[Blends-commit] [Git][blends-team/med][master] 3 commits: Recreate d/control and dependency_data
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Jan 12 20:08:42 GMT 2022
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
004e6ad2 by Andreas Tille at 2022-01-12T20:41:53+01:00
Recreate d/control and dependency_data
- - - - -
ec1a7db3 by Andreas Tille at 2022-01-12T20:44:16+01:00
Update changelog entry
- - - - -
86a7efe0 by Andreas Tille at 2022-01-12T20:45:19+01:00
Upload to unstable
- - - - -
3 changed files:
- debian/changelog
- debian/control
- + dependency_data/debian-med_3.7.1.json
Changes:
=====================================
debian/changelog
=====================================
@@ -5,7 +5,52 @@ debian-med (3.7.1) unstable; urgency=medium
* Remove r-other-hms-dbmi-spp since it is r-cran-spp
* Standards-Version: 4.6.0
- -- Andreas Tille <tille at debian.org> Tue, 23 Nov 2021 08:04:35 +0100
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-bio
+ added:
+ Recommends: r-bioc-mofa2, igblast, tipp, haploview, cutesv,
+ python3-cogent3
+ Suggests: r-bioc-isoformswitchanalyzer, catfishq, nano-snakemake,
+ tandem-genotypes, illustrate
+ removed:
+ Recommends: hinge, r-bioc-pcamethods, python3-cogent,
+ r-other-hms-dbmi-spp, haploview-cran-amap, compclust,
+ gassst, ccs, ncbi-igblast
+ Suggests: r-cran-rsgcc, r-bioc-org.ce.eg.db, r-bioc-org.rn.eg.db
+ -med-bio-dev
+ added:
+ Recommends: goby-java, python3-cigar, python3-pangolearn,
+ python3-compclust
+ removed:
+ Recommends: libgoby-java, r-other-hms-dbmi-spp, pangolearn, libbiod-dev,
+ python3-hyphy
+ Suggests: r-cran-rsgcc
+ -med-bio-ngs
+ added:
+ Recommends: q2cli
+ Suggests: r-bioc-mofa2, r-bioc-isoformswitchanalyzer
+ -med-covid-19
+ added:
+ Recommends: tipp, python3-idseq-dag, r-cran-kernelheaping
+ removed:
+ Recommends: idseq-dag
+ -med-epi
+ added:
+ Recommends: r-cran-kernelheaping
+ -med-imaging
+ added:
+ Suggests: illustrate
+ -med-imaging-dev
+ added:
+ Recommends: libvtk9-dev, libinsighttoolkit5-dev
+ Suggests: libvtk7-dev
+ removed:
+ Recommends: libvtk7-dev, libinsighttoolkit4-dev
+ Suggests: libvtk6-dev
+
+ -- Andreas Tille <tille at debian.org> Wed, 12 Jan 2022 20:44:28 +0100
debian-med (3.7) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -122,6 +122,7 @@ Recommends: abacas,
baitfisher,
bali-phy,
ballview,
+ bamclipper,
bamkit,
bamtools,
bandage,
@@ -141,6 +142,7 @@ Recommends: abacas,
bio-rainbow,
bio-tradis,
bio-vcf,
+ bioawk,
biobambam2,
biosyntax,
bitseq,
@@ -186,6 +188,7 @@ Recommends: abacas,
crac,
csb,
cutadapt,
+ cutesv,
daligner,
damapper,
datamash,
@@ -221,6 +224,7 @@ Recommends: abacas,
exonerate,
fasta3,
fastahack,
+ fastani,
fastaq,
fastdnaml,
fastlink,
@@ -256,7 +260,6 @@ Recommends: abacas,
gff2ps,
gffread,
ggd-utils,
- ghemical,
ghmm,
glam2,
gmap,
@@ -278,6 +281,7 @@ Recommends: abacas,
idba,
igdiscover,
igor,
+ igv,
indelible,
infernal,
insilicoseq,
@@ -540,7 +544,6 @@ Recommends: abacas,
r-cran-webgestaltr,
r-cran-wgcna,
r-other-ascat,
- r-other-hms-dbmi-spp,
r-other-mott-happy.hbrem,
r-other-rajewsky-dropbead,
racon,
@@ -576,7 +579,6 @@ Recommends: abacas,
saint,
salmid,
salmon,
- sambamba,
samblaster,
samclip,
samtools,
@@ -653,6 +655,7 @@ Recommends: abacas,
thesias,
tiddit,
tigr-glimmer,
+ tipp,
tm-align,
tnseq-transit,
toil,
@@ -711,13 +714,11 @@ Suggests: acacia,
axpcoords,
bagpipe,
bambus,
- bamclipper,
bax2bam,
bcbio,
biceps,
big-blast,
bigsdb,
- bioawk,
bismark,
blat,
blimps-utils,
@@ -727,13 +728,12 @@ Suggests: acacia,
cactus,
caftools,
card-rgi,
- ccs,
+ catfishq,
cdna-db,
cellprofiler,
cinema,
cluster3,
cmap,
- compclust,
conda-package-handling,
condetri,
contrafold,
@@ -764,7 +764,6 @@ Suggests: acacia,
exalt,
excavator,
falcon,
- fastani,
ffp,
fieldbioinformatics,
figaro,
@@ -773,7 +772,6 @@ Suggests: acacia,
forester,
forge,
galaxy,
- gassst,
gatk,
gbrowse-syn,
genemark,
@@ -783,18 +781,20 @@ Suggests: acacia,
genographer,
gerp++,
getdata,
+ ghemical,
glimmerhmm,
gmv,
gramalign,
graphbin,
graphmap2,
- haploview-cran-amap,
+ haploview,
hawkeye,
htqc,
hts-nim-tools,
idefix,
idseq-bench,
- igv,
+ igblast,
+ illustrate,
inspect,
jbrowse,
jigsaw,
@@ -831,10 +831,10 @@ Suggests: acacia,
mugsy,
mummergpu,
mview,
+ nano-snakemake,
nanocall,
nanocomp,
nanoplot,
- ncbi-igblast,
ncbi-magicblast,
nextsv,
ngila,
@@ -875,7 +875,7 @@ Suggests: acacia,
python3-alignlib,
python3-anndata,
python3-cgecore,
- python3-cogent,
+ python3-cogent3,
python3-cyvcf2,
python3-deeptools,
python3-deeptoolsintervals,
@@ -939,10 +939,10 @@ Suggests: acacia,
r-bioc-go.db,
r-bioc-grohmm,
r-bioc-gviz,
- r-bioc-org.ce.eg.db,
+ r-bioc-isoformswitchanalyzer,
+ r-bioc-mofa2,
r-bioc-org.hs.eg.db,
r-bioc-org.mm.eg.db,
- r-bioc-org.rn.eg.db,
r-bioc-qusage,
r-bioc-savr,
r-bioc-singlecellexperiment,
@@ -965,7 +965,6 @@ Suggests: acacia,
r-cran-qqman,
r-cran-rcpphnsw,
r-cran-rentrez,
- r-cran-rsgcc,
r-cran-sctransform,
r-other-apmswapp,
r-other-fastbaps,
@@ -982,6 +981,7 @@ Suggests: acacia,
rose,
rsat,
sailfish,
+ sambamba,
sap,
science-workflow,
seq-gen,
@@ -1005,6 +1005,7 @@ Suggests: acacia,
strelka,
tab2mage,
tacg,
+ tandem-genotypes,
taverna,
taxinspector,
tetra,
@@ -1046,6 +1047,7 @@ Recommends: bio-tradis,
biosquid,
cwltool,
gffread,
+ goby-java,
libace-perl,
libai-fann-perl,
libbambamc-dev,
@@ -1075,7 +1077,6 @@ Recommends: bio-tradis,
libbio-tools-run-remoteblast-perl,
libbio-variation-perl,
libbiococoa-dev,
- libbiod-dev,
libbiojava-java,
libbiojava4-java,
libbioparser-dev,
@@ -1177,6 +1178,7 @@ Recommends: bio-tradis,
python3-biotools,
python3-bx,
python3-cgecore,
+ python3-cigar,
python3-cobra,
python3-corepywrap,
python3-csb,
@@ -1186,7 +1188,6 @@ Recommends: bio-tradis,
python3-deeptoolsintervals,
python3-dendropy,
python3-dnaio,
- python3-ete3,
python3-fast5,
python3-freecontact,
python3-gfapy,
@@ -1194,6 +1195,7 @@ Recommends: bio-tradis,
python3-htseq,
python3-intervaltree-bio,
python3-kineticstools,
+ python3-loompy,
python3-mirtop,
python3-nanoget,
python3-ngs,
@@ -1218,11 +1220,9 @@ Recommends: bio-tradis,
python3-ruffus,
python3-screed,
python3-shasta,
- python3-skbio,
python3-sqt,
python3-streamz,
python3-tinyalign,
- python3-torch,
python3-treetime,
python3-wdlparse,
r-bioc-biobase,
@@ -1232,7 +1232,6 @@ Recommends: bio-tradis,
r-cran-fitdistrplus,
r-cran-forecast,
r-cran-genetics,
- r-cran-gprofiler,
r-cran-haplo.stats,
r-cran-metamix,
r-cran-phangorn,
@@ -1251,7 +1250,6 @@ Recommends: bio-tradis,
r-cran-tsne,
r-cran-vegan,
r-cran-webgestaltr,
- r-other-hms-dbmi-spp,
ruby-bio,
ruby-crb-blast,
sbmltoolbox,
@@ -1273,7 +1271,6 @@ Suggests: bioclipse,
libfreecontact-dev,
libfreecontact-doc,
libfreecontact-perl,
- libgoby-java,
libmaus2-dev,
libmilib-java,
libminimap-dev,
@@ -1292,30 +1289,32 @@ Suggests: bioclipse,
libtfbs-perl,
libxxsds-dynamic-dev,
octace-bioinfo,
- pangolearn,
python-biopython-doc,
python3-alignlib,
python3-bcbio,
python3-bel-resources,
python3-biopython-sql,
python3-cogent3,
+ python3-compclust,
python3-consensuscore2,
python3-cooler,
python3-ctdopts,
+ python3-ete3,
python3-galaxy-lib,
- python3-hyphy,
python3-intake,
python3-joypy,
- python3-loompy,
python3-mcaller,
python3-misopy,
python3-ncls,
python3-networkx,
+ python3-pangolearn,
python3-pycosat,
python3-pyflow,
python3-roadrunner,
python3-scanpy,
python3-seqcluster,
+ python3-skbio,
+ python3-torch,
python3-unifrac,
q2-alignment,
q2-composition,
@@ -1428,6 +1427,7 @@ 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,
@@ -1444,7 +1444,6 @@ Suggests: bioclipse,
r-cran-robustrankaggreg,
r-cran-rocr,
r-cran-rook,
- r-cran-rsgcc,
r-cran-rsvd,
r-cran-shazam,
r-cran-sitmo,
@@ -1569,7 +1568,6 @@ Recommends: abyss,
prodigal,
python3-biomaj3-cli,
python3-biopython,
- python3-cogent3,
qiime,
r-bioc-edger,
r-bioc-hilbertvis,
@@ -1607,7 +1605,8 @@ Suggests: bagpipe,
blast2,
cufflinks,
embassy-phylip,
- giira
+ giira,
+ python3-cogent3
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
@@ -1649,9 +1648,7 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: epigrass,
- python3-seirsplus,
- python3-torch,
+Recommends: python3-seirsplus,
python3-treetime,
r-cran-covid19us,
r-cran-diagnosismed,
@@ -1662,6 +1659,7 @@ Recommends: epigrass,
r-cran-epir,
r-cran-epitools,
r-cran-incidence,
+ r-cran-kernelheaping,
r-cran-lexrankr,
r-cran-seroincidence,
r-cran-sf,
@@ -1669,9 +1667,11 @@ Recommends: epigrass,
r-cran-surveillance
Suggests: chime,
epifire,
+ epigrass,
netepi-analysis,
netepi-collection,
python3-epimodels,
+ python3-torch,
r-cran-cmprsk,
r-cran-covid19,
r-cran-msm,
@@ -1723,7 +1723,6 @@ Recommends: aeskulap,
bart,
bart-view,
biosig-tools,
- camitk-imp,
ctn,
ctsim,
dcm2niix,
@@ -1732,12 +1731,10 @@ Recommends: aeskulap,
dicomnifti,
dicomscope,
gdf-tools,
- ginkgocadx,
gwyddion,
imagej,
invesalius,
ismrmrd-tools,
- itksnap,
king,
libgdcm-tools,
medcon,
@@ -1759,6 +1756,7 @@ Recommends: aeskulap,
plastimatch,
python3-dipy,
python3-nibabel,
+ python3-nipy,
python3-nipype,
python3-nitime,
python3-pydicom,
@@ -1778,6 +1776,7 @@ Suggests: afni,
bioimagexd,
blox,
brainvisa,
+ camitk-imp,
caret,
cdmedicpacs,
cellprofiler,
@@ -1804,13 +1803,16 @@ Suggests: afni,
fsl,
fslview,
gimias,
+ ginkgocadx,
hid,
+ illustrate,
imagemagick,
imagevis3d,
imview,
incf-nidash-oneclick-clients,
insightapplications,
isis,
+ itksnap,
jemris,
jist,
kradview,
@@ -1845,7 +1847,6 @@ Suggests: afni,
pngquant,
pymeg,
python3-mvpa2,
- python3-nipy,
science-workflow,
slicer,
sofa-apps,
@@ -1881,12 +1882,11 @@ Recommends: cimg-dev,
gmic,
libbart-dev,
libbiosig-dev,
- libcamitk-dev,
libcifti-dev,
libedf-dev,
libgdf-dev,
libgiftiio-dev,
- libinsighttoolkit4-dev,
+ libinsighttoolkit5-dev,
libismrmrd-dev,
libmaxflow-dev,
libmdc2-dev,
@@ -1898,15 +1898,13 @@ Recommends: cimg-dev,
libodil-dev,
libopenigtlink-dev,
libopenslide-dev,
- libopensurgsim-dev,
libpapyrus3-dev,
libsight-dev,
libteem-dev,
- libvigraimpex-dev,
libvistaio-dev,
libvolpack1-dev,
libvtk-dicom-dev,
- libvtk7-dev,
+ libvtk9-dev,
libxdf-dev,
octave-bart,
octave-dicom,
@@ -1920,15 +1918,16 @@ Recommends: cimg-dev,
python3-mia,
python3-mne,
python3-nibabel,
+ python3-nipy,
python3-nipype,
python3-nitime,
python3-openslide,
python3-pydicom,
python3-pyxnat,
- python3-vigra,
r-cran-rniftilib
Suggests: emokit,
libbio-formats-java,
+ libcamitk-dev,
libcamp-dev,
libctk-dev,
libcv-dev,
@@ -1941,15 +1940,17 @@ Suggests: emokit,
libnifti-doc,
libopenmeeg-dev,
libopenslide-java,
+ libopensurgsim-dev,
libsimpleitk1-dev,
libvia-dev,
+ libvigraimpex-dev,
libvmtk-dev,
- libvtk6-dev,
+ libvtk7-dev,
libxdffileio-dev,
python-vmtk,
python3-mvpa2,
- python3-nipy,
python3-simpleitk,
+ python3-vigra,
pytorch-vision,
tifffile
Description: Debian Med image processing and visualization packages development
@@ -2035,7 +2036,6 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: entangle,
- ginkgocadx,
gnumed-client,
gnumed-server,
libchipcard-tools,
@@ -2052,6 +2052,7 @@ Suggests: clearhealth,
freemed,
freemedforms-emr,
freeshim,
+ ginkgocadx,
libctapimkt1,
medintux,
mirrormed,
=====================================
dependency_data/debian-med_3.7.1.json
=====================================
@@ -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-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", 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["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", "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
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/e3424cb2671cf7102de4ca19bd2e5b7100c837a5...86a7efe0e263316c05164d39e1f20971b0e31d2c
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/e3424cb2671cf7102de4ca19bd2e5b7100c837a5...86a7efe0e263316c05164d39e1f20971b0e31d2c
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