[Blends-commit] [SCM] med branch, master, updated. 2c219f08e548f30dc697482887b3c1a25093d0b0
Andreas Tille
tille at debian.org
Fri Dec 1 19:13:16 UTC 2017
The following commit has been merged in the master branch:
commit 41c9fc06ffc4fb408e1b17185f8c2c7a3ee0944a
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 1 20:00:13 2017 +0100
Render new dependency relations
diff --git a/debian/changelog b/debian/changelog
index 8bf4b36..e35d5cf 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,8 @@
-debian-med (3.0.2) UNRELEASED; urgency=medium
+debian-med (3.1) UNRELEASED; urgency=medium
- *
+ * Versioned Build-Depends bumped to 0.6.99 to enable Recommends in tasks
+ files
+ * s/Depends/Recommends/
-- Andreas Tille <tille at debian.org> Wed, 19 Apr 2017 21:09:03 +0200
diff --git a/debian/control b/debian/control
index 6158c05..d2b5bbd 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: misc
Priority: extra
-Build-Depends-Indep: blends-dev (>= 0.6.92.3)
+Build-Depends-Indep: blends-dev (>= 0.6.99)
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/blends/projects/med.git
Vcs-Git: https://anonscm.debian.org/git/blends/projects/med.git
@@ -112,10 +112,10 @@ Recommends: abacas,
autogrid,
axe-demultiplexer,
baitfisher,
- ballview,
bamtools,
barrnap,
bcftools,
+ beads,
beagle,
beast-mcmc,
beast2-mcmc,
@@ -133,7 +133,6 @@ Recommends: abacas,
bppsuite,
brig,
bwa,
- canu,
cassiopee,
cd-hit,
cdbfasta,
@@ -150,12 +149,12 @@ Recommends: abacas,
concavity,
conservation-code,
crac,
+ csb,
cutadapt,
daligner,
datamash,
dawg,
dazzdb,
- deepnano,
dialign,
dialign-tx,
diamond-aligner,
@@ -166,7 +165,6 @@ Recommends: abacas,
dssp,
dwgsim,
e-mem,
- ea-utils,
ecopcr,
edtsurf,
eigensoft,
@@ -188,7 +186,6 @@ Recommends: abacas,
fastx-toolkit,
ffindex,
figtree,
- filo,
fitgcp,
flexbar,
fml-asm,
@@ -229,7 +226,6 @@ Recommends: abacas,
iqtree,
iva,
jaligner,
- jalview,
jellyfish,
jmodeltest,
jmol,
@@ -254,7 +250,6 @@ Recommends: abacas,
macsyfinder,
maffilter,
mafft,
- mapdamage,
mapsembler2,
maq,
maqview,
@@ -281,7 +276,6 @@ Recommends: abacas,
murasaki,
muscle,
mustang,
- nanopolish,
nast-ier,
ncbi-blast+,
ncbi-blast+-legacy,
@@ -296,8 +290,6 @@ Recommends: abacas,
njplot,
norsnet,
norsp,
- openms,
- paleomix,
paml,
paraclu,
parsinsert,
@@ -315,6 +307,7 @@ Recommends: abacas,
perlprimer,
perm,
pftools,
+ phast,
phipack,
phybin,
phylip,
@@ -370,7 +363,6 @@ Recommends: abacas,
python-treetime,
python3-biomaj3,
qcumber,
- qiime,
qtltools,
quorum,
r-bioc-annotate,
@@ -379,7 +371,6 @@ Recommends: abacas,
r-bioc-deseq2,
r-bioc-dnacopy,
r-bioc-ebseq,
- r-bioc-edger,
r-bioc-genefilter,
r-bioc-geneplotter,
r-bioc-gviz,
@@ -404,7 +395,6 @@ Recommends: abacas,
r-cran-vegan,
r-other-mott-happy.hbrem,
radiant,
- rambo-k,
rapmap,
rasmol,
raster3d,
@@ -429,6 +419,7 @@ Recommends: abacas,
runcircos-gui,
saint,
salmon,
+ sambamba,
samtools,
scrm,
scythe,
@@ -436,7 +427,6 @@ Recommends: abacas,
seer,
seqan-apps,
seqprep,
- seqsero,
seqtk,
sga,
sibsim4,
@@ -483,7 +473,6 @@ Recommends: abacas,
tm-align,
tnseq-transit,
tophat,
- topp,
toppred,
transdecoder,
transrate-tools,
@@ -506,6 +495,7 @@ Suggests: acacia,
adun.app,
amos-assembler,
amoscmp,
+ annovar,
apollo,
arachne,
arb,
@@ -514,8 +504,10 @@ Suggests: acacia,
axparafit,
axpcoords,
bagpipe,
+ ballview,
bambus,
- beads,
+ bandage,
+ belvu,
biceps,
big-blast,
bigsdb,
@@ -530,16 +522,17 @@ Suggests: acacia,
cactus,
caftools,
cain,
- cap3,
+ canu,
card-rgi,
ccs,
cdna-db,
+ centrifuge,
cinema,
+ clonalframeml,
clonalorigin,
cluster3,
cmap,
cnvkit,
- coalesce,
compclust,
condetri,
contrafold,
@@ -554,7 +547,10 @@ Suggests: acacia,
dascrubber,
dazzle,
decipher,
+ deepnano,
+ dotter,
e-hive,
+ ea-utils,
ecell,
elph,
embassy-phylip,
@@ -574,12 +570,13 @@ Suggests: acacia,
fasta3,
ffp,
figaro,
+ filo,
finex,
- fluctuate,
forester,
forge,
galaxy,
gassst,
+ gatb-core,
gatk,
gbioseq,
gbrowse-syn,
@@ -598,9 +595,11 @@ Suggests: acacia,
hawkeye,
hexamer,
hilbertvisgui,
+ hinge,
htqc,
igv,
inspect,
+ jalview,
jbrowse,
jigsaw,
jstreeview,
@@ -616,6 +615,7 @@ Suggests: acacia,
maker2,
malt,
manta,
+ mapdamage,
martj,
maude,
maxd,
@@ -646,6 +646,8 @@ Suggests: acacia,
mummergpu,
mview,
nanocall,
+ nanook,
+ nanopolish,
nextsv,
ngila,
ngsqctoolkit,
@@ -655,8 +657,10 @@ Suggests: acacia,
obo-edit,
oligoarrayaux,
omegamap,
+ openms,
operondb,
pal2nal,
+ paleomix,
partigene,
partitionfinder,
patman,
@@ -664,7 +668,6 @@ Suggests: acacia,
pcma,
pfaat,
phagefinder,
- phast,
phpphylotree,
phylographer,
phylophlan,
@@ -681,6 +684,7 @@ Suggests: acacia,
pyrophosphate-tools,
python-orange,
python-reaper,
+ qiime,
qtlcart,
qualimap,
r-bioc-annotationhub,
@@ -696,9 +700,9 @@ Suggests: acacia,
r-other-apmswapp,
r-other-valdar-bagphenotype.library,
raccoon,
+ rambo-k,
raxml-ng,
rbs-finder,
- recombine,
repeatmasker,
rmblast,
roadtrips,
@@ -706,13 +710,15 @@ Suggests: acacia,
rose,
rosetta,
rsat,
- sambamba,
sap,
science-workflow,
+ scoary,
segemehl,
seq-gen,
+ seqsero,
sequenceconverter.app,
sift,
+ sistr,
situs,
snpeff,
sparta,
@@ -728,6 +734,7 @@ Suggests: acacia,
tide,
tigr-glimmer-mg,
tn-seqexplorer,
+ topp,
trace2dbest,
tracetuner,
treebuilder3d,
@@ -737,6 +744,7 @@ Suggests: acacia,
tvc,
twain,
ugene,
+ umap,
unc-fish,
uniprime,
varmatch,
@@ -812,7 +820,6 @@ Recommends: bio-tradis,
libngs-java,
libngs-sdk-dev,
libnhgri-blastall-perl,
- libopenms-dev,
libpal-java,
libpbbam-dev,
libpbdata-dev,
@@ -857,13 +864,14 @@ Recommends: bio-tradis,
python-pbh5tools,
python-pysam,
python-rdkit,
- python3-biomaj3 | python-biomaj3,
+ python3-biomaj3,
python3-biopython | python-biopython,
python3-biotools | python-biotools,
python3-csb | python-csb,
python3-cutadapt | python-cutadapt,
python3-dendropy | python-dendropy,
python3-fast5 | python-fast5,
+ python3-gfapy,
python3-gffutils,
python3-intervaltree-bio | python-intervaltree-bio,
python3-ngs | python-ngs,
@@ -885,12 +893,14 @@ Recommends: bio-tradis,
sbmltoolbox,
seqan-dev
Suggests: bioclipse,
+ gatb-core,
libbam-dev,
libdisorder-dev,
libforester-java,
libfreecontact-doc,
libgff-perl,
libgtextutils-dev,
+ libopenms-dev,
libpbcopper-dev,
libqcpp-dev,
libroadrunner-dev,
@@ -903,9 +913,11 @@ Suggests: bioclipse,
octace-bioinfo,
octave-bioinfo,
python-bd2k,
+ python-biomaj3,
python-biopython-doc,
python-bx,
python-consensuscore2,
+ python-ete3,
python-hyphy,
python-misopy,
python-mmtk,
@@ -917,6 +929,7 @@ Suggests: bioclipse,
python3-biopython-sql | python-biopython-sql,
python3-bx,
python3-consensuscore2,
+ python3-ete3,
python3-hyphy,
python3-misopy,
python3-pyfasta,
@@ -1008,7 +1021,6 @@ Recommends: abyss,
fastqc,
fasttree,
fastx-toolkit,
- filo,
fitgcp,
flexbar,
freecontact,
@@ -1067,8 +1079,6 @@ Recommends: abyss,
python-biopython,
python-cogent,
python3-biopython,
- qiime,
- r-bioc-edger,
r-bioc-hilbertvis,
r-cran-pvclust,
r-cran-qtl,
@@ -1104,7 +1114,9 @@ Recommends: abyss,
Suggests: bagpipe,
cufflinks,
embassy-phylip,
+ filo,
gmap,
+ qiime,
r-other-valdar-bagphenotype.library
Description: Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
@@ -1197,7 +1209,6 @@ Architecture: all
Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
Recommends: aeskulap,
amide,
- ants,
bart,
biosig-tools,
camitk-imp,
@@ -1209,7 +1220,6 @@ Recommends: aeskulap,
dicomnifti,
dicomscope,
fw4spl,
- gdf-tools,
ginkgocadx,
gwyddion,
imagej,
@@ -1228,8 +1238,6 @@ Recommends: aeskulap,
mricron,
mrtrix,
nifti-bin,
- odin,
- openmeeg-tools,
openslide-tools,
orthanc,
orthanc-wsi,
@@ -1238,18 +1246,15 @@ Recommends: aeskulap,
python-dicom,
python-mvpa2,
python-nibabel,
- python-nipy,
- python-nipype,
python-nitime,
python-surfer,
python-tifffile,
sigviewer,
sofa-apps,
- teem-apps,
- voxbo,
vtk-dicom-tools,
xmedcon
Suggests: afni,
+ ants,
bart-view,
bioimagesuite,
bioimagexd,
@@ -1280,8 +1285,8 @@ Suggests: afni,
freesurfer,
fsl,
fslview,
+ gdf-tools,
gimias,
- gofigure2,
hid,
imagemagick,
imview,
@@ -1305,9 +1310,11 @@ Suggests: afni,
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
+ odin,
omero,
opendicom.net,
openelectrophy,
+ openmeeg-tools,
opensourcepacs,
openwalnut-qt4,
orthanc-dicomweb,
@@ -1318,17 +1325,21 @@ Suggests: afni,
piano,
pngquant,
pymeg,
+ python-nipy,
+ python-nipype,
python-pyxid,
science-workflow,
slicer,
stabilitycalc,
stir,
+ teem-apps,
tempo,
trimage,
via-bin,
visit,
vmtk,
volview,
+ voxbo,
xnat
Description: Debian Med image processing and visualization packages
This metapackage will install Debian packages which might be useful in
@@ -1353,11 +1364,8 @@ Recommends: cimg-dev,
libbiosig-dev,
libcamitk-dev,
libcifti-dev,
- libcv-dev,
libedf-dev,
libgdcm2-dev,
- libgdf-dev,
- libgiftiio-dev,
libinsighttoolkit4-dev,
libismrmrd-dev,
libmaxflow-dev,
@@ -1367,50 +1375,44 @@ Recommends: cimg-dev,
libmiaviewit-dev,
libminc-dev,
libnifti-dev,
- libodil0-dev,
libopenigtlink-dev,
- libopenmeeg-dev,
libopenslide-dev,
- libopensurgsim-dev,
libpapyrus3-dev,
- libteem-dev,
libvigraimpex-dev,
libvistaio-dev,
libvolpack1-dev,
libvtk-dicom-dev,
libvtk6-dev,
octave-bart,
- octave-gdf,
- odin,
python-casmoothing,
- python-cfflib,
python-dicom,
- python-dipy,
python-imageio,
python-mia | python3-mia,
- python-mne,
python-mvpa2,
python-nibabel,
- python-nipy,
- python-nipype,
python-nitime,
python-openslide,
python-pyxnat,
python-vigra,
r-cran-rniftilib
Suggests: emokit,
- igstk-examples,
libbio-formats-java,
libcamp-dev,
libctk-dev,
+ libcv-dev,
libeegdev-dev,
libfreeimage-dev,
+ libgdf-dev,
+ libgiftiio-dev,
libics-dev,
- libigstk4-dev,
liblimereg-dev,
libmni-perllib-perl,
libnifti-doc,
+ libodil0-dev,
+ libopenmeeg-dev,
libopenslide-java,
+ libopensurgsim-dev,
+ libteem-dev,
libvia-dev,
libvmtk-dev,
libvtk-dicom-java,
@@ -1418,7 +1420,14 @@ Suggests: emokit,
libvxl1-dev,
libxdffileio-dev,
octave-dicom,
+ octave-gdf,
+ odin,
+ python-cfflib,
+ python-dipy,
python-libavg,
+ python-mne,
+ python-nipy,
+ python-nipype,
python-tifffile,
python-vmtk
Description: Debian Med image processing and visualization packages development
@@ -1468,12 +1477,12 @@ Section: metapackages
Architecture: all
Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
Recommends: biosig-tools,
- gdf-tools,
octave,
paw,
paw++,
r-base
Suggests: gate,
+ gdf-tools,
libbiosig-dev,
octave-biosig,
openvibe,
@@ -1532,7 +1541,6 @@ Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${sourc
Recommends: praat,
psignifit,
psychopy,
- python-pyepl,
r-cran-foreign,
r-cran-psy
Suggests: miscpsycho,
@@ -1540,6 +1548,7 @@ Suggests: miscpsycho,
psychometric,
psychotree,
psyphy,
+ python-pyepl,
python-pypsignifit,
python-visionegg,
science-psychophysics
@@ -1561,8 +1570,7 @@ Package: med-statistics
Section: metapackages
Architecture: all
Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
-Recommends: r-bioc-edger,
- r-bioc-limma,
+Recommends: r-bioc-limma,
r-bioc-multtest,
r-bioc-qvalue,
r-cran-ade4,
--
Debian Med metapackages
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