[Blends-commit] [Git][blends-team/med][master] 4 commits: substitute r-cran-gprofiler by r-cran-gprofiler2 (see #994212)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Jun 3 11:07:56 BST 2022
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
f6e52845 by Andreas Tille at 2022-06-03T11:54:43+02:00
substitute r-cran-gprofiler by r-cran-gprofiler2 (see #994212)
- - - - -
73d0f94a by Andreas Tille at 2022-06-03T12:00:58+02:00
Update dependencies
- - - - -
5afe49e0 by Andreas Tille at 2022-06-03T12:03:56+02:00
Update changelog
- - - - -
237d9d13 by Andreas Tille at 2022-06-03T12:05:07+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + dependency_data/debian-med_3.7.2.json
- tasks/bio
- tasks/bio-dev
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,43 @@
-debian-med (3.7.2) UNRELEASED; urgency=medium
+debian-med (3.7.2) unstable; urgency=medium
* opensurgsim is removed from Debian
+ * substitute r-cran-gprofiler by r-cran-gprofiler2 (see #994212)
- -- Andreas Tille <tille at debian.org> Tue, 18 Jan 2022 16:28:04 +0100
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-bio
+ added:
+ Recommends: megan-ce, twopaco, lamassemble, ntcard, snpsift, mcaller,
+ dnarrange, megadepth, r-bioc-megadepth, provean,
+ libpwiz-tools, rockhopper, diann
+ Suggests: r-cran-gprofiler2
+ removed:
+ Suggests: mcaller, r-cran-gprofiler
+ -med-bio-dev
+ added:
+ Recommends: libpwiz-dev, python3-cogent3, r-cran-gprofiler2
+ removed:
+ Recommends: r-cran-gprofiler
+ Suggests: python3-cogent3, python3-mcaller
+ -med-covid-19
+ added:
+ Recommends: nf-core-artic
+ removed:
+ Recommends: artic
+ -med-epi
+ added:
+ Recommends: r-cran-prevalence
+ -med-imaging
+ removed:
+ Recommends: python3-mvpa2
+ -med-imaging-dev
+ added:
+ Recommends: libopencv-dev, python3-torchvision
+ removed:
+ Recommends: python3-mvpa2, pytorch-vision, libopensurgsim-dev, libcv-dev
+
+ -- Andreas Tille <tille at debian.org> Fri, 03 Jun 2022 12:04:09 +0200
debian-med (3.7.1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -239,6 +239,7 @@ Recommends: abacas,
fitgcp,
flash,
flexbar,
+ flye,
fml-asm,
freebayes,
freecontact,
@@ -297,7 +298,6 @@ Recommends: abacas,
kalign,
kallisto,
kaptive,
- khmer,
kineticstools,
king-probe,
kissplice,
@@ -316,6 +316,7 @@ Recommends: abacas,
lastz,
leaff,
lefse,
+ libpwiz-tools,
librg-utils-perl,
libvcflib-tools,
lighter,
@@ -328,14 +329,18 @@ Recommends: abacas,
macsyfinder,
maffilter,
mafft,
+ malt,
mapdamage,
mapsembler2,
maq,
maqview,
mash,
mauve-aligner,
+ mcaller,
mecat2,
+ megadepth,
megahit,
+ megan-ce,
melting,
meryl,
metabat,
@@ -388,6 +393,7 @@ Recommends: abacas,
njplot,
norsnet,
norsp,
+ ntcard,
obitools,
openms,
optimir,
@@ -419,7 +425,6 @@ Recommends: abacas,
phyx,
picard-tools,
picopore,
- pigx-rnaseq,
piler,
pilercr,
pilon,
@@ -470,6 +475,7 @@ Recommends: abacas,
prokka,
proteinortho,
prottest,
+ provean,
pscan-chip,
pscan-tfbs,
psortb,
@@ -478,6 +484,7 @@ Recommends: abacas,
pymol,
pyscanfcs,
python3-biomaj3-daemon,
+ python3-emperor,
python3-geneimpacts,
python3-gffutils,
python3-pairtools,
@@ -572,13 +579,14 @@ Recommends: abacas,
rna-star,
rnahybrid,
roary,
+ rockhopper,
roguenarok,
rsem,
rtax,
runcircos-gui,
saint,
salmid,
- salmon,
+ sambamba,
samblaster,
samclip,
samtools,
@@ -616,7 +624,9 @@ Recommends: abacas,
snap-aligner,
sniffles,
snp-sites,
+ snpeff,
snpomatic,
+ snpsift,
soapaligner,
soapdenovo,
soapdenovo2,
@@ -675,10 +685,8 @@ Recommends: abacas,
trf,
trim-galore,
trimmomatic,
- trinityrnaseq,
tvc,
uc-echo,
- umap-learn,
umis,
uncalled,
unicycler,
@@ -749,7 +757,9 @@ Suggests: acacia,
dazzle,
deepbinner,
dendroscope,
+ diann,
dnapi,
+ dnarrange,
e-hive,
ecell,
embassy-phylip,
@@ -768,7 +778,6 @@ Suggests: acacia,
fieldbioinformatics,
figaro,
flappie,
- flye,
forester,
forge,
galaxy,
@@ -799,19 +808,19 @@ Suggests: acacia,
jbrowse,
jigsaw,
kempbasu,
+ khmer,
+ lamassemble,
libhdf5-dev,
libhnswlib-dev,
lofreq,
mach-haplotyper,
mage2tab,
maker2,
- malt,
manta,
marginphase,
martj,
maude,
maxd,
- mcaller,
medaka,
meme,
mesquite,
@@ -860,6 +869,7 @@ Suggests: acacia,
phylophlan,
phyloviz-core,
phylowin,
+ pigx-rnaseq,
pigx-scrnaseq,
pipasic,
plato,
@@ -879,7 +889,6 @@ Suggests: acacia,
python3-cyvcf2,
python3-deeptools,
python3-deeptoolsintervals,
- python3-emperor,
python3-htseq,
python3-intake,
python3-loompy,
@@ -940,6 +949,7 @@ Suggests: acacia,
r-bioc-grohmm,
r-bioc-gviz,
r-bioc-isoformswitchanalyzer,
+ r-bioc-megadepth,
r-bioc-mofa2,
r-bioc-org.hs.eg.db,
r-bioc-org.mm.eg.db,
@@ -957,7 +967,7 @@ Suggests: acacia,
r-cran-epir,
r-cran-fitdistrplus,
r-cran-forecast,
- r-cran-gprofiler,
+ r-cran-gprofiler2,
r-cran-minerva,
r-cran-optimalcutpoints,
r-cran-parmigene,
@@ -981,7 +991,7 @@ Suggests: acacia,
rose,
rsat,
sailfish,
- sambamba,
+ salmon,
sap,
science-workflow,
seq-gen,
@@ -994,7 +1004,6 @@ Suggests: acacia,
sina,
sistr,
situs,
- snpeff,
solvate,
sourmash,
sparta,
@@ -1014,12 +1023,15 @@ Suggests: acacia,
tn-seqexplorer,
tophat,
treebuilder3d,
+ trinityrnaseq,
tripal,
trnascan-se,
twain,
+ twopaco,
ufasta,
ugene,
umap,
+ umap-learn,
unc-fish,
uniprime,
varmatch,
@@ -1136,6 +1148,7 @@ Recommends: bio-tradis,
libpbseq-dev,
libpdb-redo-dev,
libpll-dev,
+ libpwiz-dev,
libqes-dev,
librcsb-core-wrapper0-dev,
librdp-taxonomy-tree-java,
@@ -1145,7 +1158,6 @@ Recommends: bio-tradis,
librostlab3-dev,
libsbml5-dev,
libseqan2-dev,
- libseqan3-dev,
libseqlib-dev,
libsmithwaterman-dev,
libsnp-sites1-dev,
@@ -1153,6 +1165,7 @@ Recommends: bio-tradis,
libspoa-dev,
libsrf-dev,
libssm-dev,
+ libssu-dev,
libssw-dev,
libssw-java,
libstaden-read-dev,
@@ -1188,6 +1201,7 @@ Recommends: bio-tradis,
python3-deeptoolsintervals,
python3-dendropy,
python3-dnaio,
+ python3-ete3,
python3-fast5,
python3-freecontact,
python3-gfapy,
@@ -1195,7 +1209,6 @@ Recommends: bio-tradis,
python3-htseq,
python3-intervaltree-bio,
python3-kineticstools,
- python3-loompy,
python3-mirtop,
python3-nanoget,
python3-ngs,
@@ -1220,10 +1233,11 @@ Recommends: bio-tradis,
python3-ruffus,
python3-screed,
python3-shasta,
+ python3-skbio,
python3-sqt,
- python3-streamz,
python3-tinyalign,
python3-treetime,
+ python3-unifrac,
python3-wdlparse,
r-bioc-biobase,
r-cran-boolnet,
@@ -1232,6 +1246,7 @@ Recommends: bio-tradis,
r-cran-fitdistrplus,
r-cran-forecast,
r-cran-genetics,
+ r-cran-gprofiler2,
r-cran-haplo.stats,
r-cran-metamix,
r-cran-phangorn,
@@ -1282,7 +1297,7 @@ Suggests: bioclipse,
libroadrunner-dev,
librostlab-blast-doc,
librostlab-doc,
- libssu-dev,
+ libseqan3-dev,
libsuma-dev,
libsvmloc-dev,
libswarm2-dev,
@@ -1299,11 +1314,10 @@ Suggests: bioclipse,
python3-consensuscore2,
python3-cooler,
python3-ctdopts,
- python3-ete3,
python3-galaxy-lib,
python3-intake,
python3-joypy,
- python3-mcaller,
+ python3-loompy,
python3-misopy,
python3-ncls,
python3-networkx,
@@ -1313,9 +1327,8 @@ Suggests: bioclipse,
python3-roadrunner,
python3-scanpy,
python3-seqcluster,
- python3-skbio,
+ python3-streamz,
python3-torch,
- python3-unifrac,
q2-alignment,
q2-composition,
q2-cutadapt,
@@ -1427,7 +1440,6 @@ Suggests: bioclipse,
r-cran-fastcluster,
r-cran-future.apply,
r-cran-future.batchtools,
- r-cran-gprofiler,
r-cran-ica,
r-cran-itertools,
r-cran-kaos,
@@ -1661,6 +1673,7 @@ Recommends: python3-seirsplus,
r-cran-incidence,
r-cran-kernelheaping,
r-cran-lexrankr,
+ r-cran-prevalence,
r-cran-seroincidence,
r-cran-sf,
r-cran-sjplot,
@@ -1723,6 +1736,7 @@ Recommends: aeskulap,
bart,
bart-view,
biosig-tools,
+ camitk-imp,
ctn,
ctsim,
dcm2niix,
@@ -1733,7 +1747,6 @@ Recommends: aeskulap,
gdf-tools,
gwyddion,
imagej,
- invesalius,
ismrmrd-tools,
king,
libgdcm-tools,
@@ -1776,7 +1789,6 @@ Suggests: afni,
bioimagexd,
blox,
brainvisa,
- camitk-imp,
caret,
cdmedicpacs,
cellprofiler,
@@ -1811,6 +1823,7 @@ Suggests: afni,
imview,
incf-nidash-oneclick-clients,
insightapplications,
+ invesalius,
isis,
itksnap,
jemris,
@@ -1846,7 +1859,6 @@ Suggests: afni,
piano,
pngquant,
pymeg,
- python3-mvpa2,
science-workflow,
slicer,
sofa-apps,
@@ -1882,6 +1894,7 @@ Recommends: cimg-dev,
gmic,
libbart-dev,
libbiosig-dev,
+ libcamitk-dev,
libcifti-dev,
libedf-dev,
libgdf-dev,
@@ -1896,11 +1909,13 @@ Recommends: cimg-dev,
libminc-dev,
libnifti2-dev,
libodil-dev,
+ libopencv-dev,
libopenigtlink-dev,
libopenslide-dev,
libpapyrus3-dev,
libsight-dev,
libteem-dev,
+ libvigraimpex-dev,
libvistaio-dev,
libvolpack1-dev,
libvtk-dicom-dev,
@@ -1924,13 +1939,12 @@ Recommends: cimg-dev,
python3-openslide,
python3-pydicom,
python3-pyxnat,
+ python3-vigra,
r-cran-rniftilib
Suggests: emokit,
libbio-formats-java,
- libcamitk-dev,
libcamp-dev,
libctk-dev,
- libcv-dev,
libeegdev-dev,
libfreeimage-dev,
libgdcm2-dev,
@@ -1940,18 +1954,14 @@ Suggests: emokit,
libnifti-doc,
libopenmeeg-dev,
libopenslide-java,
- libopensurgsim-dev,
libsimpleitk1-dev,
libvia-dev,
- libvigraimpex-dev,
libvmtk-dev,
libvtk7-dev,
libxdffileio-dev,
python-vmtk,
- python3-mvpa2,
python3-simpleitk,
- python3-vigra,
- pytorch-vision,
+ python3-torchvision,
tifffile
Description: Debian Med image processing and visualization packages development
This metapackage will install Debian packages which might be useful
=====================================
dependency_data/debian-med_3.7.2.json
=====================================
@@ -0,0 +1 @@
+{"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", "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-cogent3", "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-gprofiler2", "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-apmswapp", "r-bioc-biobase", "libffindex0-dev", "libpwiz-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-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", "python3-ete3", "python3-gfapy", "goby-java", "python3-seqcluster", 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"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": []}, "dental": {"depends": [], "suggests": [], "recommends": ["openmolar", "imagetooth", "entangle"], "ignore": [], "avoid": []}, "imaging-dev": {"depends": [], "suggests": ["libvtk7-dev", "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", "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": []}, "research": {"depends": [], "suggests": [], "recommends": ["r-cran-rpact", "openclinica"], "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": []}, "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": []}, "tools": {"depends": [], "suggests": ["cycle", "mencal", "entangle", "goldencheetah", "oscar"], "recommends": ["pcalendar", "pondus", "mssstest", "wgerman-medical", "hunspell-de-med", "quitcount", "workrave", "edfbrowser", "hunspell-en-med", "cronometer", "python3-fitbit", "r-cran-fitcoach", "r-cran-fitbitscraper", "galileo", "nut-nutrition", "nutsqlite", "pesco"], "ignore": [], "avoid": []}, "cms": {"depends": [], "suggests": ["zope-zms", "hid"], "recommends": ["xnat"], "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": []}, "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"], "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": []}, "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", "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-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", "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", "minimap2", "bwa", "nanoseq", "guppy", "chiron", "qcat", "pycoqc", "nanoplot", "fastqc", "graphmap2", "samtools", "bedtools", "multiqc", "nf-core-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", "tipp", "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-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": []}}
\ No newline at end of file
=====================================
tasks/bio
=====================================
@@ -1299,7 +1299,7 @@ Suggests: r-cran-fitdistrplus
Suggests: r-cran-forecast
-Suggests: r-cran-gprofiler
+Suggests: r-cran-gprofiler2
Suggests: r-cran-qqman
=====================================
tasks/bio-dev
=====================================
@@ -244,7 +244,7 @@ Suggests: r-cran-future.batchtools
Recommends: r-cran-genetics
-Recommends: r-cran-gprofiler
+Recommends: r-cran-gprofiler2
Recommends: r-cran-haplo.stats
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/4fb1feeffee10388ddacc0a34cdfecebbe2bca3b...237d9d13839f155524f9c74311534a0bd054690e
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/4fb1feeffee10388ddacc0a34cdfecebbe2bca3b...237d9d13839f155524f9c74311534a0bd054690e
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