[Blends-commit] [Git][blends-team/med][master] 3 commits: Re-render dependencies (med-research was manually kept)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon May 5 20:34:47 BST 2025
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
2787465d by Andreas Tille at 2025-05-05T21:29:28+02:00
Re-render dependencies (med-research was manually kept)
- - - - -
7e343143 by Andreas Tille at 2025-05-05T21:31:52+02:00
Add dependency data - no manual changes to mention in d/changelog
- - - - -
ff56ad7c by Andreas Tille at 2025-05-05T21:33:05+02:00
Upload to unstable
- - - - -
3 changed files:
- debian/changelog
- debian/control
- + dependency_data/debian-med_3.9.0.json
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+debian-med (3.9.0) unstable; urgency=medium
+
+ * Re-render dependencies (med-research was manually kept)
+
+ -- Andreas Tille <tille at debian.org> Mon, 05 May 2025 21:32:16 +0200
+
debian-med (3.8.2) unstable; urgency=medium
* mriconvert removed from Debian
=====================================
debian/control
=====================================
@@ -91,7 +91,6 @@ Depends: ${misc:Depends},
Recommends: abacas,
abpoa,
abyss,
- acedb-other,
adapterremoval,
adun-core,
aegean,
@@ -102,7 +101,6 @@ Recommends: abacas,
amap-align,
ampliconnoise,
andi,
- anfo,
any2fasta,
aragorn,
arden,
@@ -124,7 +122,6 @@ Recommends: abacas,
axe-demultiplexer,
baitfisher,
bali-phy,
- ballview,
bamclipper,
bamkit,
bamtools,
@@ -163,7 +160,6 @@ Recommends: abacas,
busco,
bustools,
bwa,
- canu,
cassiopee,
cat-bat,
cct,
@@ -176,7 +172,6 @@ Recommends: abacas,
chromhmm,
chromimpute,
cif-tools,
- circlator,
circos,
clearcut,
clonalframe,
@@ -255,7 +250,6 @@ Recommends: abacas,
freecontact,
fsa,
fsm-lite,
- gamgi,
garli,
garlic,
gasic,
@@ -272,7 +266,6 @@ Recommends: abacas,
gff2ps,
gffread,
ggd-utils,
- ghemical,
ghmm,
glam2,
gmap,
@@ -285,7 +278,6 @@ Recommends: abacas,
gwama,
harvest-tools,
hhsuite,
- hilive,
hinge,
hisat2,
hmmer,
@@ -305,12 +297,10 @@ Recommends: abacas,
jalview,
jellyfish,
jellyfish1,
- jmodeltest,
jmol,
kalign,
kallisto,
kaptive,
- khmer,
kineticstools,
king-probe,
kissplice,
@@ -330,7 +320,6 @@ Recommends: abacas,
lastz,
leaff,
lefse,
- libpwiz-tools,
librg-utils-perl,
libvcflib-tools,
lighter,
@@ -364,7 +353,6 @@ Recommends: abacas,
mhap,
microbegps,
microbiomeutil,
- mindthegap,
minexpert2,
minia,
miniasm,
@@ -377,7 +365,6 @@ Recommends: abacas,
mlv-smile,
mmb,
mmseqs2,
- mosdepth,
mothur,
mptp,
mrbayes,
@@ -389,9 +376,7 @@ Recommends: abacas,
mustang,
nanofilt,
nanolyse,
- nanook,
nanopolish,
- nanostat,
nanosv,
nast-ier,
ncbi-acc-download,
@@ -423,10 +408,7 @@ Recommends: abacas,
parsnp,
patman,
pbdagcon,
- pbhoney,
- pbjelly,
pbsim,
- pbsuite,
pdb2pqr,
perlprimer,
perm,
@@ -463,7 +445,6 @@ Recommends: abacas,
populations,
porechop,
poretools,
- pplacer,
prank,
predictnls,
presto,
@@ -506,7 +487,6 @@ Recommends: abacas,
pyscanfcs,
python3-biomaj3-daemon,
python3-bioxtasraw,
- python3-cogent3,
python3-emperor,
python3-geneimpacts,
python3-gffutils,
@@ -517,7 +497,6 @@ Recommends: abacas,
pyvcf,
qcat,
qcumber,
- qiime,
qtltools,
quicktree,
quorum,
@@ -552,7 +531,6 @@ Recommends: abacas,
r-cran-ape,
r-cran-bio3d,
r-cran-distory,
- r-cran-genabel,
r-cran-kaos,
r-cran-phangorn,
r-cran-phytools,
@@ -587,10 +565,8 @@ Recommends: abacas,
raxml,
ray,
rdp-alignment,
- rdp-classifier,
rdp-readseq,
readseq,
- readucks,
reapr,
recan,
relion,
@@ -621,7 +597,6 @@ Recommends: abacas,
seaview,
seer,
segemehl,
- sepp,
seqan-apps,
seqan-needle,
seqan-raptor,
@@ -660,6 +635,7 @@ Recommends: abacas,
soapdenovo2,
soapsnp,
sortmerna,
+ sourmash,
spaced,
spades,
spaln,
@@ -694,7 +670,6 @@ Recommends: abacas,
thesias,
tiddit,
tigr-glimmer,
- tipp,
tm-align,
tnseq-transit,
toil,
@@ -719,8 +694,6 @@ Recommends: abacas,
twopaco,
uc-echo,
ugene,
- umap-learn,
- umis,
uncalled,
unicycler,
unikmer,
@@ -730,7 +703,6 @@ Recommends: abacas,
velvet | velvet-long,
velvetoptimiser,
veryfasttree,
- vg,
virulencefinder,
vmatch,
vsearch,
@@ -743,10 +715,12 @@ Recommends: abacas,
yanagiba,
yanosim
Suggests: acacia,
+ acedb-other,
adun.app,
agat,
amos-assembler,
amoscmp,
+ anfo,
annovar,
apollo,
arachne,
@@ -756,6 +730,7 @@ Suggests: acacia,
axparafit,
axpcoords,
bagpipe,
+ ballview,
bambus,
bax2bam,
bcbio,
@@ -770,11 +745,13 @@ Suggests: acacia,
btk-core,
cactus,
caftools,
+ canu,
card-rgi,
catfishq,
cdna-db,
cellprofiler,
cinema,
+ circlator,
cluster3,
cmap,
conda-package-handling,
@@ -813,6 +790,7 @@ Suggests: acacia,
forester,
forge,
galaxy,
+ gamgi,
gatk,
gbrowse-syn,
genemark,
@@ -822,6 +800,7 @@ Suggests: acacia,
genographer,
gerp++,
getdata,
+ ghemical,
glimmerhmm,
gmv,
gramalign,
@@ -829,6 +808,7 @@ Suggests: acacia,
graphmap2,
haploview,
hawkeye,
+ hilive,
htqc,
hts-nim-tools,
idefix,
@@ -837,9 +817,12 @@ Suggests: acacia,
inspect,
jbrowse,
jigsaw,
+ jmodeltest,
kempbasu,
+ khmer,
libhdf5-dev,
libhnswlib-dev,
+ libpwiz-tools,
lofreq,
mach-haplotyper,
mage2tab,
@@ -857,11 +840,13 @@ Suggests: acacia,
metastudent-data,
metastudent-data-2,
migrate,
+ mindthegap,
minimus,
mirbase,
modeller,
molekel,
mosaik-aligner,
+ mosdepth,
mpsqed,
mrs,
msatfinder,
@@ -871,7 +856,9 @@ Suggests: acacia,
nano-snakemake,
nanocall,
nanocomp,
+ nanook,
nanoplot,
+ nanostat,
ncbi-magicblast,
nextsv,
ngila,
@@ -889,6 +876,9 @@ Suggests: acacia,
partigene,
partitionfinder,
patristic,
+ pbhoney,
+ pbjelly,
+ pbsuite,
pcma,
pfaat,
phagefinder,
@@ -901,6 +891,7 @@ Suggests: acacia,
pipasic,
plato,
pomoxis,
+ pplacer,
profit,
profphd,
prot4est,
@@ -912,6 +903,7 @@ Suggests: acacia,
python3-alignlib,
python3-anndata,
python3-cgecore,
+ python3-cogent3,
python3-cyvcf2,
python3-deeptools,
python3-deeptoolsintervals,
@@ -954,6 +946,7 @@ Suggests: acacia,
q2-vsearch,
q2cli,
q2templates,
+ qiime,
qtlcart,
qtlreaper,
qualimap,
@@ -993,6 +986,7 @@ Suggests: acacia,
r-cran-epir,
r-cran-fitdistrplus,
r-cran-forecast,
+ r-cran-genabel,
r-cran-gprofiler2,
r-cran-minerva,
r-cran-optimalcutpoints,
@@ -1006,6 +1000,8 @@ Suggests: acacia,
r-other-fastbaps,
raxml-ng,
rbs-finder,
+ rdp-classifier,
+ readucks,
relion-cuda,
relion-gui-cuda,
repeatmasker,
@@ -1018,6 +1014,7 @@ Suggests: acacia,
sailfish,
sap,
science-workflow,
+ sepp,
seq-gen,
seq-seq-pan,
seqcluster,
@@ -1028,7 +1025,6 @@ Suggests: acacia,
sistr,
situs,
solvate,
- sourmash,
sparta,
splitstree,
ssaha,
@@ -1043,6 +1039,7 @@ Suggests: acacia,
tetra,
tide,
tigr-glimmer-mg,
+ tipp,
tn-seqexplorer,
tophat,
treebuilder3d,
@@ -1051,11 +1048,14 @@ Suggests: acacia,
twain,
ufasta,
umap,
+ umap-learn,
+ umis,
unc-fish,
uniprime,
varmatch,
varscan,
vdjtools,
+ vg,
vienna-rna,
viewmol,
vmd,
@@ -1165,7 +1165,6 @@ Recommends: bio-tradis,
libpbseq-dev,
libpdb-redo-dev,
libpll-dev,
- libpwiz-dev,
libqes-dev,
librcsb-core-wrapper0-dev,
librdp-taxonomy-tree-java,
@@ -1198,13 +1197,9 @@ Recommends: bio-tradis,
libzerg-perl,
libzerg0-dev,
mcl,
- nim-hts-dev,
- nim-kexpr-dev,
- nim-lapper-dev,
ont-fast5-api,
pyfai,
python3-airr,
- python3-anndata,
python3-bcbio-gff,
python3-bioframe,
python3-biom-format,
@@ -1214,8 +1209,6 @@ Recommends: bio-tradis,
python3-bx,
python3-cgecore,
python3-cigar,
- python3-cobra,
- python3-cogent3,
python3-cooler,
python3-corepywrap,
python3-csb,
@@ -1234,7 +1227,6 @@ Recommends: bio-tradis,
python3-htseq,
python3-intervaltree-bio,
python3-kineticstools,
- python3-loompy,
python3-mirtop,
python3-nanoget,
python3-ngs,
@@ -1342,6 +1334,7 @@ Suggests: bioclipse,
libnexml-java,
libngs-sdk-dev,
libpbcopper-dev,
+ libpwiz-dev,
libqcpp-dev,
librelion-dev,
libroadrunner-dev,
@@ -1355,14 +1348,20 @@ Suggests: bioclipse,
libtfbs-perl,
libvbz-hdf-plugin-dev,
libxxsds-dynamic-dev,
+ nim-hts-dev,
+ nim-kexpr-dev,
+ nim-lapper-dev,
octace-bioinfo,
python-biopython-doc,
python3-alignlib,
+ python3-anndata,
python3-bcbio,
python3-bel-resources,
python3-bioblend,
python3-biopython-sql,
python3-cgelib,
+ python3-cobra,
+ python3-cogent3,
python3-compclust,
python3-conda-package-streaming,
python3-consensuscore2,
@@ -1370,6 +1369,7 @@ Suggests: bioclipse,
python3-galaxy-lib,
python3-intake,
python3-joypy,
+ python3-loompy,
python3-misopy,
python3-ncls,
python3-networkx,
@@ -1522,13 +1522,11 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: abyss,
- acedb-other,
aevol,
alien-hunter,
altree,
amap-align,
ampliconnoise,
- anfo,
aragorn,
arden,
autodock,
@@ -1629,8 +1627,6 @@ Recommends: abyss,
prodigal,
python3-biomaj3-cli,
python3-biopython,
- python3-cogent3,
- qiime,
r-bioc-edger,
r-bioc-hilbertvis,
r-cran-pvclust,
@@ -1662,11 +1658,15 @@ Recommends: abyss,
velvet,
veryfasttree,
wise
-Suggests: bagpipe,
+Suggests: acedb-other,
+ anfo,
+ bagpipe,
blast2,
cufflinks,
embassy-phylip,
- giira
+ giira,
+ python3-cogent3,
+ qiime
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
@@ -1724,7 +1724,6 @@ Recommends: python3-seirsplus,
r-cran-prevalence,
r-cran-seroincidence,
r-cran-sf,
- r-cran-sjplot,
r-cran-surveillance
Suggests: chime,
epifire,
@@ -1734,6 +1733,7 @@ Suggests: chime,
r-cran-cmprsk,
r-cran-covid19,
r-cran-msm,
+ r-cran-sjplot,
repast,
shiny-server,
ushahidi
@@ -1798,8 +1798,6 @@ Recommends: amide,
king,
libgdcm-tools,
medcon,
- mia-tools,
- mialmpick,
minc-tools,
mricron,
mrtrix3,
@@ -1818,7 +1816,6 @@ Recommends: amide,
python3-nitime,
python3-pydicom,
python3-pyxid,
- python3-surfer,
sightcalibrator,
sightviewer,
sigviewer,
@@ -1873,7 +1870,9 @@ Suggests: afni,
mayam,
medisnap,
mesa-test-tools,
+ mia-tools,
mia-viewit,
+ mialmpick,
micromanager,
mipav,
miview,
@@ -1899,6 +1898,7 @@ Suggests: afni,
piano,
pngquant,
pymeg,
+ python3-surfer,
science-workflow,
slicer,
sofa-apps,
@@ -1943,7 +1943,6 @@ Recommends: cimg-dev,
libismrmrd-dev,
libmaxflow-dev,
libmdc2-dev,
- libmia-2.4-dev,
libmialm-dev,
libminc-dev,
libnifti2-dev,
@@ -1971,7 +1970,6 @@ Recommends: cimg-dev,
python3-dipy,
python3-gdcm,
python3-imageio,
- python3-mia,
python3-mne,
python3-nibabel,
python3-nipy,
@@ -1980,8 +1978,7 @@ Recommends: cimg-dev,
python3-openslide,
python3-pydicom,
python3-pyxnat,
- python3-torchvision,
- python3-vigra
+ python3-torchvision
Suggests: emokit,
libbio-formats-java,
libcamp-dev,
@@ -1991,6 +1988,7 @@ Suggests: emokit,
libgdcm2-dev,
libics-dev,
liblimereg-dev,
+ libmia-2.4-dev,
libmni-perllib-perl,
libnifti-doc,
libopenmeeg-dev,
@@ -1999,6 +1997,8 @@ Suggests: emokit,
libvmtk-dev,
libxdffileio-dev,
python-vmtk,
+ python3-mia,
+ python3-vigra,
tifffile
Description: Debian Med image processing and visualization packages development
This metapackage will install Debian packages which might be useful
@@ -2042,8 +2042,8 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: chemtool,
- r-cran-dosefinding,
- r-cran-rpact
+ r-cran-dosefinding
+Suggests: r-cran-rpact
Description: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
collection of software and documentation which is useful for
@@ -2124,7 +2124,6 @@ Depends: ${misc:Depends},
Recommends: orthanc-neuro,
praat,
psignifit,
- psychopy,
python3-bioxtasraw,
r-cran-foreign,
r-cran-psy,
@@ -2132,7 +2131,8 @@ Recommends: orthanc-neuro,
r-cran-psychometric,
r-cran-psychotree,
r-cran-psyphy
-Suggests: python-pyepl,
+Suggests: psychopy,
+ python-pyepl,
python3-bids-validator,
python3-bmtk,
python3-pynwb,
@@ -2147,8 +2147,7 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: r-cran-rpact
-Suggests: openclinica
+Suggests: r-cran-rpact, openclinica
Description: Debian Med packages for medical research
This metapackage will install tools that are useful for
medical research.
@@ -2194,7 +2193,6 @@ Recommends: cronometer,
python3-fitbit,
quitcount,
r-cran-fitbitscraper,
- r-cran-fitcoach,
wgerman-medical,
workrave
Suggests: entangle,
@@ -2204,7 +2202,8 @@ Suggests: entangle,
nut-nutrition,
oscar,
pesco,
- pondus
+ pondus,
+ r-cran-fitcoach
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
=====================================
dependency_data/debian-med_3.9.0.json
=====================================
@@ -0,0 +1 @@
+{"bio-dev": {"depends": [], "suggests": ["conda-package-handling", "python3-conda-package-streaming", "cwlformat", "cwltest", "python3-biopython-sql", "python-biopython-doc", "python3-joypy", "python3-ncls", "python3-pycosat", "libbiojava4-java", "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-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", "capsule-nextflow", "libcapsule-maven-nextflow-java", "libgatk-bwamem-java", "libgatk-bwamem-jni", "libgatk-fermilite-java", "libgatk-fermilite-jni", "libgenomicsdb-java", "libgenomicsdb-dev", "libgatk-native-bindings-java", "libicb-utils-java", "libbiosoup-dev", "libvbz-hdf-plugin-dev", "python3-bioblend", "libterraces-dev", "libbtllib-dev", "libsavvy-dev", "python3-cgelib", "libbifrost-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", "libbiojava6-java", 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\ No newline at end of file
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/8cb027abf31f015419d57963865636443ff16ada...ff56ad7c25a46244e1fe28e08373cc987957ef74
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View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/8cb027abf31f015419d57963865636443ff16ada...ff56ad7c25a46244e1fe28e08373cc987957ef74
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