[Blends-commit] [Git][blends-team/med][master] 3 commits: Update changelog and dependencies

Andreas Tille (@tille) gitlab at salsa.debian.org
Tue Nov 1 15:17:29 GMT 2022



Andreas Tille pushed to branch master at Debian Blends Team / med


Commits:
37bcb4a6 by Andreas Tille at 2022-10-28T10:12:24+02:00
Update changelog and dependencies

- - - - -
871a6205 by Andreas Tille at 2022-10-28T10:13:03+02:00
Upload to unstable

- - - - -
16d239f9 by Andreas Tille at 2022-11-01T16:17:10+01:00
Add any2fasta, snippy

- - - - -


3 changed files:

- debian/changelog
- + dependency_data/debian-med_3.7.3.json
- tasks/bio


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-debian-med (3.7.3) UNRELEASED; urgency=medium
+debian-med (3.7.3) unstable; urgency=medium
 
   * Build-Depends-Indep: blends-dev (>= 0.7.5~)
     Closes: #1012341
@@ -6,7 +6,52 @@ debian-med (3.7.3) UNRELEASED; urgency=medium
   * zalign removed from Debian
   * Standards-Version: 4.6.1
 
- -- Andreas Tille <tille at debian.org>  Fri, 03 Jun 2022 12:06:56 +0200
+  * start of automatic changelog entry * 
+  
+  * Changes in metapackage dependencies
+   -med-bio
+    added:
+      Recommends:  ska, genomicsdb-tools, nxtrim, fastq-pair, unikmer,
+                   xpore, abpoa, surpyvor, metaphlan, pullseq, pyensembl,
+                   terraphast
+    removed:
+      Recommends:  metaphlan2, zalign, falcon
+   -med-bio-dev
+    added:
+      Recommends:  python3-pyabpoa, libbiojava5-java, ont-fast5-api,
+                   python3-slow5, python3-gtfparse, libslow5-dev,
+                   python3-propka, python3-pyspoa
+      Suggests:   libgatk-fermilite-java, libgatk-fermilite-jni,
+                  libvbz-hdf-plugin-dev, libterraces-dev,
+                  libcapsule-maven-nextflow-java, libgatk-bwamem-java,
+                  libicb-utils-java, libgatk-bwamem-jni, python3-bioblend,
+                  libgenomicsdb-dev, libgenomicsdb-java, capsule-nextflow,
+                  libbiosoup-dev
+   -med-cloud
+    removed:
+      Recommends:  zalign
+   -med-imaging
+    added:
+      Recommends:  heudiconv
+      Suggests:  orthanc-neuro
+   -med-imaging-dev
+    added:
+      Recommends:  python3-dcmstack
+    removed:
+      Suggests:  libvtk7-dev
+   -med-oncology
+    removed:
+      Recommends:  dicompyler
+   -med-psychology
+    added:
+      Recommends:  orthanc-neuro
+   -med-tools
+    added:
+      Recommends:  cycle
+    removed:
+      Suggests:  cycle
+
+ -- Andreas Tille <tille at debian.org>  Fri, 28 Oct 2022 10:12:35 +0200
 
 debian-med (3.7.2) unstable; urgency=medium
 


=====================================
dependency_data/debian-med_3.7.3.json
=====================================
@@ -0,0 +1 @@
+{"rehabilitation": {"depends": [], "suggests": ["aghermann"], "recommends": ["sitplus"], "ignore": [], "avoid": []}, "statistics": {"depends": [], "suggests": ["science-statistics"], "recommends": ["r-bioc-edger", "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": []}, "covid-19": {"depends": [], "suggests": ["python3-anndata", "r-bioc-rsubread", "libsimde-dev", "python3-mmtf"], "recommends": ["cwltool", "snakemake", "arvados", "augur", "auspice", "blat", "chip-seq", "fieldbioinformatics", "megahit", "python3-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-kernelheaping", "r-cran-mediana", "r-cran-spp", "recan", "trinculo", "vadr", "wtdbg2", "pigx-rnaseq", "bowtie2", 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"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": []}, "cms": {"depends": [], "suggests": ["zope-zms", "hid"], "recommends": ["xnat"], "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-prevalence", "r-cran-seroincidence", "r-cran-incidence", "r-cran-epiestim", "r-cran-kernelheaping", "ushahidi", "r-cran-lexrankr", "r-cran-sf", "r-cran-sjplot", "python3-treetime", "python3-torch", "python3-seirsplus", "chime", "netepi-analysis", "netepi-collection", "epifire"], "ignore": [], "avoid": []}, "imaging": {"depends": [], "suggests": ["imagemagick", "pngquant", "imview", "trimage", "illustrate", "conquest-dbase", "conquest-mysql", "conquest-postgres", "conquest-sqlite", "paraview", "orthanc-webviewer", "orthanc-dicomweb", "orthanc-imagej", "orthanc-postgresql", "orthanc-mysql", "orthanc-gdcm", "orthanc-neuro", "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", "heudiconv", "aeskulap", "fsl", "fslview", "via-bin", "gwyddion", "nifti2dicom", "qnifti2dicom", "sofa-apps", "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": []}, "imaging-dev": {"depends": [], "suggests": ["libnifti-doc", "libfreeimage-dev", "libics-dev", "liblimereg-dev", "emokit", "libeegdev-dev", "libxdffileio-dev", "tifffile", "python-vmtk", "libcamp-dev"], "recommends": ["ctn-dev", "cimg-dev", "libminc-dev", "libmdc2-dev", "libvtk9-dev", "libnifti2-dev", "libinsighttoolkit5-dev", "libvolpack1-dev", "libgdcm2-dev", "python3-gdcm", "python3-dcmstack", "libmaxflow-dev", "python3-nipy", "python3-nipype", "python3-nitime", "libvia-dev", "odin", "libopencv-dev", "libteem-dev", "gmic", "libgiftiio-dev", "libvistaio-dev", "libmia-2.4-dev", "libmiaviewit-dev", "libmialm-dev", "python3-mia", "libopenigtlink-dev", "r-cran-rniftilib", "libmni-perllib-perl", "python3-pydicom", "libopenmeeg-dev", "python3-nibabel", "python3-brian", "libgdf-dev", "octave-gdf", "python3-pyxnat", "python3-dipy", "libbiosig-dev", "python3-biosig", "libctk-dev", "libopenslide-dev", "python3-openslide", "libopenslide-java", "libbio-formats-java", "octave-dicom", "libcamitk-dev", "libpapyrus3-dev", "python3-mne", "libvmtk-dev", "libvigraimpex-dev", "python3-vigra", "libvtk-dicom-dev", "libedf-dev", "python3-imageio", "libismrmrd-dev", "libodil-dev", "libbart-dev", "octave-bart", "libcifti-dev", "libxdf-dev", "libsimpleitk1-dev", "python3-simpleitk", "python3-torchvision", "libsight-dev"], "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", "oscar", "orthanc", "orthanc-wsi", "medintux", "mirth", "tinyheb", "mirrormed", "elexis", "freeb", "freemed", "elementalclinic", "openemr", "clearhealth", "proteus", "thera-pi", "freeshim", "remitt", "qrisk2"], "ignore": ["clearhealth"], "avoid": []}, "psychology": {"depends": [], "suggests": ["science-psychophysics", "python-pyepl", "python3-bmtk", "python3-bids-validator"], "recommends": ["praat", "r-cran-foreign", "psignifit", "r-cran-psy", "psychopy", "r-cran-psych", "r-cran-psychometric", "r-cran-psychotree", "r-cran-psyphy", "orthanc-neuro"], "ignore": [], "avoid": []}, "pharmacy": {"depends": [], "suggests": [], "recommends": ["chemtool", "raccoon", "r-cran-dosefinding", "r-cran-rpact"], "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": []}, "data": {"depends": [], "suggests": ["oscar"], "recommends": ["freediams", "freemedforms-freedata", "python3-hl7", "drugref.org"], "ignore": [], "avoid": []}, "bio-dev": {"depends": [], "suggests": ["conda-package-handling", "cwlformat", "python3-biopython-sql", "python-biopython-doc", "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-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", 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"r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-phyloseq", "r-bioc-mofa", "r-bioc-mofa2", "r-bioc-multiassayexperiment", "r-bioc-mutationalpatterns", "r-bioc-rtracklayer", "r-bioc-scater", "r-bioc-tfbstools", "r-cran-adegenet", "r-cran-adephylo", "r-cran-ape", "r-bioc-ebseq", "r-cran-rotl", "r-cran-samr", "r-cran-distory", "r-cran-drinsight", "r-cran-kaos", "r-cran-metamix", "r-cran-phangorn", "r-cran-phytools", "r-cran-pscbs", "r-cran-seurat", "r-cran-seqinr", "r-cran-spp", "r-cran-treescape", "r-cran-tsne", "r-cran-vegan", "r-cran-webgestaltr", "r-other-apmswapp", "r-cran-spp", "r-cran-wgcna", "r-other-ascat", "r-other-fastbaps", "r-other-mott-happy.hbrem", "readucks", "recan", "relion", "relion-gui", "relion-cuda", "relion-gui-cuda", "rdp-alignment", "rdp-readseq", "rdp-classifier", "reapr", "repeatmasker-recon", "repeatmasker", "resfinder", "roadtrips", "roary", "rockhopper", "roguenarok", "rosa", "rsat", "rsem", "sambamba", "samblaster", "salmid", "salmon", "samclip", "sap", "scrappie", "scrm", "seer", "segemehl", "sepp", "tipp", "seq-seq-pan", "seqkit", "seqmagick", "seqprep", "seqsero", "seqtk", "sequenceconverter.app", "seqwish", "sga", "shasta", "shovill", "signalalign", "sibelia", "simka", "simkamin", "sina", "sistr", "situs", "sim4db", "ska", "skesa", "smalt", "smithwaterman", "smrtanalysis", "snpeff", "snpsift", "snpomatic", "solvate", "sortmerna", "snap-aligner", "sniffles", "sourmash", "spaced", "spades", "spaln", "sparta", "sprai", "srst2", "ssaha", "sspace", "ssw-align", "staden", "stacks", "strap", "strap-base", "strelka", "stringtie", "subread", "suitename", "sumatra", "sumaclust", "sumtrees", "surankco", "surpyvor", "survivor", "svim", "swarm", "tacg", "tantan", "terraphast", "thesias", "tiddit", "toppred", "transdecoder", "tnseq-transit", "tn-seqexplorer", "toil", "tombo", "tortoize", "tracetuner", "transrate-tools", "treeview", "trf", "trinityrnaseq", "twopaco", "uc-echo", "megadepth", "ufasta", "umap-learn", "umis", "uncalled", "unicycler", "unikmer", "varna", "varmatch", "varscan", "vcfanno", "vdjtools", "vg", "vienna-rna", "virulencefinder", "vmatch", "vmd", "vsearch", "vt", "xpore", "yaha", "yanagiba", "yanosim", "canu", "zodiac-zeden", "discosnp", "mapsembler2", "dnaclust", "r-cran-tcr", "r-cran-tigger", "r-cran-alakazam", "r-cran-shazam", "igor", "r-cran-sdmtools", "presto", "changeo", "igblast", "pigx-rnaseq", "pigx-scrnaseq", "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", "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", "treebuilder3d", "excavator", "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", "e-hive", "cmap", "gbrowse-syn", "tripal", "genemark", "annovar", "python3-orange", "tigr-glimmer-mg"], "ignore": ["mozilla-biofox", "riso", "catissuecore", "trapss"], "avoid": []}, "research": {"depends": [], "suggests": [], "recommends": ["r-cran-rpact", "openclinica"], "ignore": [], "avoid": []}, "dental": {"depends": [], "suggests": [], "recommends": ["openmolar", "imagetooth", "entangle"], "ignore": [], "avoid": []}, "oncology": {"depends": [], "suggests": ["python3-dicompylercore"], "recommends": ["uw-prism", "orthanc-wsi", "planunc", "simrisc"], "ignore": [], "avoid": []}, "physics": {"depends": [], "suggests": ["paw-demos", "libbiosig-dev", "python3-biosig", "octave-biosig", "openvibe", "python3-multipletau"], "recommends": ["paw++", "paw", "octave", "r-base", "biosig-tools", "gdf-tools", "gate"], "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", "pplacer", "quicktree"], "ignore": [], "avoid": []}, "typesetting": {"depends": [], "suggests": ["kbibtex", "biber", "bibus", "jabref-plugin-oo", "r-cran-qqman"], "recommends": ["texlive-science", "texlive-latex-extra", "king"], "ignore": [], "avoid": []}}
\ No newline at end of file


=====================================
tasks/bio
=====================================
@@ -441,6 +441,8 @@ Recommends: aegean
 
 Recommends: andi
 
+Recommends: any2fasta
+
 Recommends: arden
 
 Recommends: artfastqgenerator, art-nextgen-simulation-tools
@@ -1501,6 +1503,8 @@ Recommends: snap-aligner
 
 Recommends: sniffles
 
+Recommends: snippy
+
 Recommends: sourmash
 
 Recommends: spaced



View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/9e8c07b7091398d27c806b5ba58a43105c35b8f3...16d239f9ce5037406289b31a08f9bb6de0d1b0da

-- 
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/9e8c07b7091398d27c806b5ba58a43105c35b8f3...16d239f9ce5037406289b31a08f9bb6de0d1b0da
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