[Blends-commit] [Git][blends-team/med][master] 6 commits: igdiscover will be removed from Debian
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Dec 10 17:57:51 GMT 2024
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
f59d4c6b by Andreas Tille at 2024-12-10T18:37:46+01:00
igdiscover will be removed from Debian
- - - - -
3ee8719e by Andreas Tille at 2024-12-10T18:39:15+01:00
Update dependencies
- - - - -
5810375f by Andreas Tille at 2024-12-10T18:39:55+01:00
Standards-Version: 4.7.0
- - - - -
a008087b by Andreas Tille at 2024-12-10T18:40:32+01:00
Rules-Requires-Root: no
- - - - -
784142bc by Andreas Tille at 2024-12-10T18:53:16+01:00
Automated changelog
- - - - -
8cb027ab by Andreas Tille at 2024-12-10T18:54:25+01:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/control.stub
- + dependency_data/debian-med_3.8.2.json
- tasks/bio
- tasks/bio-ngs
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-debian-med (3.8.2) UNRELEASED; urgency=medium
+debian-med (3.8.2) unstable; urgency=medium
* mriconvert removed from Debian
* r-cran-treescape replaced by r-cran-treespace
@@ -9,8 +9,66 @@ debian-med (3.8.2) UNRELEASED; urgency=medium
* Cleanup tasks from several removed packages
* remove epigrass since we need to package dash first
* squizz is removed from Debian
+ * igdiscover will be removed from Debian
+ * Standards-Version: 4.7.0
+ * Rules-Requires-Root: no
- -- Andreas Tille <tille at debian.org> Tue, 04 Jul 2023 10:23:01 +0200
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-bio
+ added:
+ Recommends: bifrost, deblur, r-cran-treespace, veryfasttree,
+ python3-bioxtasraw, ctffind
+ removed:
+ Recommends: squizz, r-cran-treescape, logol, igdiscover, raccoon,
+ r-cran-metamix
+ Suggests: epigrass
+ -med-bio-dev
+ added:
+ Suggests: cwltest, libbifrost-dev, libbiojava4-java
+ removed:
+ Recommends: libbiococoa-dev, r-cran-metamix, libbiojava4-java
+ Suggests: r-bioc-deseq
+ -med-bio-ngs
+ removed:
+ Recommends: igdiscover
+ -med-bio-phylogeny
+ added:
+ Recommends: fasttree, veryfasttree
+ -med-cloud
+ added:
+ Recommends: veryfasttree
+ removed:
+ Recommends: squizz
+ -med-covid-19
+ removed:
+ Recommends: conquest-common, pyomo, python3-typed-ast, epigrass,
+ aeskulap
+ -med-dental
+ removed:
+ Recommends: openmolar
+ -med-epi
+ removed:
+ Recommends: epigrass
+ -med-imaging
+ added:
+ Recommends: sightviewer, sightcalibrator
+ removed:
+ Recommends: dicomnifti, conquest-common, mriconvert, aeskulap
+ Suggests: conquest-sqlite, conquest-postgres, conquest-dbase,
+ conquest-mysql
+ -med-imaging-dev
+ removed:
+ Recommends: libmiaviewit-dev, r-cran-rniftilib
+ -med-pharmacy
+ removed:
+ Recommends: raccoon
+ -med-psychology
+ added:
+ Suggests: python3-pynwb
+
+ -- Andreas Tille <tille at debian.org> Tue, 10 Dec 2024 18:53:30 +0100
debian-med (3.8.1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -6,10 +6,10 @@ Section: misc
Priority: optional
Build-Depends-Indep: blends-dev (>= 0.7.5~),
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.6.2
-Rules-Requires-Root: no
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
+Rules-Requires-Root: no
Package: med-tasks
Architecture: all
@@ -102,6 +102,7 @@ Recommends: abacas,
amap-align,
ampliconnoise,
andi,
+ anfo,
any2fasta,
aragorn,
arden,
@@ -140,6 +141,7 @@ Recommends: abacas,
bedtools,
belvu,
berkeley-express,
+ bifrost,
bio-eagle,
bio-rainbow,
bio-tradis,
@@ -188,9 +190,11 @@ Recommends: abacas,
comet-ms,
concavity,
conservation-code,
+ coot,
covtobed,
crac,
csb,
+ ctffind,
cutadapt,
cutesv,
daligner,
@@ -198,6 +202,7 @@ Recommends: abacas,
datamash,
dawg,
dazzdb,
+ deblur,
delly,
density-fitness,
dextractor,
@@ -329,7 +334,6 @@ Recommends: abacas,
librg-utils-perl,
libvcflib-tools,
lighter,
- logol,
loki,
ltrsift,
lucy,
@@ -354,6 +358,7 @@ Recommends: abacas,
melting,
meryl,
metabat,
+ metaeuk,
metaphlan,
metastudent,
mhap,
@@ -458,6 +463,7 @@ Recommends: abacas,
populations,
porechop,
poretools,
+ pplacer,
prank,
predictnls,
presto,
@@ -499,6 +505,7 @@ Recommends: abacas,
pymol,
pyscanfcs,
python3-biomaj3-daemon,
+ python3-bioxtasraw,
python3-cogent3,
python3-emperor,
python3-geneimpacts,
@@ -547,7 +554,6 @@ Recommends: abacas,
r-cran-distory,
r-cran-genabel,
r-cran-kaos,
- r-cran-metamix,
r-cran-phangorn,
r-cran-phytools,
r-cran-pscbs,
@@ -561,7 +567,7 @@ Recommends: abacas,
r-cran-spp,
r-cran-tcr,
r-cran-tigger,
- r-cran-treescape,
+ r-cran-treespace,
r-cran-tsne,
r-cran-vegan,
r-cran-webgestaltr,
@@ -615,6 +621,7 @@ Recommends: abacas,
seaview,
seer,
segemehl,
+ sepp,
seqan-apps,
seqan-needle,
seqan-raptor,
@@ -643,6 +650,7 @@ Recommends: abacas,
snap,
snap-aligner,
sniffles,
+ snippy,
snp-sites,
snpeff,
snpomatic,
@@ -658,7 +666,6 @@ Recommends: abacas,
spoa,
sprai,
spread-phy,
- squizz,
sra-toolkit,
srst2,
ssake,
@@ -687,6 +694,7 @@ Recommends: abacas,
thesias,
tiddit,
tigr-glimmer,
+ tipp,
tm-align,
tnseq-transit,
toil,
@@ -706,9 +714,11 @@ Recommends: abacas,
trf,
trim-galore,
trimmomatic,
+ trinityrnaseq,
tvc,
twopaco,
uc-echo,
+ ugene,
umap-learn,
umis,
uncalled,
@@ -719,6 +729,8 @@ Recommends: abacas,
vcftools,
velvet | velvet-long,
velvetoptimiser,
+ veryfasttree,
+ vg,
virulencefinder,
vmatch,
vsearch,
@@ -735,7 +747,6 @@ Suggests: acacia,
agat,
amos-assembler,
amoscmp,
- anfo,
annovar,
apollo,
arachne,
@@ -770,7 +781,6 @@ Suggests: acacia,
condetri,
contrafold,
contralign,
- coot,
copycat,
covpipe,
crossbow,
@@ -790,7 +800,6 @@ Suggests: acacia,
emboss-explorer,
ensembl,
ensembl-vep,
- epigrass,
estferret,
euler-sr,
euler2,
@@ -824,7 +833,6 @@ Suggests: acacia,
hts-nim-tools,
idefix,
idseq-bench,
- igdiscover,
illustrate,
inspect,
jbrowse,
@@ -845,7 +853,6 @@ Suggests: acacia,
meme,
mesquite,
metabit,
- metaeuk,
metarep,
metastudent-data,
metastudent-data-2,
@@ -894,7 +901,6 @@ Suggests: acacia,
pipasic,
plato,
pomoxis,
- pplacer,
profit,
profphd,
prot4est,
@@ -998,7 +1004,6 @@ Suggests: acacia,
r-cran-sctransform,
r-other-apmswapp,
r-other-fastbaps,
- raccoon,
raxml-ng,
rbs-finder,
relion-cuda,
@@ -1013,7 +1018,6 @@ Suggests: acacia,
sailfish,
sap,
science-workflow,
- sepp,
seq-gen,
seq-seq-pan,
seqcluster,
@@ -1023,7 +1027,6 @@ Suggests: acacia,
sina,
sistr,
situs,
- snippy,
solvate,
sourmash,
sparta,
@@ -1040,23 +1043,19 @@ Suggests: acacia,
tetra,
tide,
tigr-glimmer-mg,
- tipp,
tn-seqexplorer,
tophat,
treebuilder3d,
- trinityrnaseq,
tripal,
trnascan-se,
twain,
ufasta,
- ugene,
umap,
unc-fish,
uniprime,
varmatch,
varscan,
vdjtools,
- vg,
vienna-rna,
viewmol,
vmd,
@@ -1109,9 +1108,7 @@ Recommends: bio-tradis,
libbio-tools-run-alignment-tcoffee-perl,
libbio-tools-run-remoteblast-perl,
libbio-variation-perl,
- libbiococoa-dev,
libbiojava-java,
- libbiojava4-java,
libbiojava6-java,
libbioparser-dev,
libblasr-dev,
@@ -1285,7 +1282,6 @@ Recommends: bio-tradis,
r-cran-genetics,
r-cran-gprofiler2,
r-cran-haplo.stats,
- r-cran-metamix,
r-cran-phangorn,
r-cran-pheatmap,
r-cran-phylobase,
@@ -1313,10 +1309,13 @@ Suggests: bioclipse,
ctdconverter,
cthreadpool-dev,
cwlformat,
+ cwltest,
libargs-dev,
libatomicqueue-dev,
libbam-dev,
libbbhash-dev,
+ libbifrost-dev,
+ libbiojava4-java,
libbiosoup-dev,
libbtllib-dev,
libcapsule-maven-nextflow-java,
@@ -1430,7 +1429,6 @@ Suggests: bioclipse,
r-bioc-ctc,
r-bioc-cummerbund,
r-bioc-dada2,
- r-bioc-deseq,
r-bioc-deseq2,
r-bioc-dnacopy,
r-bioc-ebseq,
@@ -1530,6 +1528,7 @@ Recommends: abyss,
altree,
amap-align,
ampliconnoise,
+ anfo,
aragorn,
arden,
autodock,
@@ -1651,7 +1650,6 @@ Recommends: abyss,
snap,
soapdenovo,
soapdenovo2,
- squizz,
sra-toolkit,
ssake,
staden-io-lib-utils,
@@ -1662,9 +1660,9 @@ Recommends: abyss,
tree-puzzle | tree-ppuzzle,
vcftools,
velvet,
+ veryfasttree,
wise
-Suggests: anfo,
- bagpipe,
+Suggests: bagpipe,
blast2,
cufflinks,
embassy-phylip,
@@ -1699,7 +1697,6 @@ Depends: ${misc:Depends},
med-tasks (= ${source:Version})
Recommends: entangle,
imagetooth
-Suggests: openmolar
Description: Debian Med packages related to dental practice
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
@@ -1731,7 +1728,6 @@ Recommends: python3-seirsplus,
r-cran-surveillance
Suggests: chime,
epifire,
- epigrass,
netepi-analysis,
netepi-collection,
python3-epimodels,
@@ -1781,17 +1777,17 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: aeskulap,
- amide,
+Recommends: amide,
+ ants,
bart,
bart-view,
biosig-tools,
+ camitk-imp,
ctn,
ctsim,
dcm2niix,
dcmtk,
dicom3tools,
- dicomnifti,
dicomscope,
gdf-tools,
gwyddion,
@@ -1803,10 +1799,8 @@ Recommends: aeskulap,
libgdcm-tools,
medcon,
mia-tools,
- mia-viewit,
mialmpick,
minc-tools,
- mriconvert,
mricron,
mrtrix3,
nifti-bin,
@@ -1825,6 +1819,8 @@ Recommends: aeskulap,
python3-pydicom,
python3-pyxid,
python3-surfer,
+ sightcalibrator,
+ sightviewer,
sigviewer,
teem-apps,
tifffile,
@@ -1832,23 +1828,16 @@ Recommends: aeskulap,
vtk-dicom-tools,
xmedcon
Suggests: afni,
- ants,
bart-cuda,
bioimagesuite,
bioimagexd,
blox,
brainvisa,
- camitk-imp,
caret,
cdmedicpacs,
cellprofiler,
cmtk,
connectomeviewer,
- conquest-common,
- conquest-dbase,
- conquest-mysql,
- conquest-postgres,
- conquest-sqlite,
crea,
dcm4chee,
devide,
@@ -1884,6 +1873,7 @@ Suggests: afni,
mayam,
medisnap,
mesa-test-tools,
+ mia-viewit,
micromanager,
mipav,
miview,
@@ -1944,6 +1934,7 @@ Recommends: cimg-dev,
gmic,
libbart-dev,
libbiosig-dev,
+ libcamitk-dev,
libcifti-dev,
libedf-dev,
libgdf-dev,
@@ -1954,7 +1945,6 @@ Recommends: cimg-dev,
libmdc2-dev,
libmia-2.4-dev,
libmialm-dev,
- libmiaviewit-dev,
libminc-dev,
libnifti2-dev,
libodil-dev,
@@ -1991,11 +1981,9 @@ Recommends: cimg-dev,
python3-pydicom,
python3-pyxnat,
python3-torchvision,
- python3-vigra,
- r-cran-rniftilib
+ python3-vigra
Suggests: emokit,
libbio-formats-java,
- libcamitk-dev,
libcamp-dev,
libctk-dev,
libeegdev-dev,
@@ -2056,7 +2044,6 @@ Depends: ${misc:Depends},
Recommends: chemtool,
r-cran-dosefinding,
r-cran-rpact
-Suggests: raccoon
Description: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
collection of software and documentation which is useful for
@@ -2137,6 +2124,7 @@ Depends: ${misc:Depends},
Recommends: orthanc-neuro,
praat,
psignifit,
+ psychopy,
python3-bioxtasraw,
r-cran-foreign,
r-cran-psy,
@@ -2144,10 +2132,10 @@ Recommends: orthanc-neuro,
r-cran-psychometric,
r-cran-psychotree,
r-cran-psyphy
-Suggests: psychopy,
- python-pyepl,
+Suggests: python-pyepl,
python3-bids-validator,
python3-bmtk,
+ python3-pynwb,
science-psychophysics
Description: Debian Med packages for psychology
This metapackage contains dependencies for a collection of software
=====================================
debian/control.stub
=====================================
@@ -5,9 +5,10 @@ Section: misc
Priority: optional
Build-Depends-Indep: blends-dev (>= 0.7.5~),
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
+Rules-Requires-Root: no
Package: med-tasks
Architecture: all
=====================================
dependency_data/debian-med_3.8.2.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", "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-db-seqfeature-perl", "libbio-featureio-perl", "libbio-tools-run-remoteblast-perl", "libbio-variation-perl", "libace-perl", "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", "python3-pyspoa", "libjebl2-java", "r-cran-boolnet", "r-cran-corrplot", "r-cran-distory", 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"r-bioc-cner", "r-bioc-cummerbund", "r-bioc-deseq2", "r-bioc-edger", "r-bioc-genefilter", "r-bioc-geoquery", "r-bioc-hilbertvis", "r-bioc-htsfilter", "r-bioc-impute", "r-bioc-limma", "r-bioc-megadepth", "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-phangorn", "r-cran-phytools", "r-cran-pscbs", "r-cran-seurat", "r-cran-seqinr", "r-cran-spp", "r-cran-treespace", "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", "savvy-util", "scrappie", "scrm", "seer", "segemehl", "sepp", "tipp", "seq-seq-pan", "seqkit", "seqmagick", "seqprep", "seqsero", "seqtk", "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", "snippy", "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", "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"], "conflicts": [], "breaks": [], "ignore": ["mozilla-biofox", "riso", "catissuecore", "trapss"], "avoid": []}, "dental": {"depends": [], "suggests": [], "recommends": ["imagetooth", "entangle"], "conflicts": [], "breaks": [], "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", "libmialm-dev", "python3-mia", "libopenigtlink-dev", "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", "python3-torchvision", "libsight-dev", "python3-bioxtasraw"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "research": {"depends": [], "suggests": [], "recommends": ["r-cran-rpact", "openclinica"], "conflicts": [], "breaks": [], "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"], "conflicts": [], "breaks": [], "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"], "conflicts": [], "breaks": [], "ignore": ["clearhealth"], "avoid": []}, "tools": {"depends": [], "suggests": ["mencal", "entangle", "goldencheetah", "oscar"], "recommends": ["pcalendar", "cycle", "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"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "cms": {"depends": [], "suggests": ["zope-zms", "hid"], "recommends": ["xnat"], "conflicts": [], "breaks": [], "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"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "psychology": {"depends": [], "suggests": ["science-psychophysics", "python-pyepl", "python3-bmtk", "python3-bids-validator", "python3-pynwb"], "recommends": ["praat", "r-cran-foreign", "psignifit", "r-cran-psy", "psychopy", "r-cran-psych", "r-cran-psychometric", "r-cran-psychotree", "r-cran-psyphy", "orthanc-neuro", "python3-bioxtasraw"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "bio-phylogeny": {"depends": [], "suggests": ["python3-treetime"], "recommends": ["altree", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle", "fasttree", "veryfasttree", "probalign", "treeviewx", "phylip", "muscle", "muscle3", "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"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "imaging": {"depends": [], "suggests": ["imagemagick", "pngquant", "imview", "trimage", "illustrate", "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", "imagej", "minc-tools", "medcon", "python3-nibabel", "python3-pydicom", "xmedcon", "dcmtk", "sightviewer", "sightcalibrator", "nifti-bin", "heudiconv", "fsl", "fslview", "via-bin", "gwyddion", "sofa-apps", "python3-nipy", "python3-nipype", "python3-nitime", "caret", "libgdcm-tools", "slicer", "lipsia", "dicom3tools", "imagevis3d", "odin", "dicomscope", "pixelmed-apps", "vmtk", "ginkgocadx", "openslide-tools", "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", "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"], "conflicts": [], "breaks": [], "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", "muscle3", "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", "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", "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", "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", "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"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "rehabilitation": {"depends": [], "suggests": ["aghermann"], "recommends": ["sitplus"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "laboratory": {"depends": [], "suggests": [], "recommends": ["opencfu", "orthanc-wsi", "openelis", "openfreezer", "catissuesuite"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "pharmacy": {"depends": [], "suggests": [], "recommends": ["chemtool", "r-cran-dosefinding", "r-cran-rpact"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "data": {"depends": [], "suggests": ["oscar"], "recommends": ["freediams", "freemedforms-freedata", "python3-hl7", "drugref.org"], "conflicts": [], "breaks": [], "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"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}, "epi": {"depends": [], "suggests": ["r-cran-msm", "r-cran-cmprsk", "shiny-server", "python3-epimodels", "repast"], "recommends": ["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"], "conflicts": [], "breaks": [], "ignore": [], "avoid": []}}
\ No newline at end of file
=====================================
tasks/bio
=====================================
@@ -788,8 +788,6 @@ Recommends: idba
Recommends: idefix
-Recommends: igdiscover
-
Suggests: idseq-bench
Recommends: indelible
=====================================
tasks/bio-ngs
=====================================
@@ -130,8 +130,6 @@ Recommends: hisat2
Recommends: idba
-Recommends: igdiscover
-
Recommends: igv
Recommends: iva
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/4861ebc68eaa90ed58439c3f1c0396e44b7bb672...8cb027abf31f015419d57963865636443ff16ada
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/4861ebc68eaa90ed58439c3f1c0396e44b7bb672...8cb027abf31f015419d57963865636443ff16ada
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