[Blends-commit] [Git][blends-team/med][master] 7 commits: Standards-Version: 4.4.1
Andreas Tille
gitlab at salsa.debian.org
Sat Oct 5 12:16:39 BST 2019
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
2d167157 by Andreas Tille at 2019-10-05T09:48:41Z
Standards-Version: 4.4.1
- - - - -
4cb156b8 by Andreas Tille at 2019-10-05T09:49:32Z
Use debhelper-compat
- - - - -
4df3509b by Andreas Tille at 2019-10-05T09:58:04Z
Re-render dependencies without Python2 packages
- - - - -
160427e2 by Andreas Tille at 2019-10-05T10:02:14Z
Automatically update changelog and dependency data
- - - - -
6b42ad5d by Andreas Tille at 2019-10-05T10:04:04Z
Fix debhelper-compat
- - - - -
0f42259d by Andreas Tille at 2019-10-05T10:17:52Z
Remove duplicated entry of tifffile
- - - - -
44e76221 by Andreas Tille at 2019-10-05T11:15:55Z
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/control.stub
- + dependency_data/debian-med_3.4.json
- tasks/imaging
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,114 @@
+debian-med (3.4) unstable; urgency=medium
+
+ * Standards-Version: 4.4.1
+ * Use debhelper-compat
+ * Re-render dependencies without Python2 packages
+
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-bio
+ added:
+ Recommends: python3-deeptoolsintervals, skesa, python3-orange, vg,
+ mmseqs2, mindthegap, kaptive, r-cran-tsne,
+ python3-deeptools, r-cran-seurat, python3-cogent,
+ kleborate, python3-reaper, python3-treetime, pizzly,
+ trim-galore, pigx-scrnaseq, pigx-rnaseq,
+ r-bioc-multiassayexperiment, wham-align, r-other-wgcna,
+ r-bioc-mofa, seqcluster, r-cran-kaos, r-cran-drinsight
+ Suggests: r-bioc-tximport, r-bioc-qusage, python3-pyflow,
+ python3-alignlib, r-cran-corrplot, r-cran-fitdistrplus,
+ r-cran-dynamictreecut, python3-loompy, strelka,
+ r-cran-gprofiler, python3-py2bit, r-cran-sctransform
+ removed:
+ Recommends: python-orange, python-treetime, python-reaper, python-cogent
+ -med-bio-dev
+ added:
+ Recommends: python3-roadrunner, python3-deeptoolsintervals,
+ r-other-hms-dbmi-spp, python3-loompy, python3-py2bit,
+ r-cran-rotl, r-cran-seqinr, libseqan2-dev, r-cran-boolnet,
+ r-other-apmswapp, r-cran-vegan, r-cran-tsne, gffread,
+ python3-deeptools, r-cran-seurat, r-cran-corrplot,
+ r-cran-fitdistrplus, r-cran-qqman, r-cran-metamix,
+ r-cran-pscbs, r-cran-pheatmap, r-cran-sctransform,
+ r-cran-adephylo, r-cran-phangorn, r-cran-distory,
+ python3-htseq, libmaus2-dev, python3-rdkit, r-cran-samr,
+ r-cran-webgestaltr, python3-freecontact, libseqan3-dev,
+ r-cran-rentrez, r-cran-adegenet, r-cran-dynamictreecut,
+ r-cran-gprofiler, r-cran-forecast, libgclib,
+ python3-biom-format, r-cran-drinsight
+ Suggests: r-cran-rann, r-bioc-biostrings, r-bioc-deseq2,
+ r-bioc-mergeomics, r-cran-metap, r-bioc-qusage,
+ python3-pyflow, python3-pycosat, r-bioc-metagenomeseq,
+ r-bioc-annotate, r-bioc-cner, r-bioc-geneplotter,
+ r-bioc-ensembldb, r-bioc-rentrez, r-bioc-tximport,
+ r-bioc-rtracklayer, r-bioc-annotationhub, r-bioc-ebseq,
+ r-bioc-go.db, r-bioc-limma, r-cran-ica, r-bioc-pcamethods,
+ r-bioc-savr, r-cran-rsvd, python3-alignlib,
+ r-cran-future.batchtools, r-bioc-tfbstools, r-bioc-bitseq,
+ r-bioc-cummerbund, r-bioc-multiassayexperiment, r-bioc-gviz,
+ r-bioc-genefilter, r-bioc-phyloseq, r-bioc-impute,
+ r-bioc-aroma.light, r-cran-future.apply, r-bioc-mofa,
+ r-bioc-dnacopy
+ removed:
+ Recommends: python-htseq, python-mmtk, python-rdkit, python-screed,
+ python-biom-format, python-roadrunner, python-freecontact
+ Suggests: python-pyflow, r-cran-rentrez
+ -med-bio-ngs
+ added:
+ Recommends: wham-align
+ -med-cloud
+ removed:
+ Recommends: python-biopython
+ -med-data
+ added:
+ Recommends: python3-hl7
+ Suggests: oscar
+ removed:
+ Recommends: python-hl7
+ -med-epi
+ added:
+ Recommends: python3-treetime
+ removed:
+ Recommends: python-treetime
+ -med-imaging
+ added:
+ Recommends: python3-nibabel, python3-mvpa2, python3-dicom,
+ python3-surfer, tifffile
+ removed:
+ Recommends: python-surfer, python-mvpa2, python-dicom,
+ python-nibabel, python-tifffile
+ -med-imaging-dev
+ added:
+ Recommends: python3-mia, python3-mvpa2, python3-dicom,
+ python3-openslide, python3-gdcm, python3-imageio,
+ python3-mne, python3-nibabel
+ Suggests: tifffile
+ removed:
+ Recommends: python-mia | python3-mia, python-gdcm, python-mne,
+ python-mvpa2, python-dicom, python-nibabel,
+ python-imageio, python-openslide
+ Suggests: python-libavg, python-tifffile
+ -med-physics
+ added:
+ Suggests: python3-multipletau
+ removed:
+ Suggests: python-multipletau
+ -med-practice
+ added:
+ Recommends: oscar
+ -med-psychology
+ removed:
+ Suggests: python-visionegg
+ -med-tools
+ added:
+ Recommends: python3-fitbit
+ Suggests: oscar
+ removed:
+ Recommends: python-clips, python-fitbit
+
+ -- Andreas Tille <tille at debian.org> Sat, 05 Oct 2019 12:02:38 +0200
+
debian-med (3.3) unstable; urgency=medium
* Re-render tasks with Buster release state
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -5,8 +5,8 @@ Uploaders: Andreas Tille <tille at debian.org>
Section: misc
Priority: optional
Build-Depends-Indep: blends-dev (>= 0.7.2~),
- debhelper (>= 12~)
-Standards-Version: 4.3.0
+Build-Depends: debhelper-compat (= 12)
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
@@ -109,11 +109,11 @@ Recommends: abacas,
artfastqgenerator,
assemblytics,
atac,
+ atropos,
augustus,
autodock,
autodock-vina,
autogrid,
- avogadro,
axe-demultiplexer,
baitfisher,
bali-phy,
@@ -226,7 +226,6 @@ Recommends: abacas,
garlic,
gasic,
gatb-core,
- gbrowse,
gdpc,
gemma,
genometester,
@@ -234,6 +233,7 @@ Recommends: abacas,
gentle,
gff2aplot,
gff2ps,
+ gffread,
ghemical,
ghmm,
giira,
@@ -265,13 +265,16 @@ Recommends: abacas,
jmodeltest,
jmol,
kalign,
+ kallisto,
khmer,
- kineticstools,
king-probe,
kissplice,
+ kma,
kmc,
kmer,
+ kmerresistance,
kraken,
+ kraken2,
lagan,
lamarc,
lambda-align,
@@ -335,6 +338,7 @@ Recommends: abacas,
norsp,
obitools,
openms,
+ optimir,
pal2nal,
paleomix,
paml,
@@ -342,15 +346,10 @@ Recommends: abacas,
parsinsert,
parsnp,
patman,
- pbalign,
pbbarcode,
pbdagcon,
- pbgenomicconsensus,
pbh5tools,
- pbhoney,
- pbjelly,
pbsim,
- pbsuite,
pdb2pqr,
perlprimer,
perm,
@@ -365,6 +364,7 @@ Recommends: abacas,
phyx,
picard-tools,
piler,
+ pilercr,
pilon,
pirs,
placnet,
@@ -413,15 +413,17 @@ Recommends: abacas,
pymol,
pynast,
pyscanfcs,
- python-cogent,
python3-biomaj3-daemon,
+ python3-geneimpacts,
python3-gffutils,
python3-presto,
python3-pybedtools,
python3-pybel,
python3-sqt,
+ python3-treetime,
pyvcf,
qcumber,
+ qiime,
qtltools,
quorum,
qutemol,
@@ -440,13 +442,10 @@ Recommends: abacas,
r-bioc-impute,
r-bioc-limma,
r-bioc-mergeomics,
- r-bioc-metagenomeseq,
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,
@@ -464,8 +463,8 @@ 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,
r-other-mott-happy.hbrem,
racon,
@@ -515,6 +514,7 @@ Recommends: abacas,
sigma-align,
sim4,
sim4db,
+ skesa,
smalr,
smalt,
smithwaterman,
@@ -573,6 +573,7 @@ Recommends: abacas,
trinityrnaseq,
tvc,
uc-echo,
+ umis,
unanimity,
unicycler,
varna,
@@ -580,7 +581,9 @@ Recommends: abacas,
velvet | velvet-long,
velvetoptimiser,
viewmol,
+ virulencefinder,
vsearch,
+ wham-align,
wigeon,
wise,
yaha,
@@ -594,8 +597,8 @@ Suggests: acacia,
arachne,
arb,
asap,
- atropos,
autodocktools,
+ avogadro,
axparafit,
axpcoords,
bagpipe,
@@ -658,6 +661,7 @@ Suggests: acacia,
galaxy,
gassst,
gatk,
+ gbrowse,
gbrowse-syn,
genemark,
genesplicer,
@@ -665,7 +669,6 @@ Suggests: acacia,
genezilla,
genographer,
getdata,
- gffread,
glimmerhmm,
gmap,
gmv,
@@ -679,11 +682,10 @@ Suggests: acacia,
jalview,
jbrowse,
jigsaw,
- kallisto,
+ kaptive,
kempbasu,
- kma,
- kmerresistance,
- kraken2,
+ kineticstools,
+ kleborate,
lofreq,
mach-haplotyper,
mage2tab,
@@ -704,9 +706,11 @@ Suggests: acacia,
mgltools-pmv,
mgltools-vision,
migrate,
+ mindthegap,
minimus,
mirbase,
mirtop,
+ mmseqs2,
mobyle,
mobyle-programs,
mobyle-tutorials,
@@ -734,12 +738,16 @@ Suggests: acacia,
omegamap,
oncofuse,
operondb,
- optimir,
optitype,
paipline,
partigene,
partitionfinder,
patristic,
+ pbalign,
+ pbgenomicconsensus,
+ pbhoney,
+ pbjelly,
+ pbsuite,
pcma,
pfaat,
phagefinder,
@@ -748,8 +756,10 @@ Suggests: acacia,
phylophlan,
phyloviz-core,
phylowin,
- pilercr,
+ pigx-rnaseq,
+ pigx-scrnaseq,
pipasic,
+ pizzly,
plato,
profit,
prokka,
@@ -757,11 +767,15 @@ Suggests: acacia,
psipred,
pssh2,
pyrophosphate-tools,
- python-orange,
- python-reaper,
- python-treetime,
- python3-geneimpacts,
- qiime,
+ python3-alignlib,
+ python3-cogent,
+ python3-deeptools,
+ python3-deeptoolsintervals,
+ python3-loompy,
+ python3-orange,
+ python3-py2bit,
+ python3-pyflow,
+ python3-reaper,
qtlcart,
qualimap,
quast,
@@ -769,14 +783,31 @@ Suggests: acacia,
r-bioc-aroma.light,
r-bioc-ensembldb,
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,
+ r-cran-dynamictreecut,
+ r-cran-fitdistrplus,
r-cran-forecast,
+ r-cran-gprofiler,
+ r-cran-kaos,
r-cran-pheatmap,
r-cran-qqman,
r-cran-rentrez,
- r-cran-webgestaltr,
+ r-cran-sctransform,
+ r-cran-seurat,
+ r-cran-treescape,
+ r-cran-tsne,
r-other-apmswapp,
+ r-other-wgcna,
raccoon,
ragout,
raxml-ng,
@@ -793,6 +824,7 @@ Suggests: acacia,
science-workflow,
seq-gen,
seq-seq-pan,
+ seqcluster,
sequenceconverter.app,
sibelia,
sift,
@@ -809,6 +841,7 @@ Suggests: acacia,
ssaha,
strap,
strap-base,
+ strelka,
stringtie,
tab2mage,
tacg,
@@ -820,20 +853,20 @@ Suggests: acacia,
tn-seqexplorer,
treebuilder3d,
treetime,
+ trim-galore,
tripal,
trnascan-se,
twain,
ugene,
umap,
- umis,
unc-fish,
uniprime,
varmatch,
varscan,
vcfanno,
vdjtools,
+ vg,
vienna-rna,
- virulencefinder,
vmd,
x-tandem-pipeline,
zodiac-zeden
@@ -852,6 +885,7 @@ Recommends: bio-tradis,
bioperl-run,
biosquid,
cwltool,
+ gffread,
libace-perl,
libai-fann-perl,
libbambamc-dev,
@@ -932,6 +966,7 @@ Recommends: bio-tradis,
librostlab-blast0-dev,
librostlab3-dev,
libsbml5-dev,
+ libseqan2-dev,
libseqlib-dev,
libsmithwaterman-dev,
libsnp-sites1-dev,
@@ -953,50 +988,66 @@ Recommends: bio-tradis,
libzerg0-dev,
mcl,
pyfai,
- python-biom-format,
python-cogent,
python-corepywrap,
- python-freecontact,
- python-htseq,
- python-kineticstools,
- python-pbcommand,
python-pbcore,
python-pbh5tools,
- python-rdkit,
python3-airr,
python3-bcbio,
+ python3-biom-format,
python3-biomaj3,
python3-biopython,
python3-biotools,
python3-bx,
+ python3-cgecore,
python3-cobra,
python3-csb,
python3-cutadapt,
python3-cyvcf2,
python3-dendropy,
python3-fast5,
+ python3-freecontact,
python3-gfapy,
python3-gffutils,
- python3-intervaltree-bio,
+ python3-htseq,
python3-ngs,
python3-pbconsensuscore,
python3-presto,
+ python3-py2bit,
python3-pybedtools,
python3-pybel,
python3-pyfaidx,
python3-pymummer,
python3-pysam,
python3-pyvcf,
+ python3-rdkit,
python3-ruffus,
python3-screed,
+ python3-skbio,
python3-sqt,
python3-treetime,
r-bioc-biobase,
+ r-cran-boolnet,
+ r-cran-distory,
+ r-cran-forecast,
r-cran-genetics,
+ r-cran-gprofiler,
r-cran-haplo.stats,
+ r-cran-metamix,
+ r-cran-phangorn,
+ r-cran-pheatmap,
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-seqinr,
+ r-cran-vegan,
+ r-cran-webgestaltr,
+ r-other-hms-dbmi-spp,
ruby-bio,
ruby-crb-blast,
sbmltoolbox,
@@ -1012,8 +1063,10 @@ Suggests: bioclipse,
libdisorder-dev,
libforester-java,
libfreecontact-doc,
+ libgclib,
libgoby-java,
libgtextutils-dev,
+ libmaus2-dev,
libmilib-java,
libmodhmm-dev,
libnexml-java,
@@ -1022,6 +1075,7 @@ Suggests: bioclipse,
libroadrunner-dev,
librostlab-blast-doc,
librostlab-doc,
+ libseqan3-dev,
libsvmloc-dev,
libswarm2-dev,
mgltools-networkeditor,
@@ -1029,47 +1083,95 @@ Suggests: bioclipse,
mgltools-vision,
octace-bioinfo,
python-biopython-doc,
- python-mmtk,
- python-pyflow,
- python-roadrunner,
- python-screed,
+ python-kineticstools,
+ python-pbcommand,
+ python3-alignlib,
python3-biopython-sql,
- python3-cgecore,
python3-consensuscore2,
python3-ctdopts,
+ python3-deeptools,
+ python3-deeptoolsintervals,
python3-ete3,
python3-hyphy,
+ python3-intervaltree-bio,
+ python3-loompy,
python3-mirtop,
python3-misopy,
+ python3-pycosat,
+ python3-pyflow,
+ python3-roadrunner,
python3-seqcluster,
- python3-skbio,
r-bioc-affy,
r-bioc-affyio,
r-bioc-altcdfenvs,
+ r-bioc-annotate,
r-bioc-annotationdbi,
+ r-bioc-annotationhub,
+ r-bioc-aroma.light,
r-bioc-biocgenerics,
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-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-rentrez,
r-bioc-rsamtools,
+ 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-adegenet,
+ r-cran-adephylo,
+ r-cran-corrplot,
+ r-cran-drinsight,
+ r-cran-dynamictreecut,
+ r-cran-fitdistrplus,
+ r-cran-future.apply,
+ r-cran-future.batchtools,
+ r-cran-ica,
+ r-cran-metap,
r-cran-natserv,
- r-cran-rentrez,
+ r-cran-rann,
r-cran-rocr,
+ r-cran-rsvd,
+ r-cran-sctransform,
+ r-cran-seurat,
+ r-cran-tsne,
+ r-other-apmswapp,
ruby-rgfa,
vdjtools
Description: Debian Med packages for development of bioinformatics applications
@@ -1188,10 +1290,10 @@ Recommends: abyss,
proda,
prodigal,
pynast,
- python-biopython,
python-cogent,
python3-biomaj3-cli,
python3-biopython,
+ qiime,
r-bioc-hilbertvis,
r-cran-pvclust,
r-cran-qtl,
@@ -1227,8 +1329,7 @@ Recommends: abyss,
Suggests: bagpipe,
cufflinks,
embassy-phylip,
- gmap,
- qiime
+ gmap
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
@@ -1241,10 +1342,11 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: freediams,
- freemedforms-freedata,
- python-hl7
+Recommends: python3-hl7
Suggests: drugref.org,
+ freediams,
+ freemedforms-freedata,
+ oscar,
sleepyhead
Description: Debian Med drug databases
This metapackage will install free drug databases and related
@@ -1270,7 +1372,9 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: r-cran-diagnosismed,
+Recommends: epigrass,
+ python3-treetime,
+ r-cran-diagnosismed,
r-cran-epi,
r-cran-epibasix,
r-cran-epicalc,
@@ -1278,16 +1382,14 @@ Recommends: r-cran-diagnosismed,
r-cran-epitools,
r-cran-lexrankr,
r-cran-seroincidence,
- r-cran-sf,
r-cran-sjplot,
r-cran-surveillance
Suggests: epifire,
- epigrass,
netepi-analysis,
netepi-collection,
- python-treetime,
r-cran-cmprsk,
r-cran-msm,
+ r-cran-sf,
repast,
shiny-server,
ushahidi
@@ -1335,8 +1437,6 @@ Recommends: aeskulap,
amide,
bart,
bart-view,
- biosig-tools,
- camitk-imp,
ctn,
ctsim,
dcm2niix,
@@ -1344,15 +1444,11 @@ Recommends: aeskulap,
dicom3tools,
dicomnifti,
dicomscope,
- fw4spl,
gdf-tools,
- ginkgocadx,
gwyddion,
imagej,
- imagevis3d,
invesalius,
ismrmrd-tools,
- itksnap,
king,
libgdcm-tools,
medcon,
@@ -1366,29 +1462,25 @@ Recommends: aeskulap,
mrtrix3,
nifti-bin,
odil,
- odin,
openslide-tools,
orthanc,
orthanc-wsi,
pixelmed-apps,
- plastimatch,
- python-dicom,
- python-nibabel,
python-nipy,
- python-nipype,
python-nitime,
- python-surfer,
- sigviewer,
- sofa-apps,
- voxbo,
+ python3-dicom,
+ python3-nibabel,
+ tifffile,
vtk-dicom-tools,
xmedcon
Suggests: afni,
ants,
bioimagesuite,
bioimagexd,
+ biosig-tools,
blox,
brainvisa,
+ camitk-imp,
caret,
cdmedicpacs,
cellprofiler,
@@ -1414,13 +1506,17 @@ Suggests: afni,
freesurfer,
fsl,
fslview,
+ fw4spl,
gimias,
+ ginkgocadx,
hid,
imagemagick,
+ imagevis3d,
imview,
incf-nidash-oneclick-clients,
insightapplications,
isis,
+ itksnap,
jemris,
jist,
kradview,
@@ -1438,6 +1534,7 @@ Suggests: afni,
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
+ odin,
omero,
opendicom.net,
openelectrophy,
@@ -1451,23 +1548,27 @@ Suggests: afni,
orthanc-webviewer,
paraview,
piano,
+ plastimatch,
pngquant,
pymeg,
python-dipy,
- python-mvpa2,
+ python-nipype,
python-pyxid,
- python-tifffile,
+ python3-mvpa2,
+ python3-surfer,
science-workflow,
+ sigviewer,
slicer,
+ sofa-apps,
stabilitycalc,
stir,
teem-apps,
tempo,
- tifffile,
trimage,
via-bin,
visit,
vmtk,
+ voxbo,
xnat
Description: Debian Med image processing and visualization packages
This metapackage will install Debian packages which might be useful in
@@ -1491,14 +1592,11 @@ Recommends: cimg-dev,
ctn-dev,
gmic,
libbart-dev,
- libbiosig-dev,
- libcamitk-dev,
libcifti-dev,
libedf-dev,
libgdcm2-dev,
libgdf-dev,
libgiftiio-dev,
- libinsighttoolkit4-dev,
libismrmrd-dev,
libmaxflow-dev,
libmdc2-dev,
@@ -1510,9 +1608,7 @@ Recommends: cimg-dev,
libodil-dev,
libopenigtlink-dev,
libopenslide-dev,
- libopensurgsim-dev,
libpapyrus3-dev,
- libsimpleitk1-dev,
libvigraimpex-dev,
libvistaio-dev,
libvolpack1-dev,
@@ -1522,46 +1618,50 @@ Recommends: cimg-dev,
octave-bart,
octave-dicom,
octave-gdf,
- odin,
python-cfflib,
- python-dicom,
- python-imageio,
- python-mia | python3-mia,
- python-mne,
- python-nibabel,
python-nipy,
- python-nipype,
python-nitime,
- python-openslide,
python-pyxnat,
python-vigra,
- python3-biosig,
- python3-simpleitk,
+ python3-dicom,
+ python3-gdcm,
+ python3-imageio,
+ python3-mia,
+ python3-nibabel,
+ python3-openslide,
r-cran-rniftilib
Suggests: emokit,
libbio-formats-java,
+ libbiosig-dev,
+ libcamitk-dev,
libcamp-dev,
libctk-dev,
libcv-dev,
libeegdev-dev,
libfreeimage-dev,
libics-dev,
+ libinsighttoolkit4-dev,
liblimereg-dev,
libmni-perllib-perl,
libnifti-doc,
libopenmeeg-dev,
libopenslide-java,
+ libopensurgsim-dev,
+ libsimpleitk1-dev,
libteem-dev,
libvia-dev,
libvmtk-dev,
libvtk6-dev,
libxdffileio-dev,
+ odin,
python-dipy,
- python-gdcm,
- python-libavg,
- python-mvpa2,
- python-tifffile,
- python-vmtk
+ python-nipype,
+ python-vmtk,
+ python3-biosig,
+ python3-mne,
+ python3-mvpa2,
+ python3-simpleitk,
+ tifffile
Description: Debian Med image processing and visualization packages development
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing and
@@ -1617,19 +1717,19 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: biosig-tools,
- gdf-tools,
+Recommends: gdf-tools,
octave,
paw,
paw++,
r-base
-Suggests: gate,
+Suggests: biosig-tools,
+ gate,
libbiosig-dev,
octave-biosig,
openvibe,
paw-demos,
- python-multipletau,
- python3-biosig
+ python3-biosig,
+ python3-multipletau
Description: Debian Med packages for medical physicists
This metapackage contains dependencies for a
collection of software and documentation which is useful for
@@ -1643,10 +1743,6 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: entangle,
- freediams,
- freemedforms-emr,
- ginkgocadx,
- gnumed-client,
gnumed-server,
libchipcard-tools,
orthanc,
@@ -1658,8 +1754,12 @@ Suggests: clearhealth,
elementalclinic,
elexis,
freeb,
+ freediams,
freemed,
+ freemedforms-emr,
freeshim,
+ ginkgocadx,
+ gnumed-client,
libctapimkt1,
medintux,
mirrormed,
@@ -1667,6 +1767,7 @@ Suggests: clearhealth,
openemr,
openpms,
openrep,
+ oscar,
proteus,
remitt,
resmedicinae,
@@ -1691,7 +1792,6 @@ Recommends: praat,
r-cran-psych
Suggests: psychopy,
python-pypsignifit,
- python-visionegg,
r-cran-psychometric,
r-cran-psychotree,
r-cran-psyphy,
@@ -1748,9 +1848,7 @@ Recommends: cronometer,
hunspell-en-med,
nutsqlite,
pcalendar,
- pondus,
- python-clips,
- python-fitbit,
+ python3-fitbit,
quitcount,
r-cran-fitbitscraper,
r-cran-fitcoach,
@@ -1762,7 +1860,9 @@ Suggests: cycle,
mencal,
mssstest,
nut-nutrition,
+ oscar,
pesco,
+ pondus,
sleepyhead
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
=====================================
debian/control.stub
=====================================
@@ -4,8 +4,8 @@ Uploaders: Andreas Tille <tille at debian.org>
Section: misc
Priority: optional
Build-Depends-Indep: blends-dev (>= 0.7.2~),
- debhelper (>= 12~)
-Standards-Version: 4.3.0
+Build-Depends: debhelper-compat (= 12)
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
=====================================
dependency_data/debian-med_3.4.json
=====================================
@@ -0,0 +1 @@
+{"bio-dev": {"depends": [], "suggests": ["python3-biopython-sql", "python-biopython-doc", "python3-pycosat", "libfreecontact-doc", "r-bioc-affy", "r-bioc-affyio", "r-bioc-altcdfenvs", "r-bioc-annotate", "r-bioc-annotationdbi", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-biocgenerics", "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-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-future.apply", "r-cran-future.batchtools", "r-cran-ica", "r-cran-metap", "r-cran-natserv", "r-cran-rann", "r-cran-rocr", "r-cran-rsvd", "ruby-rgfa", "librostlab-doc", "librostlab-blast-doc", "libswarm2-dev", "libgtextutils-dev", "libbam-dev", "libpbcopper-dev", "libdisorder-dev", "python3-pyflow", "libmilib-java", "vdjtools", "python3-alignlib", "python3-ctdopts", "ctdconverter", "libmodhmm-dev", "libsvmloc-dev"], "recommends": ["bioperl", "bioperl-run", "libncbi6-dev", "mcl", "biosquid", "cwltool", "snakemake", "libvibrant6-dev", "python3-biopython", "python-cogent", "python3-screed", "python3-cutadapt", "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", "python-corepywrap", "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-dynamictreecut", "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-rncl", "r-cran-rnexml", "r-cran-phangorn", "r-cran-phylobase", "r-cran-pscbs", "r-cran-qqman", "r-cran-rotl", "r-cran-rentrez", "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", "python-pbcore", "python-pbh5tools", "python3-cobra", "libtabixpp-dev", "python3-ruffus", "python3-hyphy", "python3-dendropy", "python3-skbio", "python3-pbconsensuscore", "python3-consensuscore2", "libconsensuscore-dev", "python-pbcommand", "python3-pyvcf", "python3-pyfaidx", "python3-sqt", "python-kineticstools", "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-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", "libmaus2-dev"], "ignore": ["golang-github-biogo-hts-dev"], "avoid": []}, "oncology": {"depends": [], "suggests": [], "recommends": ["uw-prism", "orthanc-wsi", "planunc", "dicompyler"], "ignore": [], "avoid": []}, "bio-ngs": {"depends": [], "suggests": [], "recommends": ["bedtools", "bwa", "bowtie", "blasr", "daligner", "mhap", "fastx-toolkit", "last-align", "wham-align", "maq", "picard-tools", "r-bioc-hilbertvis", "rna-star", "samtools", "sra-toolkit", "ssake", "tabix", "tophat", "bcftools", "vcftools", "velvet", "libvcflib-tools", "mothur", "qiime", "microbiomeutil", "r-bioc-metagenomeseq", "rtax", "sortmerna", "srst2", "stacks", "subread", "sumatra", "sumaclust", "vsearch", "wigeon", "anfo", "arden", "bowtie", "bowtie2", "artfastqgenerator", "art-nextgen-simulation-tools", "last-align", "maq", "ssake", "velvet | velvet-long", "bamtools", "bcbio", "bcftools", "berkeley-express", "bio-rainbow", "canu", "crac", "cufflinks", "cutadapt", "deepnano", "dindel", "discosnp", "dnaclust", "dwgsim", "ea-utils", "fastaq", "fastp", "fastqc", "fastx-toolkit", "flexbar", "fml-asm", "fsm-lite", "grinder", "giira", "hinge", "hilive", "hisat2", "idba", "igdiscover", "igv", "iva", "khmer", "kissplice", "kraken", "kraken2", "macs", "mapdamage", "maqview", "mira-assembler", "mapsembler2", "nanopolish", "paleomix", "pbsuite", "pbh5tools", "pbjelly", "pbhoney", "pirs", "placnet", "poretools", "python3-gffutils", "python3-pybedtools", "python3-sqt", "qcumber", "quorum", "r-bioc-deseq2", "salmon", "sambamba", "samblaster", "scythe", "seqprep", "seqtk", "sga", "sickle", "smalt", "smrtanalysis", "snap-aligner", "sniffles", "snp-sites", "snpomatic", "soapdenovo", "soapdenovo2", "spades", "sprai", "sra-toolkit", "stringtie", "tophat", "transrate-tools", "trimmomatic", "trinityrnaseq", "uc-echo", "velvetoptimiser", "kissplice", "scoary", "umap", "dindel", "mosaik-aligner", "r-cran-tcr", "r-cran-tigger", "r-cran-alakazam", "r-cran-shazam", "igor", "python3-airr", "python3-presto", "changeo", "vdjtools", "forge", "uc-echo", "annovar"], "ignore": [], "avoid": []}, "typesetting": {"depends": [], "suggests": ["kbibtex", "biber", "bibus", "jabref-plugin-oo", "r-cran-qqman"], "recommends": ["texlive-science", "texlive-latex-extra", "king"], "ignore": [], "avoid": []}, "cloud": {"depends": [], "suggests": [], "recommends": ["altree", "clearcut", "fastdnaml", "fasttree", "parsinsert", "phyml", "phyutility", "prime-phylo", "mrbayes", "tree-puzzle | tree-ppuzzle", "alien-hunter", "bagpipe", "fastlink", "loki", "gasic", "genometools", "plink", "probabel", "r-cran-qtl", "r-other-mott-happy.hbrem", "amap-align", "blast2", "biosquid", "boxshade", "cassiopee", "cdbfasta", "cd-hit", "clustalo", "clustalw", "conservation-code", "dialign", "dialign-tx", "emboss", "embassy-domalign", "embassy-domainatrix", "embassy-domsearch", "embassy-phylip", "exonerate", "gff2aplot", "gff2ps", "glam2", "gmap", "hmmer", "jellyfish", "kalign", "mafft", "mlv-smile", "mummer", "muscle", "neobio", "poa", "prank", "probcons", "proda", "pynast", "sibsim4", "sigma-align", "sim4", "snap", "squizz", "t-coffee", "wise", "zalign", "bamtools", "bedtools", "fastx-toolkit", "flexbar", "picard-tools", "samtools", "tabix", "vcftools", "anfo", "cufflinks", "bowtie", "bowtie2", "bwa", "last-align", "maq", "perm", "tophat", "smalt", "soapdenovo", "soapdenovo2", "abyss", "mapsembler2", "idba", "minia", "mira-assembler", "ssake", "velvet", "ampliconnoise", "arden", "fastqc", "discosnp", "dnaclust", "fitgcp", "giira", "grinder", "kissplice", "macs", "mothur", "paraclu", "r-bioc-hilbertvis", "sra-toolkit", "aragorn", "infernal", "rnahybrid", "rtax", "autodock", "autodock-vina", "autogrid", "concavity", "dssp", "freecontact", "gromacs", "hhsuite", "mustang", "pdb2pqr", "raster3d", "theseus", "melting", "mipe", "ncbi-epcr", "primer3", "acedb-other", "disulfinder", "ncbi-tools-bin", "ncoils", "python-cogent", "readseq", "tigr-glimmer", "seqan-apps", "staden-io-lib-utils", "aevol", "python3-biomaj3-cli", "bioperl", "bioperl-run", "cain", "clonalframe", "circos", "datamash", "prodigal", "python3-biopython", "qiime", "r-cran-pvclust", "r-cran-vegan"], "ignore": [], "avoid": []}, "bio": {"depends": [], "suggests": ["dascrubber", "emboss-explorer", "adun.app", "cain", "science-workflow", "getdata", "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", "mobyle", "mobyle-programs", "mobyle-tutorials", "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", "tophat", "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", 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"nast-ier", "wigeon", "minia", "trimmomatic", "trim-galore", "saint", "rtax", "rate4site", "rna-star", "sailfish", "topp", "openms", "scythe", "sickle", "smalr", "kmc", "king-probe", "ncl-tools", "tvc", "libvcflib-tools", "bppsuite", "bppphyview", "acacia", "adapterremoval", "aegean", "andi", "arden", "artfastqgenerator", "art-nextgen-simulation-tools", "assemblytics", "augustus", "baitfisher", "bandage", "beagle", "bedops", "biceps", "cnvkit", "csb", "diamond-aligner", "emperor", "euler2", "euler-sr", "fitgcp", "gasic", "giira", "ipig", "aevol", "alter-sequence-alignment", "amos-assembler", "hawkeye", "anfo", "apollo", "aragorn", "ariba", "atac", "atropos", "axe-demultiplexer", "axparafit", "axpcoords", "bali-phy", "barrnap", "bamtools", "bagpipe", "bax2bam", "bcbio", "bcftools", "bigsdb", "bio-eagle", "bio-tradis", "biobambam2", "biosyntax", "bismark", "bitseq", "blat", "blobology", "bio-rainbow", "braker", "card-rgi", "cassiopee", "ccs", "cdbfasta", "centrifuge", "cellprofiler", "chromhmm", "cgview", "brig", "cct", "cinema", "circlator", "clearcut", "clonalorigin", "cluster3", "chromimpute", "codonw", "condetri", "contrafold", "crac", "crossbow", "crux-toolkit", "cutadapt", "cytoscape", "dawg", "dazzdb", "dazzle", "deepbinner", "delly", "deepnano", "dendroscope", "dindel", "dwgsim", "ea-utils", "ecell", "ecopcr", "edtsurf", "emmax", "examl", "raxml-ng", "exabayes", "berkeley-express", "falcon", "fasta3", "fasttree", "fastahack", "fastaq", "fastml", "fastp", "fastqc", "fastqtl", "ffp", "filtlong", "unc-fish", "fml-asm", "forester", "freecontact", "freebayes", "fsa", "fsm-lite", "garli", "gatb-core", "gatk", "genometester", "genometools", "gffread", "grabix", "graphlan", "gwama", "gubbins", "haploview", "harvest-tools", "hilive", "hisat2", "hmmer2", "htqc", "idba", "igdiscover", "indelible", "iqtree", "iva", "jaligner", "jbrowse", "jmodeltest", "kaptive", "kleborate", "kempbasu", "kineticstools", "kissplice", "kma", "kmerresistance", "kraken", "kraken2", "lagan", "lambda-align", "lambda-align2", "leaff", "ltrsift", "lofreq", "kallisto", "khmer", "kmer", "radiant", "lefse", "mach-haplotyper", "macs", "macsyfinder", "maffilter", "mage2tab", "tab2mage", "malt", "manta", "mapdamage", "martj", "mash", "progressivemauve", "mauve-aligner", "meme", "meryl", "metabit", "metaphlan2", "metastudent", "microbegps", "mindthegap", "miniasm", "minimac4", "minimap", "minimap2", "mirtop", "molekel", "mosaik-aligner", "mosdepth", "mmseqs2", "mpsqed", "mptp", "mugsy", "multiqc", "murasaki | murasaki-mpi", "mview", "nanocall", "nanook", "nanopolish", "ncbi-entrez-direct", "ncbi-seg", "nextsv", "ngila", "ngsqctoolkit", "nw-align", "oases", "obitools", "oncofuse", "optimir", "optitype", "paipline", "pal2nal", "paleomix", "paraclu", "parsinsert", "parsnp", "partitionfinder", "patman", "patristic", "pbalign", "pbbarcode", "pbdagcon", "pbsuite", "pbgenomicconsensus", "pbjelly", "pbhoney", "pbh5tools", "pbsim", "pcma", "perm", "pftools", "phast", "phipack", "phybin", "phylophlan", "phyloviz-core", "phyutility", "phyx", "physamp", "piler", "pilercr", "pilon", "pipasic", "inspect", "tide", "pirs", "placnet", "plasmidseeker", "plato", "plip", "poretools", "porechop", "prank", "predictprotein", "proalign", "prodigal", "prokka", "proteinortho", "prottest", "psortb", "pscan-tfbs", "pscan-chip", "psipred", "pssh2", "python3-cogent", "pycorrfit", "pyscanfcs", "python3-deeptools", "python3-deeptoolsintervals", "python3-geneimpacts", "python3-gffutils", "python3-pybel", "python3-pybedtools", "python3-sqt", "python3-reaper", "python3-treetime", "qcumber", "qtltools", "qualimap", "quast", "quorum", "ragout", "rambo-k", "rapmap", "r-bioc-rtracklayer", "r-bioc-gviz", "r-bioc-biostrings", "r-bioc-annotate", "r-bioc-genefilter", "r-bioc-deseq2", "r-bioc-dnacopy", "r-bioc-geneplotter", "r-bioc-cummerbund", "r-bioc-ebseq", "r-bioc-impute", "r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-phyloseq", "r-bioc-mofa", "r-bioc-multiassayexperiment", "r-bioc-limma", "r-bioc-bitseq", "r-bioc-pcamethods", "r-cran-samr", "r-cran-rotl", "r-cran-adegenet", "r-cran-adephylo", "r-cran-ape", "r-cran-distory", "r-cran-drinsight", "r-cran-kaos", "r-cran-metamix", "r-cran-phangorn", "r-cran-phytools", "r-cran-pscbs", "r-cran-seurat", "r-cran-seqinr", "r-bioc-tfbstools", "r-bioc-cner", "r-cran-treescape", "r-cran-tsne", "r-cran-vegan", "r-cran-webgestaltr", "r-other-apmswapp", "r-other-hms-dbmi-spp", "r-other-wgcna", "relion-bin+gui | relion-bin+mpi+gui", "relion-bin | relion-bin+mpi", "rdp-alignment", "rdp-readseq", "rdp-classifier", "reapr", "repeatmasker-recon", "repeatmasker", "roadtrips", "roary", "roguenarok", "rsat", "rsem", "sambamba", "samblaster", "salmon", "sap", "scrm", "sga", "seer", "segemehl", "seq-seq-pan", "seqmagick", "seqprep", "seqsero", "seqtk", "sequenceconverter.app", "sibelia", "sina", "sistr", "situs", "sim4db", "skesa", "smalt", "smithwaterman", "ssw-align", "smrtanalysis", "snpeff", "snpomatic", "solvate", "sortmerna", "snap-aligner", "sniffles", "sourmash", "spaced", "spades", "spaln", "sparta", "sprai", "srst2", "ssaha", "sspace", "staden", "stacks", "strap", "strap-base", "stringtie", "subread", "suitename", "sumatra", "sumaclust", "sumtrees", "surankco", "swarm", "tacg", "tantan", "toppred", "transdecoder", "tnseq-transit", "tn-seqexplorer", "toil", "tracetuner", "transrate-tools", "treeview", "trinityrnaseq", "uc-echo", "umis", "unanimity", "unicycler", "varna", "varmatch", "varscan", "vcfanno", "vdjtools", "vg", "vienna-rna", "virulencefinder", "vmd", "vsearch", "yaha", "canu", "zalign", "zodiac-zeden", "discosnp", "mapsembler2", "dnaclust", "r-cran-tcr", "r-cran-tigger", "r-cran-alakazam", "r-cran-shazam", "igor", "r-cran-sdmtools", "python3-presto", "changeo", "ncbi-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", "compclust", "treebuilder3d", "excavator", "treetime", "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", "raccoon", "racon", "spoa", "rampler", "librg-utils-perl", "snap", "pyvcf", "vcftools", "beads", "x-tandem-pipeline", "forge", "metarep", "arachne", "maker2", "rmblast", "e-hive", "cmap", "gbrowse-syn", "tripal", "genemark", "annovar", "python3-orange", "tigr-glimmer-mg"], "ignore": ["mozilla-biofox", "riso", "catissuecore", "trapss"], "avoid": []}, "dental": {"depends": [], "suggests": [], "recommends": ["openmolar", "imagetooth", "entangle"], "ignore": [], "avoid": []}, "imaging-dev": {"depends": [], "suggests": ["libvtk6-dev", "libnifti-doc", "libfreeimage-dev", "libics-dev", "liblimereg-dev", "emokit", "libeegdev-dev", "libxdffileio-dev", "tifffile", "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", "python-nipy", "python-nipype", "python-nitime", "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", "python-pyxnat", "python-dipy", "libbiosig-dev", "python3-biosig", "libctk-dev", "python-cfflib", "libopenslide-dev", "python3-openslide", "libopenslide-java", "libbio-formats-java", "octave-dicom", "libcamitk-dev", "libpapyrus3-dev", "python3-mne", "python-vmtk", "libvmtk-dev", "libvigraimpex-dev", "python-vigra", "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": []}, "research": {"depends": [], "suggests": [], "recommends": ["r-cran-rpact", "openclinica"], "ignore": [], "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": []}, "practice": {"depends": [], "suggests": ["libctapimkt1", "openpms", "resmedicinae", "sqlclinic", "openrep"], "recommends": ["gnumed-client", "gnumed-server", "libchipcard-tools", "ginkgocadx", "freediams", "freemedforms-emr", "r-cran-medadherence", "entangle", "sleepyhead", "oscar", "orthanc", "orthanc-wsi", "medintux", "mirth", "tinyheb", "mirrormed", "elexis", "freeb", "freemed", "elementalclinic", "openemr", "clearhealth", "proteus", "thera-pi", "freeshim", "remitt", "qrisk2"], "ignore": ["clearhealth"], "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": []}, "cms": {"depends": [], "suggests": ["zope-zms", "hid"], "recommends": ["xnat"], "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"], "ignore": [], "avoid": []}, "psychology": {"depends": [], "suggests": ["science-psychophysics"], "recommends": ["python-pyepl", "praat", "r-cran-foreign", "psignifit", "python-pypsignifit", "r-cran-psy", "psychopy", "r-cran-psych", "r-cran-psychometric", "r-cran-psychotree", "r-cran-psyphy"], "ignore": [], "avoid": []}, "bio-phylogeny": {"depends": [], "suggests": ["python3-treetime"], "recommends": ["altree", "fastdnaml", "njplot", "tree-puzzle | tree-ppuzzle", "probalign", "treeviewx", "phylip", "muscle", "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"], "ignore": [], "avoid": []}, "imaging": {"depends": [], "suggests": ["imagemagick", "pngquant", "imview", "trimage", "conquest-dbase", "conquest-mysql", "conquest-postgres", "conquest-sqlite", "paraview", "orthanc-webviewer", "orthanc-dicomweb", "orthanc-imagej", "orthanc-postgresql", "orthanc-mysql", "visit", "mrisim", "connectomeviewer", "eeglab", "elastix", "python-pyxid", "dtitk", "openwalnut-qt4", "miview", "cmtk", "freesurfer", "isis", "pymeg", "stabilitycalc", "hid", "incf-nidash-oneclick-clients", "science-workflow", "tifffile"], "recommends": ["amide", "ctsim", "ctn", "dicomnifti", "imagej", "minc-tools", "medcon", "python3-nibabel", "python3-dicom", "xmedcon", "dcmtk", "nifti-bin", "aeskulap", "fsl", "fslview", "via-bin", "gwyddion", "sofa-apps", "python3-mvpa2", "python-nipy", "python-nipype", "python-nitime", "caret", "libgdcm-tools", "slicer", "lipsia", "dicom3tools", "imagevis3d", "odin", "dicomscope", "pixelmed-apps", "vmtk", "ginkgocadx", "openslide-tools", "conquest-common", "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", "mrtrix", "mrtrix3", "ants", "itksnap", "mriconvert", "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", "python-dipy", "plastimatch", "medisnap", "gimias", "mayam", "xnat", "biosig-tools", "python3-surfer", "dicoogle", "cellprofiler", "bioimagexd", "omero", "king", "vtk-dicom-tools", "gdf-tools", "fw4spl", "bart", "bart-view", "dcm2niix", "orthanc-wsi", "odil"], "ignore": [], "avoid": []}, "rehabilitation": {"depends": [], "suggests": ["aghermann"], "recommends": ["sitplus"], "ignore": [], "avoid": []}, "laboratory": {"depends": [], "suggests": [], "recommends": ["opencfu", "orthanc-wsi", "openelis", "openfreezer", "catissuesuite"], "ignore": [], "avoid": []}, "pharmacy": {"depends": [], "suggests": [], "recommends": ["chemtool", "raccoon", "r-cran-dosefinding", "r-cran-rpact"], "ignore": [], "avoid": []}, "data": {"depends": [], "suggests": ["sleepyhead", "oscar"], "recommends": ["freediams", "freemedforms-freedata", "python3-hl7", "drugref.org"], "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"], "ignore": [], "avoid": []}, "epi": {"depends": [], "suggests": ["r-cran-msm", "r-cran-cmprsk", "shiny-server", "repast"], "recommends": ["epigrass", "r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi", "r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "r-cran-seroincidence", "ushahidi", "r-cran-lexrankr", "r-cran-sf", "r-cran-sjplot", "python3-treetime", "netepi-analysis", "netepi-collection", "epifire"], "ignore": [], "avoid": []}}
\ No newline at end of file
=====================================
tasks/imaging
=====================================
@@ -862,5 +862,3 @@ Recommends: dcm2niix
Recommends: orthanc-wsi
Recommends: odil
-
-Suggests: tifffile
View it on GitLab: https://salsa.debian.org/blends-team/med/compare/b01bd921cf629b9ab29c5b2cc4a8c13736ebe2c3...44e7622108b7996020911b48465e3a11a128fffb
--
View it on GitLab: https://salsa.debian.org/blends-team/med/compare/b01bd921cf629b9ab29c5b2cc4a8c13736ebe2c3...44e7622108b7996020911b48465e3a11a128fffb
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