python3-dicompylercore"], "recommends": ["uw-prism", "orthanc-wsi", "planunc", "dicompyler", "simrisc"], "ignore": [], "avoid": []}, "bio-ngs": {"depends": [], "suggests": ["python3-anndata", "graphmap2", "nanolyse", "nanoplot"], "recommends": ["bedtools", "bwa", "bowtie", "blasr", "daligner", "mhap", "last-align", "wham-align", "maq", "picard-tools", "r-bioc-edger", "r-bioc-hilbertvis", "r-bioc-rsubread", "rna-star", "samtools", "sra-toolkit", "ssake", "tabix", "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", "discosnp", "dnaclust", "dwgsim", "ea-utils", "fastaq", "fastp", "fastqc", "flexbar", "fml-asm", "fsm-lite", "grinder", "giira", "hinge", "hilive", "hisat2", "idba", "igdiscover", "igv", "iva", "khmer", "kissplice", "kraken", "kraken2", "macs", "mapdamage", "maqview", "mira-assembler", "mapsembler2", "nanopolish", "paleomix", "pbsuite", "pbjelly", "pbhoney", "pirs", "pizzly", "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", "stringtie", "transrate-tools", "trimmomatic", "trinityrnaseq", "uc-echo", "velvetoptimiser", "kissplice", "scoary", "umap", "mosaik-aligner", "r-cran-tcr", "r-cran-tigger", "r-cran-alakazam", "r-cran-shazam", "igor", "python3-airr", 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"spread-phy", "iqtree", "pplacer", "quicktree"], "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", "orthanc-gdcm", "visit", "mrisim", "connectomeviewer", "eeglab", "elastix", "dtitk", "openwalnut-qt4", "miview", "cmtk", "freesurfer", "isis", "pymeg", "stabilitycalc", "hid", "incf-nidash-oneclick-clients", "science-workflow"], "recommends": ["amide", "ctsim", "ctn", "dicomnifti", "imagej", "minc-tools", "medcon", "python3-nibabel", "python3-pydicom", "xmedcon", "dcmtk", "nifti-bin", "aeskulap", "fsl", "fslview", "via-bin", "gwyddion", "nifti2dicom", "qnifti2dicom", "sofa-apps", "python3-mvpa2", "python3-nipy", "python3-nipype", "python3-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", "mrtrix3", "ants", "itksnap", "mriconvert", "mia-tools", "mialmpick", "mia-viewit", "ismrmrd-tools", "sigviewer", "tifffile", "mni-icbm152-nlin-2009", "mni-colin27-nifti", "mipav", "jist", "openmeeg-tools", "jemris", "insightapplications", "tempo", "dti-query", "python3-pyxid", "python3-dipy", "plastimatch", "medisnap", "gimias", "mayam", "xnat", "biosig-tools", "python3-surfer", "dicoogle", "cellprofiler", "bioimagexd", "omero", "king", "vtk-dicom-tools", "gdf-tools", "vrrender", "bart", "bart-cuda", "bart-view", "dcm2niix", "orthanc-wsi", "odil"], "ignore": [], "avoid": []}, "covid-19": {"depends": [], "suggests": ["python3-anndata", "r-bioc-rsubread", "libsimde-dev", "python3-mmtf"], "recommends": ["cwltool", "snakemake", "arvados", "augur", "auspice", "blat", "chip-seq", "fieldbioinformatics", "megahit", "idseq-dag", "nextstrain-ncov", "parasail", "r-bioc-htsfilter", "r-bioc-mutationalpatterns", "r-bioc-rcpi", "r-bioc-rgsepd", "r-bioc-pwmenrich", "r-bioc-tcgabiolinks", "r-cran-mediana", "r-cran-spp", "recan", "trinculo", "vadr", "wtdbg2", "pigx-rnaseq", "bowtie2", "minimap2", "bwa", "nanoseq", "guppy", "chiron", "qcat", "pycoqc", "nanoplot", "fastqc", "graphmap2", "samtools", "bedtools", "multiqc", "artic", "viralrecon", "parallel-fastq-dump", "fastp", "picard-tools", "ivar", "varscan", "snpeff", "snpsift", "bcftools", "cutadapt", "kraken2", "spades", "unicycler", "minia", "vg", "ncbi-blast+", "abacas", "quast", "bustools", "kallisto", "salmon", "rna-star", "allelecount", "r-other-ascat", "r-other-fastbaps", "freebayes", "manta", "qualimap", "strelka", "tiddit", "umap-learn", "ensembl-vep", "busco", "cat-bat", "centrifuge", "dextractor", "drop-seq-tools", "filtlong", "mecat2", "metabat", "nanolyse", "porechop", "changeo", "muscle", "plasmidid", "pplacer", "presto", "python3-cooler", "python3-pairix", "python3-scanpy", "r-cran-alakazam", "r-cran-shazam", "r-cran-tigger", "rosa", "sepp", "seqwish", "signalalign", "tombo", "vsearch", "assembly-stats", "bamkit", "libbbhash-dev", "flappie", "flash", "flye", "lastz", "lighter", "lumpy-sv", "medaka", "ncbi-magicblast", "nanofilt", "python3-nanomath", "nanopolish", "nanook", "nanosv", "ngmlr", "oncofuse", "optitype", "pangolin", "python3-nanoget", "python3-pairtools", "python3-pauvre", "picopore", "pinfish", "pomoxis", "poretools", "prinseq-lite", "pybedtools-bin", "python3-pychopper", "pyomo", "python3-biopython", "python3-vcf", "r-bioc-rsamtools", "readucks", "sailfish", "samclip", "scrappie", "python3-seqcluster", "seqkit", "shovill", "python3-streamz", "tophat-recondition", "vienna-rna", "vt", "python3-toolz", "python3-tornado", "yanagiba", "yanosim", "ufasta", "epigrass", "r-cran-covid19", "r-cran-covid19us", "r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi", "r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "r-cran-seroincidence", "shiny-server", "r-cran-lexrankr", "r-cran-sf", "r-cran-sjplot", "python3-treetime", "chime", "aeskulap", "conquest-common", "dcmtk", "ginkgocadx", "imagej", "libgdcm-tools", "orthanc", "orthanc-wsi", "orthanc-python", "streamlit", "libtensorflow-framework2", "abyss", "bamclipper", "bbmap", "bcalm", "bcbio", "biobambam2", "clonalframeml", "python3-cyvcf2", "covpipe", "delly", "diamond-aligner", "discosnp", "python3-drmaa", "fasta3", "fastani", "genometools", "gffread", "gnumed-client", "gnumed-server", "gromacs", "gubbins", "libhtscodecs-dev", "python3-htseq", "kalign", "libchipcard-dev", "libgclib-dev", "libics-dev", "libmaus2-dev", "libmilib-java", "mmseqs2", "nthash", "odil", "orthanc-dicomweb", "paleomix", "plink1.9", "plink2", "plip", "prokka", "proteinortho", "python3-pydicom", "python3-pynn", "python3-biom-format", "python3-bx", "python3-cgecore", "python3-cogent3", "python3-depinfo", "python3-etelemetry", "python3-gffutils", "python3-pbcommand", "python3-pbcore", "python3-pyani", "python3-pyfaidx", "python3-pysam", "python3-questplus", "python3-scitrack", "python3-screed", "python3-tinyalign", "python3-typed-ast", "q2-cutadapt", "q2-feature-table", "q2-quality-filter", "r-bioc-limma", "r-cran-hms", "r-cran-msm", "r-cran-qtl", "r-cran-stringi", "ragout", "rsem", "ruby-bio", "samblaster", "libseqan3-dev", "seqmagick", "shapeit4", "smrtanalysis", "spaln", "staden-io-lib-utils", "stringtie", "sumaclust", "texlive-science", "thesias", "tnseq-transit", "toil", "uncalled", "umis", "workrave", "python3-torch", "nextflow", "quicktree", "r-cran-incidence", "r-cran-epiestim", "python3-seirsplus", "mmb"], "ignore": [], "avoid": []}, "rehabilitation": {"depends": [], "suggests": ["aghermann"], "recommends": ["sitplus"], "ignore": [], "avoid": []}, "laboratory": {"depends": [], "suggests": [], "recommends": ["opencfu", "orthanc-wsi", "openelis", "openfreezer", "catissuesuite"], "ignore": [], "avoid": []}, "pharmacy": {"depends": [], "suggests": [], "recommends": ["chemtool", "raccoon", "r-cran-dosefinding", "r-cran-rpact"], "ignore": [], "avoid": []}, "data": {"depends": [], "suggests": ["oscar"], "recommends": ["freediams", "freemedforms-freedata", "python3-hl7", "drugref.org"], "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": []}, "epi": {"depends": [], "suggests": ["r-cran-msm", "r-cran-cmprsk", "shiny-server", "python3-epimodels", "repast"], "recommends": ["epigrass", "r-cran-covid19", "r-cran-covid19us", "r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi", "r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "r-cran-seroincidence", "r-cran-incidence", "r-cran-epiestim", "ushahidi", "r-cran-lexrankr", "r-cran-sf", "r-cran-sjplot", "python3-treetime", "python3-torch", "python3-seirsplus", "chime", "netepi-analysis", "netepi-collection", "epifire"], "ignore": [], "avoid": []}}
\ Kein Zeilenumbruch am Dateiende.
diff -Nru debian-med-3.6.2/tasks/bio debian-med-3.7/tasks/bio
--- debian-med-3.6.2/tasks/bio 2021-03-01 11:33:28.000000000 +0100
+++ debian-med-3.7/tasks/bio 2021-05-03 21:28:56.000000000 +0200
@@ -274,13 +274,6 @@
Recommends: hinge
-Recommends: r-bioc-hilbertvis
-Remark: It would be interesting to package HilbertVisGUI as well.
-
-Recommends: r-other-fastbaps
-
-Recommends: r-other-mott-happy.hbrem
-
Recommends: seq-gen
Recommends: snp-sites
@@ -423,6 +416,8 @@
Recommends: bppsuite, bppphyview
+Recommends: bioawk
+
Suggests: getdata
X-Mark: Prospective packages are starting here
@@ -462,6 +457,8 @@
Recommends: biceps
Remark: Mentioned at http://www.renard.it/, developed in RKI
+Recommends: bio-vcf
+
Recommends: cnvkit
Recommends: csb
@@ -511,6 +508,8 @@
Recommends: bali-phy
+Recommends: bamclipper
+
Recommends: bamkit
Recommends: bamtools
@@ -588,6 +587,8 @@
Recommends: contrafold
+Recommends: covpipe
+
Recommends: covtobed
Recommends: crac
@@ -651,6 +652,8 @@
Recommends: fasta3
+Recommends: fastani
+
Recommends: fasttree
Recommends: fastahack
@@ -1197,6 +1200,9 @@
Suggests: r-bioc-gviz
+Recommends: r-bioc-hilbertvis
+Remark: It would be interesting to package HilbertVisGUI as well.
+
Recommends: r-bioc-htsfilter
Recommends: r-bioc-impute
@@ -1223,9 +1229,11 @@
Suggests: r-bioc-savr
+Recommends: r-bioc-scater
+
Suggests: r-bioc-singlecellexperiment
-Recommends: r-bioc-scater
+Suggests: r-bioc-structuralvariantannotation
Suggests: r-bioc-tximport
@@ -1313,6 +1321,10 @@
Recommends: r-other-ascat
+Recommends: r-other-fastbaps
+
+Recommends: r-other-mott-happy.hbrem
+
Recommends: readucks
Recommends: recan
@@ -1537,6 +1549,8 @@
Recommends: umis
+Recommends: uncalled
+
Recommends: unicycler
Recommends: varna
diff -Nru debian-med-3.6.2/tasks/bio-dev debian-med-3.7/tasks/bio-dev
--- debian-med-3.6.2/tasks/bio-dev 2021-03-01 11:33:28.000000000 +0100
+++ debian-med-3.7/tasks/bio-dev 2021-05-03 21:28:56.000000000 +0200
@@ -14,7 +14,7 @@
Recommends: biosquid
-Recommends: cwltool, snakemake
+Recommends: cwltool, snakemake, python3-wdlparse
Suggests: cwlformat
@@ -71,7 +71,9 @@
Recommends: libbio-primerdesigner-perl
-Recommends: libbio-alignio-stockholm-perl, libbio-cluster-perl, libbio-db-hts-perl, libbio-featureio-perl, libbio-tools-run-remoteblast-perl
+Recommends: libbio-alignio-stockholm-perl, libbio-cluster-perl,
+ libbio-db-biofetch-perl, libbio-db-embl-perl, libbio-db-hts-perl, libbio-db-ncbihelper-perl,
+ libbio-featureio-perl, libbio-tools-run-remoteblast-perl, libbio-variation-perl
Recommends: libace-perl
@@ -101,6 +103,8 @@
Recommends: libpal-java
+Recommends: libpdb-redo-dev
+
Recommends: libbioparser-dev, libspoa-dev, libedlib-dev, libthread-pool-dev
Recommends: libjebl2-java
@@ -205,6 +209,7 @@
r-bioc-savr,
r-bioc-shortread,
r-bioc-snpstats,
+ r-bioc-structuralvariantannotation,
r-bioc-titancna,
r-bioc-tfbstools,
r-bioc-tximport,
@@ -625,6 +630,8 @@
Recommends: python3-cooler, python3-pairix
+Recommends: pangolearn
+
Recommends: python3-pyranges
Recommends: python3-streamz
@@ -643,4 +650,4 @@
Suggests: libsuma-dev
-
+Recommends: python3-scanpy
diff -Nru debian-med-3.6.2/tasks/covid-19 debian-med-3.7/tasks/covid-19
--- debian-med-3.6.2/tasks/covid-19 2021-03-01 11:33:28.000000000 +0100
+++ debian-med-3.7/tasks/covid-19 2021-05-03 21:28:56.000000000 +0200
@@ -201,6 +201,8 @@
Recommends: python3-cooler, python3-pairix
+Recommends: python3-scanpy
+
Recommends: r-cran-alakazam, r-cran-shazam, r-cran-tigger
Recommends: rosa
@@ -416,6 +418,8 @@
X-Mark: <begin>https://lists.debian.org/debian-med/2020/03/msg00142.html
Recommends: abyss
+Recommends: bamclipper
+
Recommends: bbmap
Recommends: bcalm
@@ -428,6 +432,8 @@
Recommends: python3-cyvcf2
+Recommends: covpipe
+
Recommends: delly
Recommends: diamond-aligner
@@ -438,6 +444,8 @@
Recommends: fasta3
+Recommends: fastani
+
Recommends: genometools
Recommends: gffread
@@ -468,6 +476,8 @@
Recommends: mmseqs2
+Recommends: nthash
+
Recommends: odil
Recommends: orthanc-dicomweb
@@ -568,6 +578,8 @@
Recommends: toil
+Recommends: uncalled
+
Recommends: umis
Recommends: workrave
diff -Nru debian-med-3.6.2/tasks/epi debian-med-3.7/tasks/epi
--- debian-med-3.6.2/tasks/epi 2021-03-01 11:33:28.000000000 +0100
+++ debian-med-3.7/tasks/epi 2021-05-03 21:28:56.000000000 +0200
@@ -48,6 +48,8 @@
Recommends: chime
+Suggests: python3-epimodels
+
Recommends: netepi-analysis
Remark: See also: http://www.stockholmchallenge.se/data/2123 and
http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf
diff -Nru debian-med-3.6.2/tasks/imaging debian-med-3.7/tasks/imaging
--- debian-med-3.6.2/tasks/imaging 2021-03-01 11:33:28.000000000 +0100
+++ debian-med-3.7/tasks/imaging 2021-05-03 21:28:56.000000000 +0200
@@ -48,8 +48,7 @@
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
-Suggests: python-nipype
-Comment: py2removal
+Recommends: python3-nipype
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
@@ -835,7 +834,7 @@
Recommends: vrrender
-Recommends: bart
+Recommends: bart, bart-cuda
Recommends: bart-view
WNPP: 851431
diff -Nru debian-med-3.6.2/tasks/imaging-dev debian-med-3.7/tasks/imaging-dev
--- debian-med-3.6.2/tasks/imaging-dev 2021-03-01 11:33:28.000000000 +0100
+++ debian-med-3.7/tasks/imaging-dev 2021-05-03 21:28:56.000000000 +0200
@@ -35,8 +35,7 @@
Recommends: python3-nipy
-Suggests: python-nipype
-Comment: py2removal
+Recommends: python3-nipype
Recommends: python3-nitime
@@ -81,6 +80,8 @@
Recommends: python3-nibabel
+Recommends: python3-brian
+
Recommends: libgdf-dev, octave-gdf
; Added by blends-inject 0.0.6. [Please note here if modified manually]
@@ -132,8 +133,7 @@
Recommends: libvigraimpex-dev
-Suggests: python-vigra
-Comment: py2removal
+Recommends: python3-vigra
Recommends: libvtk-dicom-dev
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