Package: release.debian.org
Severity: normal
User: release.debian....@packages.debian.org
Usertags: unblock
Please unblock package debian-med
This is the usual update of Debian Med metapackages at the end (or
rather close to the end) of the release cycle. Since we do not expect
severe changes in the package pool regarding packages that are relevant
for the Debian Med team this upload of the metapackages is reflecting
the package pool that is expected to be released with Stretch.
Please note: Due to the creation method of the metapackages those
packages that were removed from testing were just "degraded" from
Recommends to Suggests. In the usual maintenance process also packages
that were added to unstable also end up with Suggests since this is the
usual metapackage layout users are comfortable with. While we are
aware that this avoids the "minimum change freeze policy" this feature
of metapackages was accepted in all previous release processes.
BTW, to enhance the overview about changes inside the dependency code in
a GSoC project code for automatic changelog generation was written to
possibly help the release team. In the Debian Med case I unfortunately
forgot to activate this code. It was activated in Debian Science which
on one hand has more verbose changelog on the other hand this might be
also considered "noise" (I had some unfortunately private discussion in
German about the sense of this). I'd happily receive your hint what you
would like more - the current short Debian Med packages changelog or
the long Debian Science packages changelog which will be submitted in
the next bug report.
Kind regards and thanks for your work as release team
Andreas.
unblock debian-med/3.0.1
-- System Information:
Debian Release: 8.7
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
diff -Nru debian-med-3.0/debian/changelog debian-med-3.0.1/debian/changelog
--- debian-med-3.0/debian/changelog 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/debian/changelog 2017-04-19 15:29:37.000000000 +0200
@@ -1,3 +1,9 @@
+debian-med (3.0.1) unstable; urgency=medium
+
+ * Re-render before Stretch release
+
+ -- Andreas Tille <ti...@debian.org> Wed, 19 Apr 2017 15:29:37 +0200
+
debian-med (3.0) unstable; urgency=medium
* Bump version for Stretch release
diff -Nru debian-med-3.0/debian/control debian-med-3.0.1/debian/control
--- debian-med-3.0/debian/control 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/debian/control 2017-04-19 15:29:37.000000000 +0200
@@ -123,7 +123,6 @@
bio-eagle,
bio-rainbow,
blasr,
- blast2,
bowtie,
bowtie2,
boxshade,
@@ -148,6 +147,7 @@
cutadapt,
daligner,
dascrubber,
+ datamash,
dawg,
dazzdb,
dialign,
@@ -219,7 +219,6 @@
iqtree,
iva,
jaligner,
- jalview,
jellyfish,
jmodeltest,
jmol,
@@ -273,6 +272,7 @@
nanopolish,
nast-ier,
ncbi-blast+,
+ ncbi-blast+-legacy,
ncbi-entrez-direct,
ncbi-epcr,
ncbi-seg,
@@ -284,7 +284,6 @@
njplot,
norsnet,
norsp,
- openms,
paraclu,
parsinsert,
parsnp,
@@ -351,7 +350,6 @@
pynast,
pyscanfcs,
python-cogent,
- qiime,
qtltools,
r-bioc-annotate,
r-bioc-biostrings,
@@ -458,7 +456,6 @@
tigr-glimmer,
tm-align,
tophat,
- topp,
toppred,
transdecoder,
transrate-tools,
@@ -496,6 +493,7 @@
biceps,
big-blast,
bigsdb,
+ bio-tradis,
biomaj,
biomaj-watcher,
bitseq,
@@ -515,6 +513,7 @@
clonalorigin,
cluster3,
cmap,
+ cnvkit,
coalesce,
compclust,
condetri,
@@ -544,7 +543,9 @@
estscan,
euler-sr,
euler2,
+ exabayes,
exalt,
+ examl,
excavator,
fasta,
fasta3,
@@ -565,6 +566,7 @@
genetrack,
genezilla,
genographer,
+ getdata,
glimmerhmm,
gmap,
gmv,
@@ -577,12 +579,12 @@
htqc,
igv,
inspect,
+ jalview,
jbrowse,
jigsaw,
jstreeview,
kclust,
kempbasu,
- kronatools,
lagan,
lamarc,
lofreq,
@@ -617,6 +619,7 @@
molekel,
mosaik-aligner,
mpsqed,
+ mptp,
mrs,
msatfinder,
mugsy,
@@ -632,8 +635,10 @@
obo-edit,
oligoarrayaux,
omegamap,
+ openms,
operondb,
pal2nal,
+ paleomix,
paml,
partigene,
partitionfinder,
@@ -656,10 +661,14 @@
prot4est,
pscan-tfbs,
psipred,
+ psortb,
pssh2,
pyrophosphate-tools,
python-orange,
python-reaper,
+ python3-biomaj3,
+ qcumber,
+ qiime,
qtlcart,
qualimap,
r-bioc-annotationhub,
@@ -675,19 +684,25 @@
r-other-apmswapp,
r-other-valdar-bagphenotype.library,
raccoon,
+ radiant,
+ raxml-ng,
rbs-finder,
recombine,
repeatmasker,
rmblast,
roadtrips,
roche454ace2caf,
+ roguenarok,
rose,
rosetta,
rsat,
+ runcircos-gui,
+ sambamba,
sap,
science-workflow,
segemehl,
seq-gen,
+ seqsero,
sequenceconverter.app,
sift,
situs,
@@ -704,6 +719,8 @@
tetra,
tide,
tigr-glimmer-mg,
+ tnseq-transit,
+ topp,
trace2dbest,
tracetuner,
treebuilder3d,
@@ -785,7 +802,6 @@
libngs-java,
libngs-sdk-dev,
libnhgri-blastall-perl,
- libopenms-dev,
libpal-java,
libpbbam-dev,
libpbdata-dev,
@@ -804,7 +820,6 @@
libsnp-sites1-dev,
libsort-key-top-perl,
libsrf-dev,
- libssm-dev,
libssw-dev,
libssw-java,
libstaden-read-dev,
@@ -853,18 +868,24 @@
ruby-crb-blast,
sbmltoolbox,
seqan-dev
-Suggests: bioclipse,
+Suggests: bio-tradis,
+ bioclipse,
libbam-dev,
libbio-eutilities-perl,
+ libbiod-dev,
libdisorder-dev,
libforester-java,
libfreecontact-doc,
libgff-perl,
libgtextutils-dev,
+ libopenms-dev,
libpbcopper-dev,
libqcpp-dev,
+ libroadrunner-dev,
librostlab-blast-doc,
librostlab-doc,
+ libseqlib-dev,
+ libssm-dev,
libswarm2-dev,
mgltools-networkeditor,
mgltools-pybabel,
@@ -872,15 +893,21 @@
octace-bioinfo,
octave-bioinfo,
python-bd2k,
+ python-biomaj3,
python-biopython-doc,
+ python-biotools,
python-bx,
python-consensuscore2,
python-hyphy,
python-misopy,
python-mmtk,
python-pyfasta,
+ python-pyflow,
+ python-roadrunner,
python3-bd2k,
+ python3-biomaj3,
python3-biopython-sql | python-biopython-sql,
+ python3-biotools,
python3-bx,
python3-consensuscore2,
python3-gffutils,
@@ -912,6 +939,7 @@
r-bioc-snpstats,
r-bioc-variantannotation,
r-bioc-xvector,
+ r-cran-natserv,
r-cran-rentrez,
r-cran-rocr,
ruby-rgfa
@@ -1034,7 +1062,6 @@
python-biopython,
python-cogent,
python3-biopython,
- qiime,
r-bioc-edger,
r-bioc-hilbertvis,
r-cran-pvclust,
@@ -1072,6 +1099,7 @@
cufflinks,
embassy-phylip,
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,
@@ -1120,8 +1148,10 @@
Suggests: netepi-analysis,
netepi-collection,
r-cran-cmprsk,
+ r-cran-lexrankr,
r-cran-msm,
repast,
+ shiny-server,
ushahidi
Description: Debian Med epidemiology related packages
This metapackage will install tools that are useful in epidemiological
@@ -1142,6 +1172,7 @@
openeyes,
openmaxims,
openmrs,
+ orthanc-wsi,
oscar-mcmaster,
patientos,
tryton-modules-health,
@@ -1171,7 +1202,6 @@
dicom3tools,
dicomnifti,
dicomscope,
- fslview,
gdf-tools,
ginkgocadx,
gwyddion,
@@ -1189,10 +1219,7 @@
minc-tools,
mriconvert,
mricron,
- mrtrix,
nifti-bin,
- odin,
- openmeeg-tools,
openslide-tools,
orthanc,
pixelmed-apps,
@@ -1200,8 +1227,6 @@
python-dicom,
python-mvpa2,
python-nibabel,
- python-nipy,
- python-nipype,
python-nitime,
python-surfer,
python-tifffile,
@@ -1241,6 +1266,7 @@
fiji,
freesurfer,
fsl,
+ fslview,
fw4spl,
gimias,
gofigure2,
@@ -1267,19 +1293,25 @@
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
+ mrtrix,
+ odin,
omero,
opendicom.net,
openelectrophy,
+ openmeeg-tools,
opensourcepacs,
openwalnut-qt4,
orthanc-dicomweb,
orthanc-imagej,
orthanc-postgresql,
orthanc-webviewer,
+ orthanc-wsi,
paraview,
piano,
pngquant,
pymeg,
+ python-nipy,
+ python-nipype,
python-pyxid,
science-workflow,
slicer,
@@ -1330,7 +1362,6 @@
libnifti-dev,
libodil0-dev,
libopenigtlink-dev,
- libopenmeeg-dev,
libopenslide-dev,
libopensurgsim-dev,
libpapyrus3-dev,
@@ -1342,17 +1373,13 @@
libvtk6-dev,
octave-bart,
octave-gdf,
- odin,
python-casmoothing,
python-cfflib,
python-dicom,
- python-dipy,
python-mia | python3-mia,
python-mne,
python-mvpa2,
python-nibabel,
- python-nipy,
- python-nipype,
python-nitime,
python-openslide,
python-pyxnat,
@@ -1361,7 +1388,7 @@
Suggests: emokit,
igstk-examples,
libbio-formats-java,
- libcamp0.7-dev,
+ libcamp-dev,
libcifti-dev,
libctk-dev,
libeegdev-dev,
@@ -1371,6 +1398,7 @@
liblimereg-dev,
libmni-perllib-perl,
libnifti-doc,
+ libopenmeeg-dev,
libopenslide-java,
libvia-dev,
libvmtk-dev,
@@ -1379,8 +1407,12 @@
libvxl1-dev,
libxdffileio-dev,
octave-dicom,
+ odin,
+ python-dipy,
python-imageio,
python-libavg,
+ python-nipy,
+ python-nipype,
python-tifffile,
python-vmtk
Description: Debian Med image processing and visualization packages development
@@ -1395,7 +1427,8 @@
Recommends: opencfu
Suggests: catissuesuite,
openelis,
- openfreezer
+ openfreezer,
+ orthanc-wsi
Description: Debian Med suggestions for medical laboratories
This metapackage contains dependencies for software and that could
be useful ro run a medical laboratory.
@@ -1405,7 +1438,8 @@
Architecture: all
Depends: med-tasks (= ${source:Version}), ${misc:Depends}, med-config (= ${source:Version})
Recommends: dicompyler
-Suggests: planunc,
+Suggests: orthanc-wsi,
+ planunc,
uw-prism
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
@@ -1474,6 +1508,7 @@
openemr,
openpms,
openrep,
+ orthanc-wsi,
proteus,
remitt,
resmedicinae,
@@ -1491,7 +1526,6 @@
Recommends: praat,
psignifit,
psychopy,
- python-pyepl,
r-cran-foreign,
r-cran-psy
Suggests: miscpsycho,
@@ -1499,6 +1533,7 @@
psychometric,
psychotree,
psyphy,
+ python-pyepl,
python-pypsignifit,
python-visionegg,
science-psychophysics
diff -Nru debian-med-3.0/tasks/bio debian-med-3.0.1/tasks/bio
--- debian-med-3.0/tasks/bio 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/bio 2017-04-19 15:29:37.000000000 +0200
@@ -57,7 +57,7 @@
Depends: mummer
-Depends: blast2, plast
+Depends: ncbi-blast+-legacy, plast
Depends: ncbi-blast+
@@ -173,6 +173,8 @@
X-End-Category: Genome Browser
+Depends: python3-biomaj3
+
Suggests: biomaj
Why: Suggests since mysql setup might be overkill for default client installation
@@ -208,7 +210,7 @@
Depends: staden-io-lib-utils
-Depends: samtools, bedtools, filo
+Depends: samtools, bedtools, filo, datamash
Depends: gassst
@@ -355,6 +357,8 @@
Depends: libvcflib-tools
+Suggests: getdata
+
X-Mark: Prospective packages are starting here
X-Mark: Packages in Vcs - Information about these is queried from UDD as well
@@ -382,6 +386,8 @@
Depends: biceps
Remark: Mentioned at http://www.renard.it/, developed in RKI
+Depends: cnvkit
+
Depends: diamond-aligner
Depends: emperor
@@ -430,6 +436,8 @@
Depends: bio-eagle
+Depends: bio-tradis
+
Depends: bitseq
Depends: blat
@@ -498,6 +506,10 @@
Depends: emmax
+Depends: examl, raxml-ng
+
+Depends: exabayes
+
Depends: berkeley-express
Depends: falcon
@@ -618,7 +630,7 @@
Depends: kmer
-Depends: kronatools
+Depends: radiant
Depends: lefse
@@ -676,6 +688,8 @@
Suggests: mrs
Remark: mrs might occupy a lot of space on users disk - so you want to avoid this package from the metapackage recommends
+Depends: mptp
+
Depends: mugsy
Depends: murasaki
@@ -705,6 +719,8 @@
Depends: pal2nal
+Depends: paleomix
+
Depends: paraclu
Depends: parsinsert
@@ -740,6 +756,8 @@
Depends: perm
+Depends: pftools
+
Depends: phast
Depends: phipack
@@ -787,6 +805,8 @@
Depends: prottest
+Depends: psortb
+
Depends: pscan-tfbs
Depends: psipred
@@ -799,6 +819,8 @@
Depends: python-reaper
+Depends: qcumber
+
Depends: qtltools
Depends: qualimap
@@ -863,12 +885,16 @@
Depends: roary
+Depends: roguenarok
+
Depends: rosetta
Depends: rsat
Depends: rsem
+Depends: sambamba
+
Depends: salmon
Depends: sap
@@ -885,6 +911,8 @@
Depends: seqprep
+Depends: seqsero
+
Depends: seqtk
Depends: sequenceconverter.app
@@ -971,6 +999,8 @@
Depends: transdecoder
+Depends: tnseq-transit
+
Depends: transrate-tools
Depends: treeview
@@ -2638,7 +2668,7 @@
Depends: disulfinder
-Depends: circos
+Depends: circos, runcircos-gui
Depends: populations
diff -Nru debian-med-3.0/tasks/bio-dev debian-med-3.0.1/tasks/bio-dev
--- debian-med-3.0/tasks/bio-dev 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/bio-dev 2017-04-19 15:29:37.000000000 +0200
@@ -354,3 +354,19 @@
WNPP: 851341
Depends: libbio-eutilities-perl
+
+Depends: libseqlib-dev
+
+Depends: libroadrunner-dev, python-roadrunner
+
+Depends: python3-biotools | python-biotools
+
+Depends: bio-tradis
+
+Depends: python3-biomaj3 | python-biomaj3
+
+Suggests: python-pyflow
+
+Suggests: r-cran-natserv
+
+Depends: libbiod-dev
diff -Nru debian-med-3.0/tasks/bio-ngs debian-med-3.0.1/tasks/bio-ngs
--- debian-med-3.0/tasks/bio-ngs 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/bio-ngs 2017-04-19 15:29:37.000000000 +0200
@@ -47,6 +47,10 @@
X-Mark: Packages in Vcs - Information about these is queried from UDD as well
+Depends: scoary
+
+Depends: umap
+
Depends: dindel
Depends: mosaik-aligner
diff -Nru debian-med-3.0/tasks/epi debian-med-3.0.1/tasks/epi
--- debian-med-3.0/tasks/epi 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/epi 2017-04-19 15:29:37.000000000 +0200
@@ -28,6 +28,10 @@
Depends: ushahidi
+Suggests: shiny-server
+
+Depends: r-cran-lexrankr
+
Depends: netepi-analysis
Remark: See also: http://www.stockholmchallenge.se/data/2123 and
http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf
diff -Nru debian-med-3.0/tasks/his debian-med-3.0.1/tasks/his
--- debian-med-3.0/tasks/his 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/his 2017-04-19 15:29:37.000000000 +0200
@@ -15,6 +15,8 @@
Depends: ewd-920
+Depends: orthanc-wsi
+
Depends: tryton-modules-health
Pkg-URL: http://debian.tryton.org/debian/pool/main/t/tryton-modules-health/
Remark: Docker instance and apt repository
diff -Nru debian-med-3.0/tasks/imaging debian-med-3.0.1/tasks/imaging
--- debian-med-3.0/tasks/imaging 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/imaging 2017-04-19 15:29:37.000000000 +0200
@@ -893,3 +893,5 @@
Suggests: science-workflow
Depends: dcm2niix
+
+Depends: orthanc-wsi
diff -Nru debian-med-3.0/tasks/imaging-dev debian-med-3.0.1/tasks/imaging-dev
--- debian-med-3.0/tasks/imaging-dev 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/imaging-dev 2017-04-19 15:29:37.000000000 +0200
@@ -174,6 +174,6 @@
Depends: libbart-dev, octave-bart
-Suggests: libcamp0.7-dev
+Suggests: libcamp-dev
Depends: libcifti-dev
diff -Nru debian-med-3.0/tasks/laboratory debian-med-3.0.1/tasks/laboratory
--- debian-med-3.0/tasks/laboratory 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/laboratory 2017-04-19 15:29:37.000000000 +0200
@@ -5,6 +5,8 @@
Depends: opencfu
+Depends: orthanc-wsi
+
Depends: openelis
Homepage: http://openelis.uhl.uiowa.edu/
License: UIRF Open-source Based Public Software License
diff -Nru debian-med-3.0/tasks/oncology debian-med-3.0.1/tasks/oncology
--- debian-med-3.0/tasks/oncology 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/oncology 2017-04-19 15:29:37.000000000 +0200
@@ -5,6 +5,8 @@
Depends: uw-prism
+Depends: orthanc-wsi
+
Depends: planunc
Homepage: http://planunc.radonc.unc.edu/about/
License: needs to be clarified, registration required
diff -Nru debian-med-3.0/tasks/practice debian-med-3.0.1/tasks/practice
--- debian-med-3.0/tasks/practice 2017-01-24 10:51:13.000000000 +0100
+++ debian-med-3.0.1/tasks/practice 2017-04-19 15:29:37.000000000 +0200
@@ -24,6 +24,8 @@
Depends: orthanc
+Depends: orthanc-wsi
+
Depends: medintux
Homepage: http://medintux.org/medintux/en/
License: CeCILL (free)
