[Blends-commit] [Git][blends-team/med][master] 5 commits: Rename debian/NEWS.debian to debian/NEWS
Andreas Tille
gitlab at salsa.debian.org
Mon Mar 1 10:34:59 GMT 2021
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
626d8b9f by Andreas Tille at 2021-03-01T11:18:04+01:00
Rename debian/NEWS.debian to debian/NEWS
- - - - -
021dc5a4 by Andreas Tille at 2021-03-01T11:25:56+01:00
Update to status of package pool
- - - - -
c8963160 by Andreas Tille at 2021-03-01T11:27:02+01:00
Dependency data and changelog entry
- - - - -
0d63c4d6 by Andreas Tille at 2021-03-01T11:33:19+01:00
NEWS is renamed
- - - - -
59f1f322 by Andreas Tille at 2021-03-01T11:34:12+01:00
Upload to unstable
- - - - -
5 changed files:
- debian/NEWS.Debian → debian/NEWS
- debian/changelog
- debian/control
- debian/med-config.docs
- + dependency_data/debian-med_3.6.2.json
Changes:
=====================================
debian/NEWS.Debian → debian/NEWS
=====================================
=====================================
debian/changelog
=====================================
@@ -1,8 +1,27 @@
-debian-med (3.6.2) UNRELEASED; urgency=medium
+debian-med (3.6.2) unstable; urgency=medium
* DEP5 copyright
+ * Rename debian/NEWS.debian to debian/NEWS
- -- Andreas Tille <tille at debian.org> Mon, 21 Dec 2020 18:48:35 +0100
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-bio
+ removed:
+ Recommends: pbgenomicconsensus, unanimity, dindel
+ -med-bio-dev
+ added:
+ Suggests: libxxsds-dynamic-dev, r-bioc-affxparser,
+ r-bioc-oligoclasses, r-bioc-gseabase, r-bioc-arrayexpress,
+ r-bioc-oligo, r-bioc-gsva
+ removed:
+ Recommends: seqan-dev
+ Suggests: libdynamic-dev
+ -med-bio-ngs
+ removed:
+ Recommends: dindel
+
+ -- Andreas Tille <tille at debian.org> Mon, 01 Mar 2021 11:33:28 +0100
debian-med (3.6.1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -143,6 +143,7 @@ Recommends: abacas,
biobambam2,
biosyntax,
bitseq,
+ blasr,
blixem,
bolt-lmm,
bowtie,
@@ -245,6 +246,7 @@ Recommends: abacas,
gatb-core,
gbrowse,
gdpc,
+ gemma,
genometester,
genomethreader,
genometools,
@@ -254,6 +256,7 @@ Recommends: abacas,
gffread,
ggd-utils,
ghemical,
+ ghmm,
glam2,
gmap,
grabix,
@@ -281,6 +284,7 @@ Recommends: abacas,
iqtree,
iva,
jaligner,
+ jalview,
jellyfish,
jellyfish1,
jmodeltest,
@@ -316,6 +320,7 @@ Recommends: abacas,
lucy,
lumpy-sv,
macs,
+ macsyfinder,
maffilter,
mafft,
mapdamage,
@@ -344,10 +349,12 @@ Recommends: abacas,
mira-assembler,
mirtop,
mlv-smile,
+ mmb,
mmseqs2,
mosdepth,
mothur,
mptp,
+ mrbayes,
msxpertsuite,
multiqc,
mummer,
@@ -384,9 +391,14 @@ Recommends: abacas,
paml,
paraclu,
parasail,
+ parsinsert,
parsnp,
patman,
+ pbdagcon,
+ pbhoney,
+ pbjelly,
pbsim,
+ pbsuite,
pdb2pqr,
perlprimer,
perm,
@@ -411,6 +423,7 @@ Recommends: abacas,
pirs,
pizzly,
placnet,
+ plasmidid,
plasmidomics,
plasmidseeker,
plast,
@@ -457,6 +470,7 @@ Recommends: abacas,
psortb,
pycoqc,
pycorrfit,
+ pymol,
pyscanfcs,
python3-biomaj3-daemon,
python3-geneimpacts,
@@ -467,6 +481,7 @@ Recommends: abacas,
python3-treetime,
pyvcf,
qcat,
+ qcumber,
qiime,
qtltools,
quicktree,
@@ -494,6 +509,7 @@ Recommends: abacas,
r-bioc-pcamethods,
r-bioc-phyloseq,
r-bioc-rtracklayer,
+ r-bioc-scater,
r-bioc-tfbstools,
r-cran-adegenet,
r-cran-adephylo,
@@ -512,6 +528,7 @@ Recommends: abacas,
r-cran-samr,
r-cran-sdmtools,
r-cran-seqinr,
+ r-cran-seurat,
r-cran-shazam,
r-cran-spp,
r-cran-tcr,
@@ -577,16 +594,21 @@ Recommends: abacas,
seqsero,
seqtk,
sga,
+ shasta,
+ shovill,
sibelia,
sibsim4,
sickle,
sigma-align,
sim4,
sim4db,
+ simka,
+ simkamin,
skesa,
skewer,
smalt,
smithwaterman,
+ smrtanalysis,
snap,
snap-aligner,
sniffles,
@@ -643,6 +665,7 @@ Recommends: abacas,
transdecoder,
transrate-tools,
transtermhp,
+ tree-puzzle | tree-ppuzzle,
treeview,
treeviewx,
trf,
@@ -651,6 +674,7 @@ Recommends: abacas,
trinityrnaseq,
tvc,
uc-echo,
+ umap-learn,
umis,
unicycler,
varna,
@@ -663,6 +687,7 @@ Recommends: abacas,
vmatch,
vsearch,
vt,
+ wham-align,
wigeon,
wise,
yaha,
@@ -690,7 +715,6 @@ Suggests: acacia,
big-blast,
bigsdb,
bismark,
- blasr,
blat,
blimps-utils,
blobology,
@@ -746,7 +770,6 @@ Suggests: acacia,
gassst,
gatk,
gbrowse-syn,
- gemma,
genemark,
genesplicer,
genetrack,
@@ -754,7 +777,6 @@ Suggests: acacia,
genographer,
gerp++,
getdata,
- ghmm,
glimmerhmm,
gmv,
gramalign,
@@ -768,7 +790,6 @@ Suggests: acacia,
idseq-bench,
igv,
inspect,
- jalview,
jbrowse,
jigsaw,
kempbasu,
@@ -776,7 +797,6 @@ Suggests: acacia,
libhnswlib-dev,
lofreq,
mach-haplotyper,
- macsyfinder,
mage2tab,
maker2,
malt,
@@ -796,12 +816,10 @@ Suggests: acacia,
migrate,
minimus,
mirbase,
- mmb,
modeller,
molekel,
mosaik-aligner,
mpsqed,
- mrbayes,
mrs,
msatfinder,
mugsy,
@@ -825,15 +843,9 @@ Suggests: acacia,
optitype,
paipline,
pangolin,
- parsinsert,
partigene,
partitionfinder,
patristic,
- pbdagcon,
- pbgenomicconsensus,
- pbhoney,
- pbjelly,
- pbsuite,
pcma,
pfaat,
phagefinder,
@@ -844,7 +856,6 @@ Suggests: acacia,
phylowin,
pigx-scrnaseq,
pipasic,
- plasmidid,
plato,
pomoxis,
profit,
@@ -854,7 +865,6 @@ Suggests: acacia,
pssh2,
pufferfish,
purple,
- pymol,
pyrophosphate-tools,
python3-alignlib,
python3-anndata,
@@ -903,7 +913,6 @@ Suggests: acacia,
q2-vsearch,
q2cli,
q2templates,
- qcumber,
qtlcart,
qtlreaper,
qualimap,
@@ -930,7 +939,6 @@ Suggests: acacia,
r-bioc-org.rn.eg.db,
r-bioc-qusage,
r-bioc-savr,
- r-bioc-scater,
r-bioc-singlecellexperiment,
r-bioc-tximport,
r-cran-amap,
@@ -952,7 +960,6 @@ Suggests: acacia,
r-cran-rentrez,
r-cran-rsgcc,
r-cran-sctransform,
- r-cran-seurat,
r-other-apmswapp,
r-other-fastbaps,
raccoon,
@@ -975,16 +982,11 @@ Suggests: acacia,
seqcluster,
sequenceconverter.app,
seqwish,
- shasta,
- shovill,
sift,
signalalign,
- simka,
- simkamin,
sina,
sistr,
situs,
- smrtanalysis,
snpeff,
solvate,
sourmash,
@@ -1003,7 +1005,6 @@ Suggests: acacia,
tigr-glimmer-mg,
tn-seqexplorer,
tophat,
- tree-puzzle | tree-ppuzzle,
treebuilder3d,
tripal,
trnascan-se,
@@ -1011,8 +1012,6 @@ Suggests: acacia,
ufasta,
ugene,
umap,
- umap-learn,
- unanimity,
unc-fish,
uniprime,
varmatch,
@@ -1021,7 +1020,6 @@ Suggests: acacia,
vienna-rna,
viewmol,
vmd,
- wham-align,
x-tandem-pipeline,
zodiac-zeden
Description: Debian Med bioinformatics packages
@@ -1037,6 +1035,7 @@ Depends: ${misc:Depends},
Recommends: bio-tradis,
biobambam2,
bioperl,
+ bioperl-run,
biosquid,
cwltool,
gffread,
@@ -1060,12 +1059,16 @@ Recommends: bio-tradis,
libbio-primerdesigner-perl,
libbio-samtools-perl,
libbio-scf-perl,
+ libbio-tools-phylo-paml-perl,
+ libbio-tools-run-alignment-clustalw-perl,
+ libbio-tools-run-alignment-tcoffee-perl,
libbio-tools-run-remoteblast-perl,
libbiococoa-dev,
libbiod-dev,
libbiojava-java,
libbiojava4-java,
libbioparser-dev,
+ libblasr-dev,
libbpp-core-dev,
libbpp-phyl-dev,
libbpp-phyl-omics-dev,
@@ -1103,6 +1106,7 @@ Recommends: bio-tradis,
libkmer-dev,
libmems-dev,
libminimap2-dev,
+ libmmblib-dev,
libmuscle-dev,
libncbi-vdb-dev,
libncbi6-dev,
@@ -1115,8 +1119,12 @@ Recommends: bio-tradis,
libpal-java,
libparasail-dev,
libpbbam-dev,
+ libpbdata-dev,
+ libpbihdf-dev,
+ libpbseq-dev,
libpll-dev,
libqes-dev,
+ librcsb-core-wrapper0-dev,
librdp-taxonomy-tree-java,
librg-blast-parser-perl,
librg-reprof-bundle-perl,
@@ -1147,7 +1155,9 @@ Recommends: bio-tradis,
nim-hts-dev,
nim-kexpr-dev,
nim-lapper-dev,
+ pyfai,
python3-airr,
+ python3-anndata,
python3-bcbio-gff,
python3-biom-format,
python3-biomaj3,
@@ -1156,6 +1166,7 @@ Recommends: bio-tradis,
python3-bx,
python3-cgecore,
python3-cobra,
+ python3-corepywrap,
python3-csb,
python3-cutadapt,
python3-cyvcf2,
@@ -1194,10 +1205,12 @@ Recommends: bio-tradis,
python3-rdkit,
python3-ruffus,
python3-screed,
+ python3-shasta,
python3-skbio,
python3-sqt,
python3-streamz,
python3-tinyalign,
+ python3-torch,
python3-treetime,
r-bioc-biobase,
r-cran-boolnet,
@@ -1221,6 +1234,7 @@ Recommends: bio-tradis,
r-cran-samr,
r-cran-sctransform,
r-cran-seqinr,
+ r-cran-seurat,
r-cran-tsne,
r-cran-vegan,
r-cran-webgestaltr,
@@ -1231,7 +1245,6 @@ Recommends: bio-tradis,
snakemake,
toil
Suggests: bioclipse,
- bioperl-run,
conda-package-handling,
ctdconverter,
cthreadpool-dev,
@@ -1240,13 +1253,8 @@ Suggests: bioclipse,
libatomicqueue-dev,
libbam-dev,
libbbhash-dev,
- libbio-tools-phylo-paml-perl,
- libbio-tools-run-alignment-clustalw-perl,
- libbio-tools-run-alignment-tcoffee-perl,
- libblasr-dev,
libconcurrentqueue-dev,
libdisorder-dev,
- libdynamic-dev,
libfast-perl,
libforester-java,
libfreecontact-dev,
@@ -1256,15 +1264,10 @@ Suggests: bioclipse,
libmaus2-dev,
libmilib-java,
libminimap-dev,
- libmmblib-dev,
libmodhmm-dev,
libnexml-java,
libpbcopper-dev,
- libpbdata-dev,
- libpbihdf-dev,
- libpbseq-dev,
libqcpp-dev,
- librcsb-core-wrapper0-dev,
librelion-dev,
libroadrunner-dev,
librostlab-blast-doc,
@@ -1274,18 +1277,16 @@ Suggests: bioclipse,
libsvmloc-dev,
libswarm2-dev,
libtfbs-perl,
+ libxxsds-dynamic-dev,
octace-bioinfo,
- pyfai,
python-biopython-doc,
python3-alignlib,
- python3-anndata,
python3-bcbio,
python3-bel-resources,
python3-biopython-sql,
python3-cogent3,
python3-consensuscore2,
python3-cooler,
- python3-corepywrap,
python3-ctdopts,
python3-galaxy-lib,
python3-hyphy,
@@ -1300,8 +1301,6 @@ Suggests: bioclipse,
python3-pyflow,
python3-roadrunner,
python3-seqcluster,
- python3-shasta,
- python3-torch,
python3-unifrac,
q2-alignment,
q2-composition,
@@ -1330,6 +1329,7 @@ Suggests: bioclipse,
q2lint,
q2templates,
qiime,
+ r-bioc-affxparser,
r-bioc-affy,
r-bioc-affyio,
r-bioc-altcdfenvs,
@@ -1337,6 +1337,7 @@ Suggests: bioclipse,
r-bioc-annotationdbi,
r-bioc-annotationhub,
r-bioc-aroma.light,
+ r-bioc-arrayexpress,
r-bioc-biocgenerics,
r-bioc-biocneighbors,
r-bioc-biomart,
@@ -1367,6 +1368,8 @@ Suggests: bioclipse,
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,
@@ -1378,6 +1381,8 @@ Suggests: bioclipse,
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,
@@ -1425,7 +1430,6 @@ Suggests: bioclipse,
r-cran-rook,
r-cran-rsgcc,
r-cran-rsvd,
- r-cran-seurat,
r-cran-shazam,
r-cran-sitmo,
r-cran-venndiagram,
@@ -1458,6 +1462,7 @@ Recommends: abyss,
bamtools,
bedtools,
bioperl,
+ bioperl-run,
biosquid,
bowtie,
bowtie2,
@@ -1520,6 +1525,7 @@ Recommends: abyss,
mira-assembler,
mlv-smile,
mothur,
+ mrbayes,
mummer,
muscle,
mustang,
@@ -1528,6 +1534,7 @@ Recommends: abyss,
ncoils,
neobio,
paraclu,
+ parsinsert,
pdb2pqr,
perm,
phyml,
@@ -1546,6 +1553,7 @@ Recommends: abyss,
prodigal,
python3-biomaj3-cli,
python3-biopython,
+ python3-cogent3,
qiime,
r-bioc-edger,
r-bioc-hilbertvis,
@@ -1574,20 +1582,16 @@ Recommends: abyss,
tabix,
theseus,
tigr-glimmer,
+ tree-puzzle | tree-ppuzzle,
vcftools,
velvet,
wise,
zalign
Suggests: bagpipe,
- bioperl-run,
blast2,
cufflinks,
embassy-phylip,
- giira,
- mrbayes,
- parsinsert,
- python3-cogent3,
- tree-puzzle | tree-ppuzzle
+ giira
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
@@ -1631,6 +1635,7 @@ Depends: ${misc:Depends},
med-tasks (= ${source:Version})
Recommends: epigrass,
python3-seirsplus,
+ python3-torch,
python3-treetime,
r-cran-covid19us,
r-cran-diagnosismed,
@@ -1650,7 +1655,6 @@ Suggests: chime,
epifire,
netepi-analysis,
netepi-collection,
- python3-torch,
r-cran-cmprsk,
r-cran-covid19,
r-cran-msm,
@@ -1670,10 +1674,10 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: orthanc-wsi
+Recommends: fis-gtm,
+ orthanc-wsi
Suggests: care2x,
ewd-920,
- fis-gtm,
hkma-cms,
ipath,
openeyes,
@@ -1743,6 +1747,8 @@ Recommends: aeskulap,
python3-pyxid,
python3-surfer,
qnifti2dicom,
+ sigviewer,
+ teem-apps,
tifffile,
vrrender,
vtk-dicom-tools,
@@ -1823,12 +1829,10 @@ Suggests: afni,
python3-mvpa2,
python3-nipy,
science-workflow,
- sigviewer,
slicer,
sofa-apps,
stabilitycalc,
stir,
- teem-apps,
tempo,
trimage,
via-bin,
@@ -1872,12 +1876,14 @@ Recommends: cimg-dev,
libmialm-dev,
libmiaviewit-dev,
libminc-dev,
+ libnifti2-dev,
libodil-dev,
libopenigtlink-dev,
libopenslide-dev,
libopensurgsim-dev,
libpapyrus3-dev,
libsight-dev,
+ libteem-dev,
libvigraimpex-dev,
libvistaio-dev,
libvolpack1-dev,
@@ -1912,11 +1918,9 @@ Suggests: emokit,
liblimereg-dev,
libmni-perllib-perl,
libnifti-doc,
- libnifti2-dev,
libopenmeeg-dev,
libopenslide-java,
libsimpleitk1-dev,
- libteem-dev,
libvia-dev,
libvmtk-dev,
libvtk6-dev,
=====================================
debian/med-config.docs
=====================================
@@ -1 +1 @@
-debian/NEWS.Debian
+debian/NEWS
=====================================
dependency_data/debian-med_3.6.2.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-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-rsgcc", "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", 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\ No newline at end of file
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/9e40b5326745237e9fe6f89a18be378454f89532...59f1f3226c4cac4e2fc4c0f19ba9bda78f1cacf2
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View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/9e40b5326745237e9fe6f89a18be378454f89532...59f1f3226c4cac4e2fc4c0f19ba9bda78f1cacf2
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