[Blends-commit] [Git][blends-team/med][master] 6 commits: Python2 packages only suggested
Andreas Tille
gitlab at salsa.debian.org
Thu Nov 28 08:29:03 GMT 2019
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
b62520c8 by Andreas Tille at 2019-11-28T07:57:36Z
Python2 packages only suggested
- - - - -
a57ab0f6 by Andreas Tille at 2019-11-28T07:59:12Z
giira from Recommends to Suggests since it needs tophat
- - - - -
3ea3810a by Andreas Tille at 2019-11-28T08:11:12Z
Rerender with Python2 packages only suggested
- - - - -
66bbba14 by Andreas Tille at 2019-11-28T08:17:20Z
Update changelog entry
- - - - -
0dd52d78 by Andreas Tille at 2019-11-28T08:25:38Z
lintian-override for field-too-long Recommends
- - - - -
1ac5e2e7 by Andreas Tille at 2019-11-28T08:27:36Z
Upload to unstable
- - - - -
10 changed files:
- debian/changelog
- debian/control
- + debian/med-bio.lintian-overrides
- + dependency_data/debian-med_3.5.json
- tasks/bio
- tasks/bio-dev
- tasks/cloud
- tasks/imaging
- tasks/imaging-dev
- tasks/psychology
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,63 @@
+debian-med (3.5) unstable; urgency=medium
+
+ * Python2 packages only suggested
+ Closes: #945659
+ * Remove tophat since deprecated by upstream
+ * giira from Recommends to Suggests since it needs tophat
+ * lintian-override for field-too-long Recommends
+
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-bio
+ added:
+ Recommends: idefix, resfinder, purple, pufferfish
+ Suggests: skewer, giira
+ removed:
+ Recommends: giira, tophat
+ Suggests: mobyle-programs, mobyle-tutorials, mobyle
+ -med-bio-dev
+ added:
+ Recommends: python3-dnaio, python3-pyani, biobambam2, libcdk-java
+ Suggests: r-bioc-dada2, python-pbcommand, python-pbh5tools,
+ r-cran-dt, r-cran-proc, python-kineticstools, libfast-perl,
+ python-corepywrap, libmaus2-dev, python-pbcore,
+ r-cran-pcapp, r-cran-dynamictreecut, python-cogent,
+ r-cran-kaos
+ removed:
+ Recommends: python-pbh5tools, python-pbcommand, python-kineticstools,
+ python-corepywrap, libmaus2-dev, python-pbcore,
+ r-cran-dynamictreecut, python-cogent
+ -med-bio-ngs
+ removed:
+ Recommends: tophat
+ -med-cloud
+ added:
+ Recommends: hisat2
+ Suggests: python-cogent
+ removed:
+ Recommends: python-cogent, tophat
+ -med-imaging
+ added:
+ Suggests: python-nipype, python-nitime, python-dipy, python-nipy
+ removed:
+ Recommends: python-nipype, python-nitime, python-dipy, python-nipy
+ Suggests: tifffile
+ -med-imaging-dev
+ added:
+ Suggests: python-vigra, python-nipype, python-cfflib, python-nitime,
+ python-pyxnat, python-nipy, python-vmtk, python-dipy
+ removed:
+ Recommends: python-vigra, python-nipype, python-cfflib, python-nitime,
+ python-pyxnat, python-nipy, python-vmtk, python-dipy
+ -med-psychology
+ added:
+ Suggests: python-pyepl
+ removed:
+ Recommends: python-pypsignifit, python-pyepl
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Nov 2019 09:25:44 +0100
+
debian-med (3.4) unstable; urgency=medium
* Standards-Version: 4.4.1
=====================================
debian/control
=====================================
@@ -183,7 +183,6 @@ Recommends: abacas,
dialign-tx,
diamond-aligner,
dindel,
- discosnp,
disulfinder,
dnaclust,
dotter,
@@ -199,6 +198,7 @@ Recommends: abacas,
embassy-domalign,
embassy-domsearch,
emboss,
+ emmax,
estscan,
examl,
exonerate,
@@ -236,7 +236,6 @@ Recommends: abacas,
gffread,
ghemical,
ghmm,
- giira,
glam2,
grabix,
graphlan,
@@ -313,6 +312,7 @@ Recommends: abacas,
mipe,
mira-assembler,
mlv-smile,
+ mmseqs2,
mothur,
mptp,
mrbayes,
@@ -334,7 +334,6 @@ Recommends: abacas,
ncoils,
neobio,
njplot,
- norsnet,
norsp,
obitools,
openms,
@@ -346,11 +345,8 @@ Recommends: abacas,
parsinsert,
parsnp,
patman,
- pbbarcode,
pbdagcon,
- pbh5tools,
pbsim,
- pdb2pqr,
perlprimer,
perm,
pftools,
@@ -380,7 +376,6 @@ Recommends: abacas,
poretools,
prank,
predictnls,
- predictprotein,
prime-phylo,
primer3,
proalign,
@@ -389,18 +384,6 @@ Recommends: abacas,
probcons,
proda,
prodigal,
- profbval,
- profisis,
- profnet-bval,
- profnet-chop,
- profnet-con,
- profnet-isis,
- profnet-md,
- profnet-norsnet,
- profnet-prof,
- profnet-snapfun,
- profphd,
- profphd-net,
profphd-utils,
proftmb,
progressivemauve,
@@ -442,15 +425,19 @@ Recommends: abacas,
r-bioc-impute,
r-bioc-limma,
r-bioc-mergeomics,
+ r-bioc-multiassayexperiment,
r-bioc-pcamethods,
r-bioc-phyloseq,
r-bioc-rtracklayer,
r-bioc-tfbstools,
+ r-cran-adegenet,
+ r-cran-adephylo,
r-cran-alakazam,
r-cran-ape,
r-cran-bio3d,
r-cran-distory,
r-cran-genabel,
+ r-cran-kaos,
r-cran-metamix,
r-cran-phangorn,
r-cran-phytools,
@@ -463,6 +450,7 @@ Recommends: abacas,
r-cran-shazam,
r-cran-tcr,
r-cran-tigger,
+ r-cran-treescape,
r-cran-vegan,
r-cran-webgestaltr,
r-other-hms-dbmi-spp,
@@ -515,7 +503,6 @@ Recommends: abacas,
sim4,
sim4db,
skesa,
- smalr,
smalt,
smithwaterman,
snap,
@@ -558,7 +545,6 @@ Recommends: abacas,
tm-align,
tnseq-transit,
toil,
- tophat,
topp,
toppred,
trace2dbest,
@@ -574,7 +560,6 @@ Recommends: abacas,
tvc,
uc-echo,
umis,
- unanimity,
unicycler,
varna,
vcftools,
@@ -638,11 +623,11 @@ Suggests: acacia,
dazzle,
deepbinner,
dendroscope,
+ discosnp,
e-hive,
ecell,
embassy-phylip,
emboss-explorer,
- emmax,
emperor,
ensembl,
estferret,
@@ -669,6 +654,7 @@ Suggests: acacia,
genezilla,
genographer,
getdata,
+ giira,
glimmerhmm,
gmap,
gmv,
@@ -676,6 +662,7 @@ Suggests: acacia,
haploview,
hawkeye,
htqc,
+ idefix,
igdiscover,
igv,
inspect,
@@ -710,10 +697,6 @@ Suggests: acacia,
minimus,
mirbase,
mirtop,
- mmseqs2,
- mobyle,
- mobyle-programs,
- mobyle-tutorials,
modeller,
molekel,
mosaik-aligner,
@@ -731,6 +714,7 @@ Suggests: acacia,
nextsv,
ngila,
ngsqctoolkit,
+ norsnet,
nw-align,
oases,
obo-edit,
@@ -744,11 +728,14 @@ Suggests: acacia,
partitionfinder,
patristic,
pbalign,
+ pbbarcode,
pbgenomicconsensus,
+ pbh5tools,
pbhoney,
pbjelly,
pbsuite,
pcma,
+ pdb2pqr,
pfaat,
phagefinder,
phpphylotree,
@@ -761,11 +748,26 @@ Suggests: acacia,
pipasic,
pizzly,
plato,
+ predictprotein,
+ profbval,
+ profisis,
profit,
+ profnet-bval,
+ profnet-chop,
+ profnet-con,
+ profnet-isis,
+ profnet-md,
+ profnet-norsnet,
+ profnet-prof,
+ profnet-snapfun,
+ profphd,
+ profphd-net,
prokka,
prot4est,
psipred,
pssh2,
+ pufferfish,
+ purple,
pyrophosphate-tools,
python3-alignlib,
python3-cogent,
@@ -785,12 +787,9 @@ Suggests: acacia,
r-bioc-go.db,
r-bioc-metagenomeseq,
r-bioc-mofa,
- r-bioc-multiassayexperiment,
r-bioc-qusage,
r-bioc-savr,
r-bioc-tximport,
- r-cran-adegenet,
- r-cran-adephylo,
r-cran-boolnet,
r-cran-corrplot,
r-cran-drinsight,
@@ -798,13 +797,11 @@ Suggests: acacia,
r-cran-fitdistrplus,
r-cran-forecast,
r-cran-gprofiler,
- r-cran-kaos,
r-cran-pheatmap,
r-cran-qqman,
r-cran-rentrez,
r-cran-sctransform,
r-cran-seurat,
- r-cran-treescape,
r-cran-tsne,
r-other-apmswapp,
r-other-wgcna,
@@ -813,6 +810,7 @@ Suggests: acacia,
raxml-ng,
rbs-finder,
repeatmasker,
+ resfinder,
rmblast,
roadtrips,
roche454ace2caf,
@@ -831,6 +829,8 @@ Suggests: acacia,
sina,
sistr,
situs,
+ skewer,
+ smalr,
smrtanalysis,
snpeff,
solvate,
@@ -859,6 +859,7 @@ Suggests: acacia,
twain,
ugene,
umap,
+ unanimity,
unc-fish,
uniprime,
varmatch,
@@ -895,7 +896,6 @@ Recommends: bio-tradis,
libbio-coordinate-perl,
libbio-das-lite-perl,
libbio-eutilities-perl,
- libbio-graphics-perl,
libbio-mage-perl,
libbio-mage-utils-perl,
libbio-primerdesigner-perl,
@@ -917,6 +917,7 @@ Recommends: bio-tradis,
libbpp-raa-dev,
libbpp-seq-dev,
libbpp-seq-omics-dev,
+ libcdk-java,
libchado-perl,
libconsensuscore-dev,
libdivsufsort-dev,
@@ -987,11 +988,6 @@ Recommends: bio-tradis,
libzerg-perl,
libzerg0-dev,
mcl,
- pyfai,
- python-cogent,
- python-corepywrap,
- python-pbcore,
- python-pbh5tools,
python3-airr,
python3-bcbio,
python3-biom-format,
@@ -1005,6 +1001,7 @@ Recommends: bio-tradis,
python3-cutadapt,
python3-cyvcf2,
python3-dendropy,
+ python3-dnaio,
python3-fast5,
python3-freecontact,
python3-gfapy,
@@ -1027,8 +1024,11 @@ Recommends: bio-tradis,
python3-sqt,
python3-treetime,
r-bioc-biobase,
+ r-cran-adegenet,
+ r-cran-adephylo,
r-cran-boolnet,
r-cran-distory,
+ r-cran-fitdistrplus,
r-cran-forecast,
r-cran-genetics,
r-cran-gprofiler,
@@ -1054,13 +1054,16 @@ Recommends: bio-tradis,
seqan-dev,
snakemake,
toil
-Suggests: bioclipse,
+Suggests: biobambam2,
+ bioclipse,
ctdconverter,
galaxy-lib,
libbam-dev,
libbigwig-dev,
+ libbio-graphics-perl,
libbiod-dev,
libdisorder-dev,
+ libfast-perl,
libforester-java,
libfreecontact-doc,
libgclib,
@@ -1082,9 +1085,14 @@ Suggests: bioclipse,
mgltools-pybabel,
mgltools-vision,
octace-bioinfo,
+ pyfai,
python-biopython-doc,
+ python-cogent,
+ python-corepywrap,
python-kineticstools,
python-pbcommand,
+ python-pbcore,
+ python-pbh5tools,
python3-alignlib,
python3-biopython-sql,
python3-consensuscore2,
@@ -1097,6 +1105,7 @@ Suggests: bioclipse,
python3-loompy,
python3-mirtop,
python3-misopy,
+ python3-pyani,
python3-pycosat,
python3-pyflow,
python3-roadrunner,
@@ -1117,6 +1126,7 @@ Suggests: bioclipse,
r-bioc-bsgenome,
r-bioc-cner,
r-bioc-cummerbund,
+ r-bioc-dada2,
r-bioc-deseq2,
r-bioc-dnacopy,
r-bioc-ebseq,
@@ -1154,17 +1164,18 @@ Suggests: bioclipse,
r-bioc-tximport,
r-bioc-variantannotation,
r-bioc-xvector,
- r-cran-adegenet,
- r-cran-adephylo,
r-cran-corrplot,
r-cran-drinsight,
+ r-cran-dt,
r-cran-dynamictreecut,
- r-cran-fitdistrplus,
r-cran-future.apply,
r-cran-future.batchtools,
r-cran-ica,
+ r-cran-kaos,
r-cran-metap,
r-cran-natserv,
+ r-cran-pcapp,
+ r-cran-proc,
r-cran-rann,
r-cran-rocr,
r-cran-rsvd,
@@ -1221,7 +1232,6 @@ Recommends: abyss,
datamash,
dialign,
dialign-tx,
- discosnp,
disulfinder,
dnaclust,
dssp,
@@ -1247,6 +1257,7 @@ Recommends: abyss,
grinder,
gromacs,
hhsuite,
+ hisat2,
hmmer,
idba,
infernal,
@@ -1275,7 +1286,6 @@ Recommends: abyss,
neobio,
paraclu,
parsinsert,
- pdb2pqr,
perm,
phyml,
phyutility,
@@ -1290,7 +1300,6 @@ Recommends: abyss,
proda,
prodigal,
pynast,
- python-cogent,
python3-biomaj3-cli,
python3-biopython,
qiime,
@@ -1320,7 +1329,6 @@ Recommends: abyss,
tabix,
theseus,
tigr-glimmer,
- tophat,
tree-puzzle | tree-ppuzzle,
vcftools,
velvet,
@@ -1328,8 +1336,11 @@ Recommends: abyss,
zalign
Suggests: bagpipe,
cufflinks,
+ discosnp,
embassy-phylip,
- gmap
+ gmap,
+ pdb2pqr,
+ python-cogent
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
@@ -1382,6 +1393,7 @@ Recommends: epigrass,
r-cran-epitools,
r-cran-lexrankr,
r-cran-seroincidence,
+ r-cran-sf,
r-cran-sjplot,
r-cran-surveillance
Suggests: epifire,
@@ -1389,7 +1401,6 @@ Suggests: epifire,
netepi-collection,
r-cran-cmprsk,
r-cran-msm,
- r-cran-sf,
repast,
shiny-server,
ushahidi
@@ -1459,15 +1470,12 @@ Recommends: aeskulap,
mriconvert,
mricron,
mrtrix,
- mrtrix3,
nifti-bin,
odil,
openslide-tools,
orthanc,
orthanc-wsi,
pixelmed-apps,
- python-nipy,
- python-nitime,
python3-dicom,
python3-nibabel,
tifffile,
@@ -1534,6 +1542,7 @@ Suggests: afni,
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
+ mrtrix3,
odin,
omero,
opendicom.net,
@@ -1552,7 +1561,9 @@ Suggests: afni,
pngquant,
pymeg,
python-dipy,
+ python-nipy,
python-nipype,
+ python-nitime,
python-pyxid,
python3-mvpa2,
python3-surfer,
@@ -1597,6 +1608,7 @@ Recommends: cimg-dev,
libgdcm2-dev,
libgdf-dev,
libgiftiio-dev,
+ libinsighttoolkit4-dev,
libismrmrd-dev,
libmaxflow-dev,
libmdc2-dev,
@@ -1618,11 +1630,6 @@ Recommends: cimg-dev,
octave-bart,
octave-dicom,
octave-gdf,
- python-cfflib,
- python-nipy,
- python-nitime,
- python-pyxnat,
- python-vigra,
python3-dicom,
python3-gdcm,
python3-imageio,
@@ -1640,7 +1647,6 @@ Suggests: emokit,
libeegdev-dev,
libfreeimage-dev,
libics-dev,
- libinsighttoolkit4-dev,
liblimereg-dev,
libmni-perllib-perl,
libnifti-doc,
@@ -1654,8 +1660,13 @@ Suggests: emokit,
libvtk6-dev,
libxdffileio-dev,
odin,
+ python-cfflib,
python-dipy,
+ python-nipy,
python-nipype,
+ python-nitime,
+ python-pyxnat,
+ python-vigra,
python-vmtk,
python3-biosig,
python3-mne,
@@ -1673,9 +1684,9 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: opencfu,
- orthanc-wsi
+Recommends: orthanc-wsi
Suggests: catissuesuite,
+ opencfu,
openelis,
openfreezer
Description: Debian Med suggestions for medical laboratories
@@ -1786,12 +1797,11 @@ Depends: ${misc:Depends},
med-tasks (= ${source:Version})
Recommends: praat,
psignifit,
- python-pyepl,
r-cran-foreign,
r-cran-psy,
r-cran-psych
Suggests: psychopy,
- python-pypsignifit,
+ python-pyepl,
r-cran-psychometric,
r-cran-psychotree,
r-cran-psyphy,
=====================================
debian/med-bio.lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# We really have a lot of recommends
+med-bio: field-too-long Recommends (* chars > 5000)
=====================================
dependency_data/debian-med_3.5.json
=====================================
@@ -0,0 +1 @@
+{"cms": {"depends": [], "suggests": ["zope-zms", "hid"], "recommends": ["xnat"], "ignore": [], "avoid": []}, "bio": {"depends": [], "suggests": ["dascrubber", "emboss-explorer", "adun.app", "cain", "skewer", "science-workflow", "getdata", "giira", "metastudent-data", "metastudent-data-2", "metastudent-data-3", "mrs", "python3-alignlib", "python3-loompy", "python3-py2bit", "r-bioc-tximport", "r-cran-corrplot", "r-cran-dynamictreecut", "r-cran-forecast", "r-cran-gprofiler", "r-cran-fitdistrplus", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-ensembldb", "r-bioc-go.db", "r-bioc-qusage", "r-cran-qqman", "r-cran-rentrez", "r-cran-boolnet", "r-cran-pheatmap", "r-bioc-savr", "r-cran-sctransform", "r-bioc-tximport", "strelka", "python3-pyflow", "maude"], "recommends": ["altree", "beast-mcmc", "beast2-mcmc", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle", "probalign", "treeviewx", "figtree", "hyphy-mpi | hyphy-pt", "spread-phy", "omegamap", "sweed", "phylip", "fastlink", "loki", "plink", "plink1.9", "r-cran-qtl", "r-cran-genabel", "gemma", "bolt-lmm", "amap-align", "boxshade", "fastx-toolkit", "gff2aplot", "muscle", "sim4", "sibsim4", "tabix", "wise", "maqview", "blasr", "daligner", "mhap", "bwa", "mummer", "e-mem", "ncbi-blast+-legacy", "plast", "ncbi-blast+", "mafft", "sra-toolkit", "t-coffee", "kalign", "ghmm", "hmmer", "gramalign", "exonerate", "elph", "dialign", "dialign-tx", "poa", "probcons", "proda", "seaview", "sigma-align", "wham-align", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "arb", "clustalx", "clustalo", "clustalw", "mothur", "bowtie", "bowtie2", "transtermhp", "last-align", "maq", "ssake", "velvet | velvet-long", "qiime", "scoary", "umap", "infernal", "rnahybrid", "adun-core", "avogadro", "garlic", "gamgi", "gdpc", "ghemical", "jmol", "pymol", "r-cran-bio3d", "msxpertsuite", "gromacs", "rasmol", "viewmol", "qutemol", "modeller", "plasmidomics", "gff2ps", "ncbi-epcr", "ncbi-tools-bin", "ncbi-tools-x11", "perlprimer", "readseq", "tigr-glimmer", "melting", "mipe", "primer3", "artemis", "gbrowse", "python3-biomaj3-daemon", "glam2", "raster3d", "phyml", "autodock", "autogrid", "autodock-vina", "autodocktools", "mgltools-pmv", "mgltools-vision", "mgltools-cadd", "mustang", "probabel", "theseus", "staden-io-lib-utils", "samtools", "bedtools", "datamash", "gassst", "hinge", "r-bioc-hilbertvis", "r-other-mott-happy.hbrem", "seq-gen", "snp-sites", "mira-assembler", "alien-hunter", "seqan-apps", "ncoils", "gentle", "gmap", "igv", "picard-tools", "acedb-other", "blixem", "dotter", "belvu", "paml", "velvetoptimiser", "ensembl", "mrbayes", "pdb2pqr", "squizz", "clonalframe", "clonalframeml", "dssp", "jellyfish", "jellyfish1", "ballview", "pynast", "pizzly", "raxml", "seqcluster", "mlv-smile", "cd-hit", "cufflinks", "eigensoft", "grinder", "jalview", "reprof", "tm-align", "norsnet", "norsp", "predictnls", "prime-phylo", "proftmb", "profbval", "profisis", "hhsuite", "ffindex", 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"r-bioc-biomart", "r-bioc-biomformat", "r-bioc-biostrings", "r-bioc-biovizbase", "r-bioc-bitseq", "r-bioc-bsgenome", "r-bioc-cner", "r-bioc-cummerbund", "r-bioc-dada2", "r-bioc-deseq2", "r-bioc-dnacopy", "r-bioc-ebseq", "r-bioc-ensembldb", "r-bioc-genefilter", "r-bioc-geneplotter", "r-bioc-genomeinfodb", "r-bioc-genomicalignments", "r-bioc-genomicfeatures", "r-bioc-genomicranges", "r-bioc-go.db", "r-bioc-graph", "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-pcamethods", "r-bioc-phyloseq", "r-bioc-preprocesscore", "r-bioc-qusage", "r-bioc-rbgl", "r-bioc-rsamtools", "r-bioc-rentrez", "r-bioc-rtracklayer", "r-bioc-savr", "r-bioc-shortread", "r-bioc-snpstats", "r-bioc-tfbstools", "r-bioc-tximport", "r-bioc-variantannotation", "r-bioc-xvector", "r-cran-dt", "r-cran-dynamictreecut", "r-cran-future.apply", "r-cran-future.batchtools", "r-cran-ica", "r-cran-kaos", "r-cran-metap", "r-cran-natserv", "r-cran-pcapp", "r-cran-proc", "r-cran-rann", "r-cran-rocr", "r-cran-rsvd", "ruby-rgfa", "librostlab-doc", "librostlab-blast-doc", "libswarm2-dev", "libgtextutils-dev", "python-pbcore", "python-pbh5tools", "python-pbcommand", "python-kineticstools", "libbam-dev", "libfast-perl", "libpbcopper-dev", "libdisorder-dev", "python3-pyflow", "libmilib-java", "vdjtools", "python3-alignlib", "python3-ctdopts", "ctdconverter", "libmodhmm-dev", "libsvmloc-dev", "libmaus2-dev"], "recommends": ["bioperl", "bioperl-run", "libncbi6-dev", "mcl", "biosquid", "cwltool", "snakemake", "libvibrant6-dev", "python3-biopython", "python3-screed", "python3-cutadapt", "python3-dnaio", "ruby-bio", "libbiojava-java", "libbiojava4-java", "libgenome-dev", "libmuscle-dev", "libmems-dev", "libhtsjdk-java", "libai-fann-perl", "libbio-mage-perl", "libnhgri-blastall-perl", "libtfbs-perl", "libfreecontact-dev", "libfreecontact-perl", "libgo-perl", "libbio-graphics-perl", "libbio-coordinate-perl", "libbio-primerdesigner-perl", "libace-perl", "libbiococoa-dev", "libstaden-read-dev", "libsrf-dev", "libzerg0-dev", "libzerg-perl", "librg-reprof-bundle-perl", "librcsb-core-wrapper0-dev", "libsbml5-dev", "sbmltoolbox", "seqan-dev", "libseqan2-dev", "libseqan3-dev", "libbio-mage-utils-perl", "libchado-perl", "libpal-java", "libbioparser-dev", "libspoa-dev", "libedlib-dev", "libthread-pool-dev", "libjebl2-java", "r-cran-adegenet", "r-cran-adephylo", "r-cran-boolnet", "r-cran-corrplot", "r-cran-distory", "r-cran-drinsight", "r-cran-forecast", "r-cran-fitdistrplus", "r-cran-genetics", "r-cran-gprofiler", "r-cran-haplo.stats", "r-cran-metamix", "r-cran-phangorn", "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-cran-pheatmap", "r-other-hms-dbmi-spp", "r-other-apmswapp", "r-bioc-biobase", "libffindex0-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", "bioclipse", "libgff-dev", "python3-pysam", "python3-cobra", "libtabixpp-dev", "python3-ruffus", "python3-hyphy", "python3-dendropy", "python3-skbio", "python3-pbconsensuscore", "python3-consensuscore2", "libconsensuscore-dev", "python3-pyvcf", "python3-pyfaidx", "python3-sqt", "libqes-dev", "libfast5-dev", "python3-fast5", "libpbseq-dev", "libpbdata-dev", "libpbihdf-dev", "libblasr-dev", "libminimap-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", "mgltools-networkeditor", "mgltools-vision", "mgltools-pybabel", "libssw-dev", "libssw-java", "libfml-dev", "libgkarrays-dev", "libjloda-java", "libvcflib-dev", "libswiss-perl", "python3-pybedtools", "python3-gffutils", "python3-bx", "toil", "galaxy-lib", "libbio-eutilities-perl", "libseqlib-dev", "libroadrunner-dev", "python3-roadrunner", "python3-biotools", "bio-tradis", "python3-biomaj3", "libbiod-dev", "python3-ete3", "python3-gfapy", "libgoby-java", "python3-seqcluster", "python3-cyvcf2", "libgatbcore-dev", "python3-airr", "python3-presto", "python3-bcbio", "libpll-dev", "libstatgen-dev", "python3-pyani", "python3-screed", "python3-treetime", "libbio-tools-run-alignment-tcoffee-perl", "libbio-asn1-entrezgene-perl", "libbio-chado-schema-perl", "libbio-samtools-perl", "libbio-scf-perl", "libbio-tools-phylo-paml-perl", "libbio-tools-run-alignment-clustalw-perl", "python3-pybel", "python3-mirtop", "libnexml-java", "python3-cgecore", "python3-deeptools", "python3-deeptoolsintervals", "python3-py2bit", "python3-loompy", "gffread", "libgclib", "biobambam2", "libcdk-java"], "ignore": ["golang-github-biogo-hts-dev"], "avoid": []}, "statistics": {"depends": [], "suggests": ["science-statistics"], "recommends": ["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": []}, "tools": {"depends": [], "suggests": ["cycle", "mencal", "entangle", "goldencheetah", "sleepyhead", "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": []}, "imaging-dev": {"depends": [], "suggests": ["libvtk6-dev", "libnifti-doc", "libfreeimage-dev", "libics-dev", "liblimereg-dev", "python-nipy", "python-nipype", "python-nitime", "emokit", "python-pyxnat", "python-dipy", "python-cfflib", "libeegdev-dev", "libxdffileio-dev", "tifffile", "python-vmtk", "python-vigra", "libcamp-dev"], "recommends": ["ctn-dev", "cimg-dev", "libminc-dev", "libmdc2-dev", "libvtk7-dev", "libnifti-dev", "libinsighttoolkit4-dev", "libvolpack1-dev", "libgdcm2-dev", "python3-gdcm", "libopensurgsim-dev", "libmaxflow-dev", "python3-mvpa2", "libvia-dev", "odin", "libcv-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-dicom", "libopenmeeg-dev", "python3-nibabel", "libgdf-dev", "octave-gdf", "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", "libvtk-dicom-dev", "libedf-dev", "python3-imageio", "libismrmrd-dev", "libodil-dev", "libbart-dev", "octave-bart", "libcifti-dev", "libxdf-dev", "libsimpleitk1-dev", "python3-simpleitk"], "ignore": [], "avoid": []}}
\ No newline at end of file
=====================================
tasks/bio
=====================================
@@ -427,7 +427,8 @@ Recommends: fitgcp
Recommends: gasic
-Recommends: giira
+Suggests: giira
+Comment: Needs deprecated tophat
Recommends: ipig
=====================================
tasks/bio-dev
=====================================
@@ -20,7 +20,8 @@ Recommends: python3-biopython
Suggests: python3-biopython-sql, python-biopython-doc
-Recommends: python-cogent
+Suggests: python-cogent
+Comment: py2removal
Suggests: python3-pycosat
@@ -67,7 +68,10 @@ Recommends: libzerg0-dev, libzerg-perl
Recommends: librg-reprof-bundle-perl
-Recommends: python-corepywrap, librcsb-core-wrapper0-dev
+Suggests: python-corepywrap
+Comment: py2removal
+
+Recommends: librcsb-core-wrapper0-dev
Recommends: libsbml5-dev, sbmltoolbox
@@ -332,7 +336,8 @@ Recommends: libgff-dev
Recommends: python3-pysam
-Recommends: python-pbcore, python-pbh5tools
+Suggests: python-pbcore, python-pbh5tools
+Comment: py2removal
Recommends: python3-cobra
@@ -350,7 +355,8 @@ Recommends: python3-pbconsensuscore
Recommends: python3-consensuscore2, libconsensuscore-dev
-Recommends: python-pbcommand
+Suggests: python-pbcommand
+Comment: py2removal
Recommends: python3-pyvcf
@@ -358,7 +364,8 @@ Recommends: python3-pyfaidx
Recommends: python3-sqt
-Recommends: python-kineticstools
+Suggests: python-kineticstools
+Comment: py2removal
Suggests: libbam-dev
=====================================
tasks/cloud
=====================================
@@ -59,8 +59,11 @@ X-Begin-Category: Tools for the molecular biologist.
Recommends: melting, mipe, ncbi-epcr, primer3
Comment: Oligonucleotides and PCR
-Recommends: acedb-other, disulfinder, ncbi-tools-bin, ncoils, python-cogent,
+Recommends: acedb-other, disulfinder, ncbi-tools-bin, ncoils,
readseq, tigr-glimmer, seqan-apps, staden-io-lib-utils
+
+Suggests: python-cogent
+Comment: py2removal
X-End-Category: Tools for the molecular biologist.
X-Begin-Category: Others
=====================================
tasks/imaging
=====================================
@@ -42,15 +42,18 @@ Recommends: sofa-apps
Recommends: python3-mvpa2
Why: Suggested by maintainer Michael Hanke <michael.hanke at gmail.com>
-Recommends: python-nipy
+Suggests: python-nipy
+Comment: py2removal
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
-Recommends: python-nipype
+Suggests: python-nipype
+Comment: py2removal
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
-Recommends: python-nitime
+Suggests: python-nitime
+Comment: py2removal
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
@@ -635,7 +638,9 @@ Registration: http://sccn.ucsd.edu/eeglab/install.html
Suggests: elastix
Suggests: python-pyxid
-Recommends: python-dipy
+
+Suggests: python-dipy
+Comment: py2removal
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
=====================================
tasks/imaging-dev
=====================================
@@ -33,11 +33,14 @@ Suggests: liblimereg-dev
Recommends: python3-mvpa2
Why: Suggested by maintainer Michael Hanke <michael.hanke at gmail.com>
-Recommends: python-nipy
+Suggests: python-nipy
+Comment: py2removal
-Recommends: python-nipype
+Suggests: python-nipype
+Comment: py2removal
-Recommends: python-nitime
+Suggests: python-nitime
+Comment: py2removal
Recommends: libvia-dev
@@ -92,15 +95,18 @@ Vcs-Git: git://github.com/daeken/Emokit.git
Pkg-Description: Emotiv EPOC headset Python interface
Emotive is an interface to a budget Emotiv EPOC EEG headset.
-Recommends: python-pyxnat
+Suggests: python-pyxnat
+Comment: py2removal
-Recommends: python-dipy
+Suggests: python-dipy
+Comment: py2removal
Recommends: libbiosig-dev, python3-biosig
Recommends: libctk-dev
-Recommends: python-cfflib
+Suggests: python-cfflib
+Comment: py2removal
Recommends: libopenslide-dev
@@ -126,9 +132,15 @@ Recommends: python3-mne
Suggests: tifffile
-Recommends: python-vmtk, libvmtk-dev
+Recommends: libvmtk-dev
-Recommends: libvigraimpex-dev, python-vigra
+Suggests: python-vmtk
+Comment: py2removal
+
+Recommends: libvigraimpex-dev
+
+Suggests: python-vigra
+Comment: py2removal
Recommends: libvtk-dicom-dev
=====================================
tasks/psychology
=====================================
@@ -6,12 +6,12 @@ Description: Debian Med packages for psychology
Suggests: science-psychophysics
Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/psychophysics
-Recommends: python-pyepl
+Suggests: python-pyepl
+Comment: py2removal
Recommends: praat
-Recommends: r-cran-foreign, psignifit, python-pypsignifit
-Why: analysis packages of particular relevance for psych. data
+Recommends: r-cran-foreign, psignifit
Recommends: r-cran-psy
Remark: r-cran-psy is orphaned upstream.
View it on GitLab: https://salsa.debian.org/blends-team/med/compare/97d887604435dda6527a8a213d71ed2ae940562c...1ac5e2e73b4572c66daa7c4fa6a34757c4ecacd5
--
View it on GitLab: https://salsa.debian.org/blends-team/med/compare/97d887604435dda6527a8a213d71ed2ae940562c...1ac5e2e73b4572c66daa7c4fa6a34757c4ecacd5
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