[Blends-commit] [Git][blends-team/med][master] 7 commits: Standards-Version: 4.3.0
Andreas Tille
gitlab at salsa.debian.org
Thu Jan 24 14:10:22 GMT 2019
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
056cc758 by Andreas Tille at 2019-01-24T13:32:59Z
Standards-Version: 4.3.0
- - - - -
c31f878e by Andreas Tille at 2019-01-24T13:33:56Z
debhelper 12
- - - - -
6ad8b43a by Andreas Tille at 2019-01-24T13:34:50Z
Versioned Build-Depends: blends-dev (>= 0.7.2~)
- - - - -
5aaa66bb by Andreas Tille at 2019-01-24T13:45:19Z
Re-render dependencies
- - - - -
078e4a50 by Andreas Tille at 2019-01-24T13:51:32Z
Autogenerate changelog and dependency data
- - - - -
4d1d3565 by Andreas Tille at 2019-01-24T14:07:48Z
Add missing ${misc:Depends}
- - - - -
acee915b by Andreas Tille at 2019-01-24T14:09:10Z
Upload to unstable
- - - - -
6 changed files:
- debian-med-tasks.desc
- debian/changelog
- debian/compat
- debian/control
- debian/control.stub
- + dependency_data/debian-med_3.2.json
Changes:
=====================================
debian-med-tasks.desc
=====================================
@@ -162,6 +162,24 @@ Description: Debian Med packages for psychology
Key:
med-psychology
+Task: med-rehabilitation
+Parent: debian-med
+Section: debian-med
+Description: Debian Med packages for rehabilitation technologies
+ This metapackage will install tools that are useful for
+ rehabilitation and therapy.
+Key:
+ med-rehabilitation
+
+Task: med-research
+Parent: debian-med
+Section: debian-med
+Description: Debian Med packages for medical research
+ This metapackage will install tools that are useful for
+ medical research.
+Key:
+ med-research
+
Task: med-statistics
Parent: debian-med
Section: debian-med
=====================================
debian/changelog
=====================================
@@ -1,8 +1,103 @@
-debian-med (3.2) UNRELEASED; urgency=medium
+debian-med (3.2) unstable; urgency=medium
* Fix broken reference to alioth
+ * Standards-Version: 4.3.0
+ * debhelper 12
+ * Versioned Build-Depends: blends-dev (>= 0.7.2~)
+ * Add missing ${misc:Depends}
- -- Andreas Tille <tille at debian.org> Sun, 29 Jul 2018 02:22:44 +0200
+ * start of automatic changelog entry *
+
+ * Changes in metapackage dependencies
+ -med-bio
+ added:
+ Recommends: r-cran-sdmtools, delly, python3-pybedtools, r-cran-tcr,
+ qutemol, r-cran-tigger, bax2bam, python3-gffutils,
+ vdjtools, r-cran-shazam, r-cran-alakazam, gramalign,
+ igor, deepbinner, python3-sqt, minimap2, sourmash,
+ samblaster, murasaki | murasaki-mpi, biosyntax, paipline,
+ pyvcf, r-bioc-cner, igdiscover, fastp, ncbi-igblast,
+ pybel, jellyfish1, minimac4, lambda-align2, sweed,
+ viewmol, seq-seq-pan, yaha, python3-biomaj3-daemon,
+ changeo, mirtop, python3-presto, cct, unanimity,
+ plasmidseeker
+ removed:
+ Recommends: hilbertvisgui, decipher, hyphygui, jstreeview,
+ biosyntax-gedit, python3-biomaj3, spice, rosetta,
+ hexamer, murasaki, gbioseq, finex, das-proserver, est-db
+ -med-bio-dev
+ added:
+ Recommends: python3-screed, python3-misopy, python3-pyvcf,
+ python3-biomaj3, python3-ngs, toil, python3-cutadapt,
+ python3-ruffus, python3-biotools, python3-sqt,
+ libmems-dev, python3-hyphy, libstatgen-dev, python3-cobra,
+ python3-biopython, python3-pysam, python3-airr,
+ python3-dendropy, libgenome-dev, python3-fast5,
+ python3-cyvcf2, libpll-dev, python3-bx, libmuscle-dev,
+ python3-treetime, python3-presto, python3-pbconsensuscore,
+ python3-csb, python3-intervaltree-bio, python3-seqcluster,
+ python3-ete3, python3-bcbio, python3-pyfaidx, galaxy-lib,
+ python3-consensuscore2, snakemake
+ Suggests: ctdconverter, libmodhmm-dev, libsvmloc-dev, vdjtools,
+ python3-ctdopts, python3-biopython-sql, libmilib-java
+ removed:
+ Recommends: python3-biotools | python-biotools, octave-bioinfo,
+ python3-pyvcf | python-pyvcf,
+ python3-biomaj3 | python-biomaj3,
+ python3-pbconsensuscore | python-pbconsensuscore,
+ libmuscle-3.7-dev, python3-pyfaidx | python-pyfaidx,
+ python3-consensuscore2 | python-consensuscore2,
+ python-bd2k, python3-bx | python-bx,
+ python3-ete3 | python-ete3, python3-ruffus | python-ruffus,
+ python3-fast5 | python-fast5,
+ python3-dendropy | python-dendropy, python-pysam,
+ python3-cutadapt | python-cutadapt, libgff-perl,
+ python3-ngs | python-ngs, python3-pyfasta | python-pyfasta,
+ python3-csb | python-csb, libgenome-1.3-dev,
+ python3-biopython | python-biopython,
+ python3-hyphy | python-hyphy, python-cobra,
+ libmems-1.6-dev,
+ python3-intervaltree-bio | python-intervaltree-bio,
+ python3-misopy | python-misopy
+ Suggests: python3-biopython-sql | python-biopython-sql
+ -med-bio-ngs
+ added:
+ Recommends: python3-presto, changeo, bcbio, igor, python3-pybedtools,
+ igdiscover, python3-airr, r-cran-tcr, r-cran-tigger,
+ python3-sqt, python3-gffutils, fastp, vdjtools,
+ samblaster, r-cran-shazam, r-cran-alakazam
+ -med-bio-phylogeny
+ added:
+ Suggests: python3-treetime
+ -med-epi
+ added:
+ Recommends: epifire
+ -med-imaging
+ added:
+ Recommends: mrtrix3, odil
+ Suggests: orthanc-mysql, tifffile
+ -med-imaging-dev
+ added:
+ Recommends: libsimpleitk1-dev, python3-biosig, libodil-dev,
+ python3-simpleitk, libxdf-dev
+ removed:
+ Recommends: libodil0-dev
+ -med-pharmacy
+ added:
+ Recommends: r-cran-rpact
+ -med-physics
+ added:
+ Suggests: python3-biosig
+ removed:
+ Suggests: python-biosig
+ -med-research
+ added:
+ Recommends: r-cran-rpact
+ -med-typesetting
+ removed:
+ Suggests: referencer
+
+ -- Andreas Tille <tille at debian.org> Thu, 24 Jan 2019 15:07:55 +0100
debian-med (3.1) unstable; urgency=medium
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-9
+12
=====================================
debian/control
=====================================
@@ -4,19 +4,20 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: misc
Priority: optional
-Build-Depends-Indep: blends-dev (>= 0.7~)
-Standards-Version: 4.1.4
+Build-Depends-Indep: blends-dev (>= 0.7.2~),
+ debhelper (>= 12~)
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
Package: med-tasks
Architecture: all
-Depends: tasksel
+Depends: tasksel, ${misc:Depends}
Description: Debian Med tasks for tasksel
This package provides Debian Med tasks in tasksel.
.
These tasks are described in detail at
- http://debian-med.alioth.debian.org/tasks/
+ https://blends.debian.org/med/tasks/
Package: med-config
Architecture: all
@@ -73,6 +74,8 @@ Suggests: med-cloud,
med-physics,
med-practice,
med-psychology,
+ med-rehabilitation,
+ med-research,
med-tools,
med-typesetting
Description: Default selection of tasks for Debian Med
@@ -103,6 +106,7 @@ Recommends: abacas,
arden,
ariba,
art-nextgen-simulation-tools,
+ artemis,
artfastqgenerator,
assemblytics,
atac,
@@ -114,12 +118,16 @@ Recommends: abacas,
axe-demultiplexer,
baitfisher,
bali-phy,
+ ballview,
bamtools,
+ bandage,
barrnap,
+ bcbio,
bcftools,
beads,
beagle,
beast-mcmc,
+ beast2-mcmc,
bedops,
bedtools,
belvu,
@@ -127,7 +135,7 @@ Recommends: abacas,
bio-eagle,
bio-rainbow,
bio-tradis,
- biosyntax-gedit,
+ biosyntax,
bitseq,
blasr,
blixem,
@@ -141,10 +149,12 @@ Recommends: abacas,
bwa,
canu,
cassiopee,
+ cct,
cd-hit,
cdbfasta,
centrifuge,
cgview,
+ changeo,
chimeraslayer,
chromhmm,
chromimpute,
@@ -157,6 +167,7 @@ Recommends: abacas,
clustalo,
clustalw,
clustalx,
+ cnvkit,
codonw,
concavity,
conservation-code,
@@ -168,6 +179,7 @@ Recommends: abacas,
dawg,
dazzdb,
deepnano,
+ delly,
dialign,
dialign-tx,
diamond-aligner,
@@ -183,10 +195,12 @@ Recommends: abacas,
ecopcr,
edtsurf,
eigensoft,
+ elph,
embassy-domainatrix,
embassy-domalign,
embassy-domsearch,
emboss,
+ estscan,
examl,
exonerate,
falcon,
@@ -195,6 +209,7 @@ Recommends: abacas,
fastdnaml,
fastlink,
fastml,
+ fastp,
fastqc,
fastqtl,
fasttree,
@@ -212,14 +227,17 @@ Recommends: abacas,
garli,
garlic,
gasic,
+ gatb-core,
gbrowse,
gdpc,
gemma,
+ genometester,
genometools,
gentle,
gff2aplot,
gff2ps,
ghemical,
+ ghmm,
giira,
glam2,
grabix,
@@ -236,7 +254,6 @@ Recommends: abacas,
hmmer,
hmmer2,
hyphy-mpi | hyphy-pt,
- hyphygui,
idba,
indelible,
infernal,
@@ -244,7 +261,9 @@ Recommends: abacas,
iqtree,
iva,
jaligner,
+ jalview,
jellyfish,
+ jellyfish1,
jmodeltest,
jmol,
kalign,
@@ -255,8 +274,10 @@ Recommends: abacas,
kmc,
kmer,
kraken,
+ lagan,
lamarc,
lambda-align,
+ lambda-align2,
last-align,
leaff,
lefse,
@@ -265,6 +286,7 @@ Recommends: abacas,
logol,
loki,
ltrsift,
+ lucy,
macs,
macsyfinder,
maffilter,
@@ -284,7 +306,9 @@ Recommends: abacas,
microbiomeutil,
minia,
miniasm,
+ minimac4,
minimap,
+ minimap2,
mipe,
mira-assembler,
mlv-smile,
@@ -293,7 +317,7 @@ Recommends: abacas,
mrbayes,
msxpertsuite,
mummer,
- murasaki,
+ murasaki | murasaki-mpi,
muscle,
mustang,
nanook,
@@ -312,6 +336,8 @@ Recommends: abacas,
njplot,
norsnet,
norsp,
+ obitools,
+ openms,
pal2nal,
paleomix,
paml,
@@ -339,17 +365,21 @@ Recommends: abacas,
phyml,
physamp,
phyutility,
+ phyx,
picard-tools,
piler,
+ pilon,
pirs,
placnet,
plasmidomics,
+ plasmidseeker,
plast,
plink,
plink1.9,
plip,
poa,
populations,
+ porechop,
poretools,
prank,
predictnls,
@@ -387,14 +417,20 @@ Recommends: abacas,
pynast,
pyscanfcs,
python-cogent,
- python-treetime,
- python3-biomaj3,
+ python3-biomaj3-daemon,
+ python3-gffutils,
+ python3-presto,
+ python3-pybedtools,
+ pyvcf,
qcumber,
+ qiime,
qtltools,
quorum,
+ qutemol,
r-bioc-annotate,
r-bioc-biostrings,
r-bioc-bitseq,
+ r-bioc-cner,
r-bioc-cummerbund,
r-bioc-deseq2,
r-bioc-dnacopy,
@@ -410,25 +446,36 @@ Recommends: abacas,
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-metamix,
r-cran-phangorn,
r-cran-phytools,
r-cran-pscbs,
r-cran-qtl,
r-cran-rotl,
+ r-cran-samr,
+ r-cran-sdmtools,
r-cran-seqinr,
+ r-cran-shazam,
+ r-cran-tcr,
+ r-cran-tigger,
r-cran-treescape,
r-cran-vegan,
r-other-hms-dbmi-spp,
r-other-mott-happy.hbrem,
+ racon,
radiant,
rambo-k,
+ rampler,
rapmap,
+ rasmol,
raster3d,
rate4site,
raxml,
@@ -438,6 +485,8 @@ Recommends: abacas,
rdp-readseq,
readseq,
reapr,
+ relion-bin | relion-bin+mpi,
+ relion-bin+gui | relion-bin+mpi+gui,
repeatmasker-recon,
reprof,
rna-star,
@@ -450,11 +499,13 @@ Recommends: abacas,
saint,
salmon,
sambamba,
+ samblaster,
samtools,
scrm,
scythe,
seaview,
seer,
+ segemehl,
seqan-apps,
seqmagick,
seqprep,
@@ -482,6 +533,7 @@ Recommends: abacas,
sortmerna,
spaced,
spades,
+ spoa,
sprai,
spread-phy,
squizz,
@@ -500,6 +552,7 @@ Recommends: abacas,
sumtrees,
surankco,
swarm,
+ sweed,
t-coffee,
tabix,
tantan,
@@ -507,8 +560,12 @@ Recommends: abacas,
tigr-glimmer,
tm-align,
tnseq-transit,
+ toil,
tophat,
+ topp,
toppred,
+ trace2dbest,
+ tracetuner,
transdecoder,
transrate-tools,
transtermhp,
@@ -517,14 +574,19 @@ Recommends: abacas,
treeviewx,
trimmomatic,
trinityrnaseq,
+ tvc,
uc-echo,
+ unanimity,
+ unicycler,
varna,
vcftools,
velvet | velvet-long,
velvetoptimiser,
+ viewmol,
vsearch,
wigeon,
wise,
+ yaha,
zalign
Suggests: acacia,
adun.app,
@@ -534,17 +596,13 @@ Suggests: acacia,
apollo,
arachne,
arb,
- artemis,
asap,
autodocktools,
axparafit,
axpcoords,
bagpipe,
- ballview,
bambus,
- bandage,
- bcbio,
- beast2-mcmc,
+ bax2bam,
biceps,
big-blast,
bigsdb,
@@ -562,7 +620,6 @@ Suggests: acacia,
cinema,
cluster3,
cmap,
- cnvkit,
compclust,
condetri,
contrafold,
@@ -573,21 +630,17 @@ Suggests: acacia,
crux-toolkit,
cufflinks,
cytoscape,
- das-proserver,
dascrubber,
dazzle,
- decipher,
+ deepbinner,
e-hive,
ecell,
- elph,
embassy-phylip,
emboss-explorer,
emmax,
emperor,
ensembl,
- est-db,
estferret,
- estscan,
euler-sr,
euler2,
exabayes,
@@ -596,41 +649,33 @@ Suggests: acacia,
fasta3,
ffp,
figaro,
- finex,
forester,
forge,
galaxy,
gassst,
- gatb-core,
gatk,
- gbioseq,
gbrowse-syn,
genemark,
genesplicer,
genetrack,
genezilla,
genographer,
- genometester,
getdata,
- ghmm,
glimmerhmm,
gmap,
gmv,
+ gramalign,
haploview,
hawkeye,
- hexamer,
- hilbertvisgui,
htqc,
+ igdiscover,
+ igor,
igv,
inspect,
- jalview,
jbrowse,
jigsaw,
- jstreeview,
kempbasu,
- lagan,
lofreq,
- lucy,
mach-haplotyper,
mage2tab,
maker2,
@@ -653,6 +698,7 @@ Suggests: acacia,
migrate,
minimus,
mirbase,
+ mirtop,
mobyle,
mobyle-programs,
mobyle-tutorials,
@@ -666,17 +712,17 @@ Suggests: acacia,
mummergpu,
mview,
nanocall,
+ ncbi-igblast,
nextsv,
ngila,
ngsqctoolkit,
nw-align,
oases,
- obitools,
obo-edit,
oligoarrayaux,
omegamap,
- openms,
operondb,
+ paipline,
partigene,
partitionfinder,
patristic,
@@ -688,20 +734,19 @@ Suggests: acacia,
phylophlan,
phyloviz-core,
phylowin,
- phyx,
- pilon,
pipasic,
plato,
- porechop,
profit,
prokka,
prot4est,
psipred,
pssh2,
+ pybel,
pyrophosphate-tools,
python-orange,
python-reaper,
- qiime,
+ python-treetime,
+ python3-sqt,
qtlcart,
qualimap,
r-bioc-annotationhub,
@@ -709,44 +754,34 @@ Suggests: acacia,
r-bioc-ensembldb,
r-bioc-go.db,
r-bioc-savr,
- r-bioc-tfbstools,
r-cran-boolnet,
- r-cran-metamix,
r-cran-pheatmap,
r-cran-qqman,
r-cran-rentrez,
- r-cran-samr,
r-other-apmswapp,
raccoon,
- racon,
- rampler,
- rasmol,
raxml-ng,
rbs-finder,
- relion-bin | relion-bin+mpi,
- relion-bin+gui | relion-bin+mpi+gui,
repeatmasker,
rmblast,
roadtrips,
roche454ace2caf,
rose,
- rosetta,
rsat,
sap,
science-workflow,
scoary,
- segemehl,
seq-gen,
+ seq-seq-pan,
sequenceconverter.app,
sift,
sistr,
situs,
snpeff,
solvate,
+ sourmash,
sparta,
- spice,
splitstree,
- spoa,
ssaha,
strap,
strap-base,
@@ -758,23 +793,18 @@ Suggests: acacia,
tide,
tigr-glimmer-mg,
tn-seqexplorer,
- toil,
- topp,
- trace2dbest,
- tracetuner,
treebuilder3d,
treetime,
tripal,
trnascan-se,
- tvc,
twain,
ugene,
umap,
unc-fish,
- unicycler,
uniprime,
varmatch,
varscan,
+ vdjtools,
vienna-rna,
vmd,
x-tandem-pipeline,
@@ -809,6 +839,7 @@ Recommends: bio-tradis,
libbiod-dev,
libbiojava-java,
libbiojava4-java,
+ libbioparser-dev,
libblasr-dev,
libbpp-core-dev,
libbpp-phyl-dev,
@@ -821,13 +852,15 @@ Recommends: bio-tradis,
libchado-perl,
libconsensuscore-dev,
libdivsufsort-dev,
+ libedlib-dev,
libfast5-dev,
libfastahack-dev,
libffindex0-dev,
libfml-dev,
libfreecontact-dev,
libfreecontact-perl,
- libgenome-1.3-dev,
+ libgatbcore-dev,
+ libgenome-dev,
libgenome-model-tools-music-perl,
libgenome-perl,
libgenometools0-dev,
@@ -840,23 +873,26 @@ Recommends: bio-tradis,
libjebl2-java,
libjloda-java,
libkmer-dev,
- libmems-1.6-dev,
+ libmems-dev,
libminimap-dev,
- libmuscle-3.7-dev,
+ libmuscle-dev,
libncbi-vdb-dev,
libncbi6-dev,
libncl-dev,
libngs-java,
libngs-sdk-dev,
libnhgri-blastall-perl,
+ libopenms-dev,
libpal-java,
libpbbam-dev,
libpbdata-dev,
libpbihdf-dev,
libpbseq-dev,
+ libpll-dev,
libqes-dev,
librcsb-core-wrapper0-dev,
librdp-taxonomy-tree-java,
+ librelion-dev,
librg-blast-parser-perl,
librg-reprof-bundle-perl,
librostlab-blast0-dev,
@@ -866,23 +902,24 @@ Recommends: bio-tradis,
libsmithwaterman-dev,
libsnp-sites1-dev,
libsort-key-top-perl,
+ libspoa-dev,
libsrf-dev,
libssm-dev,
libssw-dev,
libssw-java,
libstaden-read-dev,
+ libstatgen-dev,
libswiss-perl,
libtabixpp-dev,
libtfbs-perl,
+ libthread-pool-dev,
libvcflib-dev,
libvibrant6-dev,
libzerg-perl,
libzerg0-dev,
mcl,
pyfai,
- python-bd2k,
python-biom-format,
- python-cobra,
python-cogent,
python-corepywrap,
python-freecontact,
@@ -891,73 +928,81 @@ Recommends: bio-tradis,
python-pbcommand,
python-pbcore,
python-pbh5tools,
- python-pysam,
+ python-rdkit,
+ python3-airr,
+ python3-bcbio,
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-biopython,
+ python3-biotools,
+ python3-bx,
+ python3-cobra,
+ python3-csb,
+ python3-cutadapt,
+ python3-cyvcf2,
+ python3-dendropy,
+ python3-fast5,
python3-gfapy,
- python3-intervaltree-bio | python-intervaltree-bio,
- python3-ngs | python-ngs,
- python3-pbconsensuscore | python-pbconsensuscore,
- python3-pyfaidx | python-pyfaidx,
+ python3-gffutils,
+ python3-intervaltree-bio,
+ python3-ngs,
+ python3-pbconsensuscore,
+ python3-presto,
+ python3-pybedtools,
+ python3-pyfaidx,
python3-pymummer,
- python3-pyvcf | python-pyvcf,
- python3-ruffus | python-ruffus,
+ python3-pysam,
+ python3-pyvcf,
+ python3-ruffus,
+ python3-screed,
python3-skbio,
+ python3-treetime,
r-bioc-biobase,
r-cran-genetics,
r-cran-haplo.stats,
r-cran-phylobase,
r-cran-rncl,
r-cran-rnexml,
+ ruby-bio,
+ ruby-crb-blast,
sbmltoolbox,
- seqan-dev
+ seqan-dev,
+ snakemake,
+ toil
Suggests: bioclipse,
+ ctdconverter,
+ galaxy-lib,
libbam-dev,
- libbioparser-dev,
libdisorder-dev,
- libedlib-dev,
libforester-java,
libfreecontact-doc,
- libgatbcore-dev,
- libgff-perl,
libgoby-java,
libgtextutils-dev,
- libopenms-dev,
+ libmilib-java,
+ libmodhmm-dev,
libpbcopper-dev,
libqcpp-dev,
- librelion-dev,
libroadrunner-dev,
librostlab-blast-doc,
librostlab-doc,
- libspoa-dev,
+ libsvmloc-dev,
libswarm2-dev,
- libthread-pool-dev,
mgltools-networkeditor,
mgltools-pybabel,
mgltools-vision,
octace-bioinfo,
- octave-bioinfo,
- python-biomaj3,
python-biopython-doc,
python-mmtk,
python-pyflow,
- python-rdkit,
python-roadrunner,
python-screed,
- python3-biopython-sql | python-biopython-sql,
- python3-bx | python-bx,
- python3-consensuscore2 | python-consensuscore2,
- python3-ete3 | python-ete3,
- python3-gffutils,
- python3-hyphy | python-hyphy,
- python3-misopy | python-misopy,
- python3-pybedtools,
- python3-pyfasta | python-pyfasta,
+ python3-biopython-sql,
+ python3-consensuscore2,
+ python3-ctdopts,
+ python3-ete3,
+ python3-hyphy,
+ python3-misopy,
+ python3-seqcluster,
+ python3-sqt,
r-bioc-affy,
r-bioc-affyio,
r-bioc-altcdfenvs,
@@ -985,9 +1030,8 @@ Suggests: bioclipse,
r-cran-natserv,
r-cran-rentrez,
r-cran-rocr,
- ruby-bio,
- ruby-crb-blast,
- ruby-rgfa
+ ruby-rgfa,
+ vdjtools
Description: Debian Med packages for development of bioinformatics applications
This metapackage will install Debian packages which might be helpful
for development of applications for biological research.
@@ -1108,6 +1152,7 @@ Recommends: abyss,
python-cogent,
python3-biomaj3-cli,
python3-biopython,
+ qiime,
r-bioc-hilbertvis,
r-cran-pvclust,
r-cran-qtl,
@@ -1143,8 +1188,7 @@ 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
@@ -1174,8 +1218,8 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: entangle,
- imagetooth,
- openmolar
+ imagetooth
+Suggests: openmolar
Description: Debian Med packages related to dental practice
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
@@ -1186,7 +1230,7 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: python-treetime,
+Recommends: epigrass,
r-cran-diagnosismed,
r-cran-epi,
r-cran-epibasix,
@@ -1195,14 +1239,15 @@ Recommends: python-treetime,
r-cran-epitools,
r-cran-lexrankr,
r-cran-seroincidence,
+ r-cran-sf,
+ r-cran-sjplot,
r-cran-surveillance
-Suggests: epigrass,
+Suggests: epifire,
netepi-analysis,
netepi-collection,
+ python-treetime,
r-cran-cmprsk,
r-cran-msm,
- r-cran-sf,
- r-cran-sjplot,
repast,
shiny-server,
ushahidi
@@ -1248,6 +1293,7 @@ Depends: ${misc:Depends},
med-tasks (= ${source:Version})
Recommends: aeskulap,
amide,
+ ants,
bart,
bart-view,
biosig-tools,
@@ -1259,6 +1305,7 @@ Recommends: aeskulap,
dicom3tools,
dicomnifti,
dicomscope,
+ fw4spl,
gdf-tools,
ginkgocadx,
gwyddion,
@@ -1277,23 +1324,30 @@ Recommends: aeskulap,
mriconvert,
mricron,
mrtrix,
+ mrtrix3,
nifti-bin,
+ odil,
+ odin,
openslide-tools,
orthanc,
orthanc-wsi,
+ pixelmed-apps,
plastimatch,
python-dicom,
+ python-dipy,
+ python-mvpa2,
python-nibabel,
python-nipy,
python-nipype,
python-nitime,
- python-tifffile,
+ python-surfer,
sigviewer,
sofa-apps,
+ teem-apps,
+ voxbo,
vtk-dicom-tools,
xmedcon
Suggests: afni,
- ants,
bioimagesuite,
bioimagexd,
blox,
@@ -1323,7 +1377,6 @@ Suggests: afni,
freesurfer,
fsl,
fslview,
- fw4spl,
gimias,
hid,
imagemagick,
@@ -1348,7 +1401,6 @@ Suggests: afni,
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
- odin,
omero,
opendicom.net,
openelectrophy,
@@ -1357,28 +1409,25 @@ Suggests: afni,
openwalnut-qt4,
orthanc-dicomweb,
orthanc-imagej,
+ orthanc-mysql,
orthanc-postgresql,
orthanc-webviewer,
paraview,
piano,
- pixelmed-apps,
pngquant,
pymeg,
- python-dipy,
- python-mvpa2,
python-pyxid,
- python-surfer,
+ python-tifffile,
science-workflow,
slicer,
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
@@ -1418,21 +1467,30 @@ Recommends: cimg-dev,
libmiaviewit-dev,
libminc-dev,
libnifti-dev,
- libodil0-dev,
+ libodil-dev,
libopenigtlink-dev,
libopenslide-dev,
+ libopensurgsim-dev,
libpapyrus3-dev,
+ libsimpleitk1-dev,
+ libteem-dev,
libvigraimpex-dev,
libvistaio-dev,
libvolpack1-dev,
libvtk-dicom-dev,
libvtk6-dev,
+ libxdf-dev,
octave-bart,
+ octave-dicom,
octave-gdf,
+ odin,
+ python-cfflib,
python-dicom,
- python-gdcm,
+ python-dipy,
python-imageio,
python-mia | python3-mia,
+ python-mne,
+ python-mvpa2,
python-nibabel,
python-nipy,
python-nipype,
@@ -1440,6 +1498,8 @@ Recommends: cimg-dev,
python-openslide,
python-pyxnat,
python-vigra,
+ python3-biosig,
+ python3-simpleitk,
r-cran-rniftilib
Suggests: emokit,
libbio-formats-java,
@@ -1454,18 +1514,11 @@ Suggests: emokit,
libnifti-doc,
libopenmeeg-dev,
libopenslide-java,
- libopensurgsim-dev,
- libteem-dev,
libvia-dev,
libvmtk-dev,
libxdffileio-dev,
- octave-dicom,
- odin,
- python-cfflib,
- python-dipy,
+ python-gdcm,
python-libavg,
- python-mne,
- python-mvpa2,
python-tifffile,
python-vmtk
Description: Debian Med image processing and visualization packages development
@@ -1509,7 +1562,8 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: chemtool,
- r-cran-dosefinding
+ r-cran-dosefinding,
+ r-cran-rpact
Suggests: raccoon
Description: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
@@ -1533,8 +1587,8 @@ Suggests: gate,
octave-biosig,
openvibe,
paw-demos,
- python-biosig,
- python-multipletau
+ python-multipletau,
+ python3-biosig
Description: Debian Med packages for medical physicists
This metapackage contains dependencies for a
collection of software and documentation which is useful for
@@ -1590,15 +1644,15 @@ Depends: ${misc:Depends},
med-tasks (= ${source:Version})
Recommends: praat,
psignifit,
+ psychopy,
+ python-pyepl,
r-cran-foreign,
r-cran-psy
Suggests: miscpsycho,
psych,
psychometric,
- psychopy,
psychotree,
psyphy,
- python-pyepl,
python-pypsignifit,
python-visionegg,
science-psychophysics
@@ -1606,6 +1660,30 @@ Description: Debian Med packages for psychology
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
+Package: med-rehabilitation
+Section: metapackages
+Architecture: all
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
+Recommends: sitplus
+Suggests: aghermann
+Description: Debian Med packages for rehabilitation technologies
+ This metapackage will install tools that are useful for
+ rehabilitation and therapy.
+
+Package: med-research
+Section: metapackages
+Architecture: all
+Depends: ${misc:Depends},
+ med-config (= ${source:Version}),
+ med-tasks (= ${source:Version})
+Recommends: r-cran-rpact
+Suggests: openclinica
+Description: Debian Med packages for medical research
+ This metapackage will install tools that are useful for
+ medical research.
+
Package: med-statistics
Section: metapackages
Architecture: all
@@ -1675,8 +1753,7 @@ Suggests: biber,
bibus,
jabref-plugin-oo,
kbibtex,
- r-cran-qqman,
- referencer
+ r-cran-qqman
Description: Debian Med support for typesetting and publishing
This metapackage will install Debian packages that might be helpful
for typesetting and publishing in medical care and structural
=====================================
debian/control.stub
=====================================
@@ -3,14 +3,15 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: misc
Priority: optional
-Build-Depends-Indep: blends-dev (>= 0.7~)
-Standards-Version: 4.1.4
+Build-Depends-Indep: blends-dev (>= 0.7.2~),
+ debhelper (>= 12~)
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
Package: med-tasks
Architecture: all
-Depends: tasksel
+Depends: tasksel, ${misc:Depends}
Description: Debian Med tasks for tasksel
This package provides Debian Med tasks in tasksel.
.
=====================================
dependency_data/debian-med_3.2.json
=====================================
@@ -0,0 +1 @@
+{"cms": {"depends": [], "suggests": ["zope-zms", "xnat", "hid"], "recommends": [], "ignore": [], "avoid": []}, "bio": {"depends": [], "suggests": ["dascrubber", "emboss-explorer", "adun.app", "melting-gui", "cain", "science-workflow", "getdata", "metastudent-data", "metastudent-data-2", "metastudent-data-3", "mrs", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-ensembldb", "r-bioc-go.db", "r-bioc-savr", "r-cran-qqman", "r-cran-rentrez", "r-cran-boolnet", "r-cran-pheatmap", "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", "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", "python-cogent", "paml", "velvetoptimiser", "ensembl", "mrbayes", "pdb2pqr", "squizz", "clonalframe", "clonalframeml", "dssp", "jellyfish", "jellyfish1", "ballview", "pynast", "raxml", "mlv-smile", "cd-hit", "cufflinks", "r-bioc-cummerbund", "eigensoft", "grinder", "jalview", "reprof", "tm-align", "norsnet", "norsp", "predictnls", "prime-phylo", "proftmb", "profbval", "profisis", "hhsuite", "ffindex", "flexbar", "blimps-utils", "sift", "neobio", "ray", "ugene", "logol", "soapdenovo", "soapdenovo2", "soapsnp", "soapaligner", "microbiomeutil", "chimeraslayer", "nast-ier", "wigeon", "minia", "trimmomatic", "saint", "rtax", "rate4site", "rna-star", "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", "axe-demultiplexer", "axparafit", "axpcoords", "bali-phy", "barrnap", "bamtools", "bagpipe", "bax2bam", "bcbio", "bcftools", "bigsdb", "bio-eagle", "bio-tradis", "biosyntax", "bitseq", "blat", "blobology", "bio-rainbow", "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", "dindel", "dwgsim", "ea-utils", "ecell", "ecopcr", "edtsurf", "emmax", "examl", "raxml-ng", "exabayes", "berkeley-express", "falcon", "fasta3", "fasttree", "fastahack", "fastaq", "fastml", "fastp", "fastqc", "fastqtl", "ffp", "unc-fish", "fml-asm", "forester", "freecontact", "freebayes", "fsa", "fsm-lite", "garli", "gatb-core", "gatk", "genometester", "genometools", "grabix", "graphlan", "gwama", "gubbins", "haploview", "harvest-tools", "hilive", "hisat2", "hmmer2", "htqc", "idba", "igdiscover", "indelible", "iqtree", "iva", "jaligner", "jbrowse", "jmodeltest", "kempbasu", "kineticstools", "kissplice", "kraken", "lagan", "lambda-align", "lambda-align2", "leaff", "ltrsift", "lofreq", "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", "miniasm", "minimac4", "minimap", "minimap2", "mirtop", "molekel", "mosaik-aligner", "mpsqed", "mptp", "mugsy", "murasaki | murasaki-mpi", "mview", "nanocall", "nanook", "nanopolish", "ncbi-entrez-direct", "ncbi-seg", "nextsv", "ngila", "ngsqctoolkit", "nw-align", "oases", "obitools", "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", "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", "pybel", "pycorrfit", "pyscanfcs", "python3-gffutils", "python3-pybedtools", "python3-sqt", "python-reaper", "python-treetime", "qcumber", "qtltools", "qualimap", "quorum", "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-impute", "r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-phyloseq", "r-bioc-ebseq", "r-bioc-limma", "r-bioc-bitseq", "r-bioc-pcamethods", "r-cran-samr", "r-bioc-tfbstools", "r-bioc-cner", "r-cran-metamix", "r-cran-rotl", "r-cran-adegenet", "r-cran-adephylo", "r-cran-distory", "r-cran-metamix", "r-cran-phangorn", "r-cran-pscbs", "r-cran-seqinr", "r-cran-vegan", "r-other-hms-dbmi-spp", "r-other-apmswapp", "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", "sistr", "situs", "sim4db", "smalt", "smithwaterman", "ssw-align", "smrtanalysis", "snpeff", "snpomatic", "solvate", "sortmerna", "snap-aligner", "sniffles", "sourmash", "spaced", "spades", "sparta", "sprai", "srst2", "ssaha", "sspace", "staden", "stacks", "strap", "strap-base", "subread", "suitename", "sumatra", "sumaclust", "sumtrees", "surankco", "swarm", "tacg", "tantan", "toppred", "transdecoder", "tnseq-transit", "tn-seqexplorer", "toil", "tracetuner", "transrate-tools", "treeview", "trinityrnaseq", "uc-echo", "unanimity", "unicycler", "varna", "varmatch", "varscan", "vdjtools", "vienna-rna", "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", "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", "r-cran-ape", "r-cran-phytools", "r-cran-treescape", "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", "python-orange", "tigr-glimmer-mg"], "ignore": ["mozilla-biofox", "riso", "catissuecore", "trapss"], "avoid": []}, "research": {"depends": [], "suggests": [], "recommends": ["r-cran-rpact", "openclinica"], "ignore": [], "avoid": []}, "data": {"depends": [], "suggests": ["sleepyhead"], "recommends": ["freediams", "freemedforms-freedata", "python-hl7", "drugref.org"], "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", 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View it on GitLab: https://salsa.debian.org/blends-team/med/compare/57a386aa7ea187781a8989ba85077098837a19c7...acee915bb52d1c85eb7742d23d90ae5fdf1dd10c
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View it on GitLab: https://salsa.debian.org/blends-team/med/compare/57a386aa7ea187781a8989ba85077098837a19c7...acee915bb52d1c85eb7742d23d90ae5fdf1dd10c
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