[Blends-commit] [Git][blends-team/med][master] 7 commits: routine-update: Standards-Version: 4.5.0
Andreas Tille
gitlab at salsa.debian.org
Fri Aug 14 21:39:41 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
3099c67b by Andreas Tille at 2020-08-14T21:38:47+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
fde8f3e5 by Andreas Tille at 2020-08-14T21:38:48+02:00
routine-update: debhelper-compat 13
- - - - -
11c67185 by Andreas Tille at 2020-08-14T21:40:37+02:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
8abe9356 by Andreas Tille at 2020-08-14T22:29:32+02:00
Refresh control information to match current package pool information
- - - - -
e68f2ace by Andreas Tille at 2020-08-14T22:36:17+02:00
Bump version to 3.6 to mark the COVID-19 effort
- - - - -
d1d8a711 by Andreas Tille at 2020-08-14T22:36:56+02:00
Create dependency data
- - - - -
06f895d8 by Andreas Tille at 2020-08-14T22:37:55+02:00
Upload to unstable
- - - - -
5 changed files:
- Makefile
- debian/changelog
- debian/control
- debian/control.stub
- + dependency_data/debian-med_3.6.json
Changes:
=====================================
Makefile
=====================================
@@ -24,3 +24,6 @@ endif
dummy:
@echo $(err)
+
+dep_data:
+ make statusdump
=====================================
debian/changelog
=====================================
@@ -1,13 +1,17 @@
-debian-med (3.5.2) UNRELEASED; urgency=medium
+debian-med (3.6) unstable; urgency=medium
+ * COVID-19 sprint release
* Drop autodocktools since it depends mgltools-pmv which is about to
be removed
* Drop all mgltools-* packages since these are unmaintained and there
is no Python3 port
* Remove cain from tasks since there is close to no chance to port it
to Python3
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Trim trailing whitespace.
- -- Andreas Tille <tille at debian.org> Sat, 07 Dec 2019 09:05:02 +0100
+ -- Andreas Tille <tille at debian.org> Fri, 14 Aug 2020 22:37:10 +0200
debian-med (3.5.1) unstable; urgency=medium
@@ -15,8 +19,8 @@ debian-med (3.5.1) unstable; urgency=medium
libgtextutils has issued with gcc9
* Drop mgltools-pmv which is constantly broken for several years
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-bio
added:
@@ -45,8 +49,8 @@ debian-med (3.5) unstable; urgency=medium
* giira from Recommends to Suggests since it needs tophat
* lintian-override for field-too-long Recommends
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-bio
added:
@@ -103,8 +107,8 @@ debian-med (3.4) unstable; urgency=medium
* Use debhelper-compat
* Re-render dependencies without Python2 packages
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-bio
added:
@@ -212,8 +216,8 @@ debian-med (3.3) unstable; urgency=medium
* Re-render tasks with Buster release state
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-bio
added:
@@ -272,8 +276,8 @@ debian-med (3.2) unstable; urgency=medium
* Versioned Build-Depends: blends-dev (>= 0.7.2~)
* Add missing ${misc:Depends}
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-bio
added:
@@ -389,8 +393,8 @@ debian-med (3.0) unstable; urgency=medium
* Bump version for Stretch release
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-tools
added:
@@ -428,8 +432,8 @@ debian-med (2.4) unstable; urgency=medium
* rebuild using blends-dev 0.6.96
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-tools
added:
@@ -458,8 +462,8 @@ debian-med (2.3) unstable; urgency=medium
* med-bio: Add mgltools-pmv, mgltools-vision, mgltools-cadd
Closes: #732069
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-tools
added:
@@ -576,8 +580,8 @@ debian-med (2.2) unstable; urgency=medium
* Moved to Git
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-tools
removed:
@@ -650,8 +654,8 @@ debian-med (1.99) unstable; urgency=low
- debhelper 9
* d/source/format: 3.0 (native)
- * start of automatic changelog entry *
-
+ * start of automatic changelog entry *
+
* Changes in metapackage dependencies
-med-pharmacy
added:
@@ -875,7 +879,7 @@ debian-med (1.8) unstable; urgency=low
[Steffen Möller]
* Added task cloud: Cloud computing image for Debian Med
-
+
[Andreas Tille]
* config/control: Depends: blends-common (>= 0.6.15)
* debian/control.stub: Build-Depends-Indep: blends-dev (>= 0.6.15)
@@ -926,7 +930,7 @@ debian-med (1.4) unstable; urgency=low
Closes: #562553
* No need to Build-Depends from debhelper because blends-dev
does depend from it
- * Several new package
+ * Several new package
-- Andreas Tille <tille at debian.org> Mon, 28 Dec 2009 08:58:27 +0100
@@ -1135,7 +1139,7 @@ debian-med (0.14) unstable; urgency=low
* med-imaging-dev: cimg-dev
decreased libgtkimreg-dev from Recommends to Suggests
* med-practice: libchipcard3c1, libchipcard3d0
-
+
-- Andreas Tille <tille at debian.org> Sat, 11 Aug 2007 17:50:29 +0200
debian-med (0.13) unstable; urgency=low
@@ -1170,7 +1174,7 @@ debian-med (0.12) unstable; urgency=low
Moved vrom Suggests to Depends: seaview (now really free)
Suggests: wise-doc
* med-imaging: Depends: libfslio0, libniftiio0, nifti-bin
- Suggests:
+ Suggests:
* med-imaging-dev: Depends: libfslio0-dev, libniftiio0-dev
Suggests: libnifti-doc
@@ -1187,7 +1191,7 @@ debian-med (0.11) unstable; urgency=low
Suggests: mozilla-biofox
* debian/compat: 5
* Uploaders: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-
+
-- Andreas Tille <tille at debian.org> Wed, 16 Aug 2006 10:07:41 +0200
debian-med (0.10.1) unstable; urgency=low
@@ -1216,7 +1220,7 @@ debian-med (0.9) unstable; urgency=low
* Removed gnutrion from tools because it was removed from Debian at all
* Rebuilded with cdd-dev 0.3.10 version
- * med-bio:
+ * med-bio:
Depends: muscle, gff2aplot, t-coffee, gff2ps, gdpc
Suggests: arb
* med-bio-dev
@@ -1230,7 +1234,7 @@ debian-med (0.9) unstable; urgency=low
paul now Recommends not Depends
Depends: dcmtk
Recommends: pngquant
- * med-tools:
+ * med-tools:
Depends: cycle
Suggests: cl-pubmed
Strong dependency would cost installing a large amount
=====================================
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~),
-Build-Depends: debhelper-compat (= 12)
-Standards-Version: 4.4.1
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
@@ -107,21 +107,27 @@ Recommends: abacas,
art-nextgen-simulation-tools,
artemis,
artfastqgenerator,
+ assembly-stats,
assemblytics,
atac,
+ ataqv,
atropos,
+ augur,
augustus,
autodock,
autodock-vina,
autogrid,
+ avogadro,
axe-demultiplexer,
baitfisher,
bali-phy,
ballview,
+ bamkit,
bamtools,
bandage,
barrnap,
- bcbio,
+ bbmap,
+ bcalm,
bcftools,
beads,
beagle,
@@ -134,6 +140,7 @@ Recommends: abacas,
bio-eagle,
bio-rainbow,
bio-tradis,
+ biobambam2,
biosyntax,
bitseq,
blasr,
@@ -145,9 +152,12 @@ Recommends: abacas,
bppphyview,
bppsuite,
brig,
+ busco,
+ bustools,
bwa,
canu,
cassiopee,
+ cat-bat,
cct,
cd-hit,
cdbfasta,
@@ -170,6 +180,7 @@ Recommends: abacas,
codonw,
concavity,
conservation-code,
+ covtobed,
crac,
csb,
cutadapt,
@@ -179,13 +190,16 @@ Recommends: abacas,
dazzdb,
deepnano,
delly,
+ dextractor,
dialign,
dialign-tx,
diamond-aligner,
dindel,
+ discosnp,
disulfinder,
dnaclust,
dotter,
+ drop-seq-tools,
dssp,
dwgsim,
e-mem,
@@ -202,6 +216,8 @@ Recommends: abacas,
estscan,
examl,
exonerate,
+ falcon,
+ fasta3,
fastahack,
fastaq,
fastdnaml,
@@ -213,7 +229,9 @@ Recommends: abacas,
fasttree,
ffindex,
figtree,
+ filtlong,
fitgcp,
+ flash,
flexbar,
fml-asm,
freebayes,
@@ -225,9 +243,11 @@ Recommends: abacas,
garlic,
gasic,
gatb-core,
+ gbrowse,
gdpc,
gemma,
genometester,
+ genomethreader,
genometools,
gentle,
gff2aplot,
@@ -236,6 +256,7 @@ Recommends: abacas,
ghemical,
ghmm,
glam2,
+ gmap,
grabix,
graphlan,
grinder,
@@ -251,22 +272,28 @@ Recommends: abacas,
hmmer2,
hyphy-mpi | hyphy-pt,
idba,
+ igdiscover,
igor,
indelible,
infernal,
+ insilicoseq,
ipig,
iqtree,
iva,
jaligner,
+ jalview,
jellyfish,
jellyfish1,
jmodeltest,
jmol,
kalign,
kallisto,
+ kaptive,
khmer,
+ kineticstools,
king-probe,
kissplice,
+ kleborate,
kma,
kmc,
kmer,
@@ -278,14 +305,17 @@ Recommends: abacas,
lambda-align,
lambda-align2,
last-align,
+ lastz,
leaff,
lefse,
librg-utils-perl,
libvcflib-tools,
+ lighter,
logol,
loki,
ltrsift,
lucy,
+ lumpy-sv,
macs,
macsyfinder,
maffilter,
@@ -298,11 +328,13 @@ Recommends: abacas,
mauve-aligner,
melting,
meryl,
+ metabat,
metaphlan2,
metastudent,
mhap,
microbegps,
microbiomeutil,
+ mindthegap,
minia,
miniasm,
minimac4,
@@ -310,18 +342,25 @@ Recommends: abacas,
minimap2,
mipe,
mira-assembler,
+ mirtop,
mlv-smile,
+ mmb,
mmseqs2,
mothur,
mptp,
mrbayes,
+ msxpertsuite,
+ multiqc,
mummer,
murasaki | murasaki-mpi,
muscle,
mustang,
+ nanofilt,
nanook,
nanopolish,
+ nanosv,
nast-ier,
+ ncbi-acc-download,
ncbi-blast+,
ncbi-blast+-legacy,
ncbi-entrez-direct,
@@ -332,7 +371,9 @@ Recommends: abacas,
ncl-tools,
ncoils,
neobio,
+ ngmlr,
njplot,
+ norsnet,
norsp,
obitools,
openms,
@@ -341,11 +382,17 @@ Recommends: abacas,
paleomix,
paml,
paraclu,
+ parasail,
parsinsert,
parsnp,
patman,
pbdagcon,
+ pbgenomicconsensus,
+ pbhoney,
+ pbjelly,
pbsim,
+ pbsuite,
+ pdb2pqr,
perlprimer,
perm,
pftools,
@@ -358,9 +405,11 @@ Recommends: abacas,
phyutility,
phyx,
picard-tools,
+ picopore,
piler,
pilercr,
pilon,
+ pique,
pirs,
placnet,
plasmidomics,
@@ -373,24 +422,42 @@ Recommends: abacas,
populations,
porechop,
poretools,
+ pplacer,
prank,
predictnls,
+ predictprotein,
+ presto,
prime-phylo,
primer3,
+ prinseq-lite,
proalign,
probabel,
probalign,
probcons,
proda,
prodigal,
+ profbval,
+ profisis,
+ profnet-bval,
+ profnet-chop,
+ profnet-con,
+ profnet-isis,
+ profnet-md,
+ profnet-norsnet,
+ profnet-prof,
+ profnet-snapfun,
+ profphd,
+ profphd-net,
profphd-utils,
proftmb,
progressivemauve,
+ prokka,
proteinortho,
prottest,
pscan-chip,
pscan-tfbs,
psortb,
+ pycoqc,
pycorrfit,
pymol,
pynast,
@@ -398,15 +465,16 @@ Recommends: abacas,
python3-biomaj3-daemon,
python3-geneimpacts,
python3-gffutils,
- python3-presto,
+ python3-pairtools,
python3-pybedtools,
- python3-pybel,
python3-sqt,
python3-treetime,
pyvcf,
+ qcat,
qcumber,
qiime,
qtltools,
+ quicktree,
quorum,
qutemol,
r-bioc-annotate,
@@ -415,16 +483,19 @@ Recommends: abacas,
r-bioc-cner,
r-bioc-cummerbund,
r-bioc-deseq2,
- r-bioc-dnacopy,
r-bioc-ebseq,
+ r-bioc-edger,
r-bioc-genefilter,
- r-bioc-geneplotter,
- r-bioc-gviz,
+ r-bioc-geoquery,
r-bioc-hilbertvis,
+ r-bioc-htsfilter,
r-bioc-impute,
r-bioc-limma,
r-bioc-mergeomics,
+ r-bioc-metagenomeseq,
+ r-bioc-mofa,
r-bioc-multiassayexperiment,
+ r-bioc-mutationalpatterns,
r-bioc-pcamethods,
r-bioc-phyloseq,
r-bioc-rtracklayer,
@@ -446,16 +517,22 @@ Recommends: abacas,
r-cran-samr,
r-cran-sdmtools,
r-cran-seqinr,
+ r-cran-seurat,
r-cran-shazam,
+ r-cran-spp,
r-cran-tcr,
r-cran-tigger,
r-cran-treescape,
+ r-cran-tsne,
r-cran-vegan,
r-cran-webgestaltr,
+ r-cran-wgcna,
+ r-other-ascat,
r-other-hms-dbmi-spp,
r-other-mott-happy.hbrem,
racon,
radiant,
+ ragout,
rambo-k,
rampler,
rapmap,
@@ -468,11 +545,14 @@ Recommends: abacas,
rdp-classifier,
rdp-readseq,
readseq,
+ readucks,
reapr,
+ recan,
relion-bin | relion-bin+mpi,
relion-bin+gui | relion-bin+mpi+gui,
repeatmasker-recon,
reprof,
+ resfinder,
rna-star,
rnahybrid,
roary,
@@ -482,9 +562,12 @@ Recommends: abacas,
runcircos-gui,
saint,
salmon,
+ sambamba,
samblaster,
+ samclip,
samtools,
scoary,
+ scrappie,
scrm,
scythe,
seaview,
@@ -496,14 +579,18 @@ Recommends: abacas,
seqsero,
seqtk,
sga,
+ shovill,
+ sibelia,
sibsim4,
sickle,
sigma-align,
sim4,
sim4db,
skesa,
+ skewer,
smalt,
smithwaterman,
+ smrtanalysis,
snap,
snap-aligner,
sniffles,
@@ -516,6 +603,7 @@ Recommends: abacas,
sortmerna,
spaced,
spades,
+ spaln,
spoa,
sprai,
spread-phy,
@@ -528,6 +616,7 @@ Recommends: abacas,
stacks,
staden,
staden-io-lib-utils,
+ stringtie,
subread,
suitename,
sumaclust,
@@ -540,9 +629,14 @@ Recommends: abacas,
tabix,
tantan,
theseus,
+ thesias,
+ tiddit,
tigr-glimmer,
tm-align,
+ tnseq-transit,
toil,
+ tombo,
+ tophat-recondition,
topp,
toppred,
trace2dbest,
@@ -553,23 +647,32 @@ Recommends: abacas,
tree-puzzle | tree-ppuzzle,
treeview,
treeviewx,
+ trf,
+ trim-galore,
trimmomatic,
trinityrnaseq,
tvc,
uc-echo,
+ umap-learn,
umis,
+ unanimity,
unicycler,
varna,
vcftools,
velvet | velvet-long,
velvetoptimiser,
+ vg,
viewmol,
virulencefinder,
+ vmatch,
vsearch,
+ vt,
wham-align,
wigeon,
wise,
yaha,
+ yanagiba,
+ yanosim,
zalign
Suggests: acacia,
adun.app,
@@ -579,18 +682,17 @@ Suggests: acacia,
apollo,
arachne,
arb,
+ arvados,
asap,
- autodocktools,
- avogadro,
axparafit,
axpcoords,
bagpipe,
bambus,
bax2bam,
+ bcbio,
biceps,
big-blast,
bigsdb,
- biobambam2,
bismark,
blat,
blimps-utils,
@@ -599,7 +701,6 @@ Suggests: acacia,
btk-core,
cactus,
caftools,
- cain,
card-rgi,
ccs,
cdna-db,
@@ -608,6 +709,7 @@ Suggests: acacia,
cluster3,
cmap,
compclust,
+ conda-package-handling,
condetri,
contrafold,
contralign,
@@ -617,83 +719,81 @@ Suggests: acacia,
crux-toolkit,
cufflinks,
cytoscape,
+ damapper,
dascrubber,
dazzle,
deepbinner,
dendroscope,
- discosnp,
+ dnapi,
e-hive,
ecell,
embassy-phylip,
emboss-explorer,
- emperor,
ensembl,
+ ensembl-vep,
+ epigrass,
estferret,
euler-sr,
euler2,
exabayes,
exalt,
excavator,
- falcon,
- fasta3,
ffp,
+ fieldbioinformatics,
figaro,
- filtlong,
+ flappie,
+ flye,
forester,
forge,
galaxy,
gassst,
gatk,
- gbrowse,
gbrowse-syn,
genemark,
genesplicer,
genetrack,
genezilla,
genographer,
+ gerp++,
getdata,
- giira,
glimmerhmm,
- gmap,
gmv,
gramalign,
- haploview,
+ graphbin,
+ graphmap2,
+ haploview-cran-amap,
hawkeye,
htqc,
idefix,
- igdiscover,
+ idseq-bench,
igv,
inspect,
- jalview,
jbrowse,
jigsaw,
- kaptive,
kempbasu,
- kineticstools,
- kleborate,
+ libhdf5-dev,
lofreq,
mach-haplotyper,
mage2tab,
maker2,
malt,
manta,
+ marginphase,
martj,
maude,
maxd,
+ mecat2,
+ medaka,
+ megahit,
meme,
mesquite,
metabit,
metarep,
metastudent-data,
metastudent-data-2,
- metastudent-data-3,
- mgltools-cadd,
- mgltools-vision,
migrate,
- mindthegap,
minimus,
mirbase,
- mirtop,
modeller,
molekel,
mosaik-aligner,
@@ -701,17 +801,17 @@ Suggests: acacia,
mpsqed,
mrs,
msatfinder,
- msxpertsuite,
mugsy,
- multiqc,
mummergpu,
mview,
nanocall,
+ nanolyse,
+ nanoplot,
ncbi-igblast,
+ ncbi-magicblast,
nextsv,
ngila,
ngsqctoolkit,
- norsnet,
nw-align,
oases,
obo-edit,
@@ -724,15 +824,7 @@ Suggests: acacia,
partigene,
partitionfinder,
patristic,
- pbalign,
- pbbarcode,
- pbgenomicconsensus,
- pbh5tools,
- pbhoney,
- pbjelly,
- pbsuite,
pcma,
- pdb2pqr,
pfaat,
phagefinder,
phpphylotree,
@@ -744,22 +836,10 @@ Suggests: acacia,
pigx-scrnaseq,
pipasic,
pizzly,
+ plasmidid,
plato,
- predictprotein,
- profbval,
- profisis,
+ pomoxis,
profit,
- profnet-bval,
- profnet-chop,
- profnet-con,
- profnet-isis,
- profnet-md,
- profnet-norsnet,
- profnet-prof,
- profnet-snapfun,
- profphd,
- profphd-net,
- prokka,
prot4est,
psipred,
pssh2,
@@ -767,80 +847,120 @@ Suggests: acacia,
purple,
pyrophosphate-tools,
python3-alignlib,
+ python3-anndata,
+ python3-cgecore,
python3-cogent,
+ python3-cyvcf2,
python3-deeptools,
python3-deeptoolsintervals,
+ python3-emperor,
+ python3-htseq,
+ python3-intake,
python3-loompy,
+ python3-nanomath,
+ python3-ncls,
python3-orange,
python3-py2bit,
+ python3-pybel,
+ python3-pychopper,
+ python3-pyfaidx,
python3-pyflow,
- python3-reaper,
+ python3-pyranges,
+ python3-pyrle,
+ python3-pysam,
+ python3-tinyalign,
+ q2-alignment,
+ q2-composition,
+ q2-cutadapt,
+ q2-dada2,
+ q2-deblur,
+ q2-demux,
+ q2-diversity,
+ q2-emperor,
+ q2-feature-classifier,
+ q2-feature-table,
+ q2-fragment-insertion,
+ q2-gneiss,
+ q2-longitudinal,
+ q2-metadata,
+ q2-phylogeny,
+ q2-quality-control,
+ q2-quality-filter,
+ q2-sample-classifier,
+ q2-taxa,
+ q2-types,
+ q2-vsearch,
+ q2cli,
+ q2templates,
qtlcart,
+ qtlreaper,
qualimap,
quast,
r-bioc-annotationhub,
r-bioc-aroma.light,
+ r-bioc-biosingular,
+ r-bioc-ctc,
+ r-bioc-dnacopy,
r-bioc-ensembldb,
- r-bioc-geoquery,
+ r-bioc-experimenthub,
+ r-bioc-geneplotter,
r-bioc-go.db,
- r-bioc-metagenomeseq,
- r-bioc-mofa,
+ r-bioc-grohmm,
+ r-bioc-gviz,
r-bioc-qusage,
r-bioc-savr,
r-bioc-tximport,
+ r-cran-amap,
+ r-cran-biwt,
r-cran-boolnet,
r-cran-corrplot,
r-cran-drinsight,
r-cran-dynamictreecut,
+ r-cran-epir,
r-cran-fitdistrplus,
r-cran-forecast,
r-cran-gprofiler,
+ r-cran-minerva,
+ r-cran-optimalcutpoints,
+ r-cran-parmigene,
r-cran-pheatmap,
r-cran-qqman,
r-cran-rentrez,
+ r-cran-rsgcc,
r-cran-sctransform,
- r-cran-seurat,
- r-cran-tsne,
- r-cran-wgcna,
r-other-apmswapp,
raccoon,
- ragout,
raxml-ng,
rbs-finder,
repeatmasker,
- resfinder,
- rmblast,
roadtrips,
roche454ace2caf,
+ rosa,
rose,
rsat,
sailfish,
- sambamba,
sap,
science-workflow,
+ sepp,
seq-gen,
seq-seq-pan,
- seqcluster,
+ seqkit,
sequenceconverter.app,
- sibelia,
+ seqwish,
sift,
+ signalalign,
sina,
sistr,
situs,
- skewer,
- smalr,
- smrtanalysis,
snpeff,
solvate,
sourmash,
- spaln,
sparta,
splitstree,
ssaha,
strap,
strap-base,
strelka,
- stringtie,
tab2mage,
tacg,
taverna,
@@ -849,23 +969,20 @@ Suggests: acacia,
tide,
tigr-glimmer-mg,
tn-seqexplorer,
- tnseq-transit,
+ tophat,
treebuilder3d,
- treetime,
- trim-galore,
tripal,
trnascan-se,
twain,
+ ufasta,
ugene,
umap,
- unanimity,
unc-fish,
uniprime,
varmatch,
varscan,
vcfanno,
vdjtools,
- vg,
vienna-rna,
vmd,
x-tandem-pipeline,
@@ -881,6 +998,7 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: bio-tradis,
+ biobambam2,
bioperl,
bioperl-run,
biosquid,
@@ -890,6 +1008,7 @@ Recommends: bio-tradis,
libai-fann-perl,
libbambamc-dev,
libbamtools-dev,
+ libbigwig-dev,
libbio-asn1-entrezgene-perl,
libbio-chado-schema-perl,
libbio-coordinate-perl,
@@ -905,6 +1024,7 @@ Recommends: bio-tradis,
libbio-tools-run-alignment-clustalw-perl,
libbio-tools-run-alignment-tcoffee-perl,
libbiococoa-dev,
+ libbiod-dev,
libbiojava-java,
libbiojava4-java,
libbioparser-dev,
@@ -926,9 +1046,8 @@ Recommends: bio-tradis,
libfastahack-dev,
libffindex0-dev,
libfml-dev,
- libfreecontact-dev,
- libfreecontact-perl,
libgatbcore-dev,
+ libgclib-dev,
libgenome-dev,
libgenome-model-tools-music-perl,
libgenome-perl,
@@ -936,14 +1055,17 @@ Recommends: bio-tradis,
libgff-dev,
libgkarrays-dev,
libgo-perl,
+ libhdf5-dev,
libhmsbeagle-dev,
libhts-dev,
+ libhtscodecs-dev,
libhtsjdk-java,
libjebl2-java,
libjloda-java,
libkmer-dev,
libmems-dev,
- libminimap-dev,
+ libminimap2-dev,
+ libmmblib-dev,
libmuscle-dev,
libncbi-vdb-dev,
libncbi6-dev,
@@ -951,8 +1073,10 @@ Recommends: bio-tradis,
libngs-java,
libngs-sdk-dev,
libnhgri-blastall-perl,
+ libopenmm-dev,
libopenms-dev,
libpal-java,
+ libparasail-dev,
libpbbam-dev,
libpbdata-dev,
libpbihdf-dev,
@@ -968,6 +1092,7 @@ Recommends: bio-tradis,
librostlab3-dev,
libsbml5-dev,
libseqan2-dev,
+ libseqan3-dev,
libseqlib-dev,
libsmithwaterman-dev,
libsnp-sites1-dev,
@@ -981,15 +1106,14 @@ Recommends: bio-tradis,
libstatgen-dev,
libswiss-perl,
libtabixpp-dev,
- libtfbs-perl,
libthread-pool-dev,
libvcflib-dev,
libvibrant6-dev,
libzerg-perl,
libzerg0-dev,
mcl,
+ pyfai,
python3-airr,
- python3-bcbio,
python3-biom-format,
python3-biomaj3,
python3-biopython,
@@ -997,20 +1121,34 @@ Recommends: bio-tradis,
python3-bx,
python3-cgecore,
python3-cobra,
+ python3-cooler,
+ python3-corepywrap,
python3-csb,
python3-cutadapt,
python3-cyvcf2,
+ python3-deeptools,
+ python3-deeptoolsintervals,
python3-dendropy,
python3-dnaio,
+ python3-ete3,
python3-fast5,
python3-freecontact,
python3-gfapy,
python3-gffutils,
python3-htseq,
+ python3-intervaltree-bio,
+ python3-kineticstools,
+ python3-loompy,
+ python3-mirtop,
+ python3-nanoget,
python3-ngs,
+ python3-parasail,
+ python3-pbcommand,
python3-pbconsensuscore,
+ python3-pbcore,
python3-presto,
python3-py2bit,
+ python3-pyani,
python3-pybedtools,
python3-pybel,
python3-pyfaidx,
@@ -1020,12 +1158,14 @@ Recommends: bio-tradis,
python3-rdkit,
python3-ruffus,
python3-screed,
+ python3-skbio,
python3-sqt,
+ python3-streamz,
+ python3-tinyalign,
python3-treetime,
r-bioc-biobase,
- r-cran-adegenet,
- r-cran-adephylo,
r-cran-boolnet,
+ r-cran-corrplot,
r-cran-distory,
r-cran-fitdistrplus,
r-cran-forecast,
@@ -1043,7 +1183,10 @@ Recommends: bio-tradis,
r-cran-rnexml,
r-cran-rotl,
r-cran-samr,
+ r-cran-sctransform,
r-cran-seqinr,
+ r-cran-seurat,
+ r-cran-tsne,
r-cran-vegan,
r-cran-webgestaltr,
r-other-hms-dbmi-spp,
@@ -1053,21 +1196,22 @@ Recommends: bio-tradis,
seqan-dev,
snakemake,
toil
-Suggests: biobambam2,
- bioclipse,
+Suggests: bioclipse,
+ conda-package-handling,
ctdconverter,
- galaxy-lib,
+ cthreadpool-dev,
libbam-dev,
- libbigwig-dev,
- libbiod-dev,
+ libbbhash-dev,
libdisorder-dev,
libfast-perl,
libforester-java,
+ libfreecontact-dev,
libfreecontact-doc,
- libgclib,
+ libfreecontact-perl,
libgoby-java,
libmaus2-dev,
libmilib-java,
+ libminimap-dev,
libmodhmm-dev,
libnexml-java,
libpbcopper-dev,
@@ -1075,39 +1219,34 @@ Suggests: biobambam2,
libroadrunner-dev,
librostlab-blast-doc,
librostlab-doc,
- libseqan3-dev,
+ libssu-dev,
libsvmloc-dev,
libswarm2-dev,
- mgltools-networkeditor,
- mgltools-pybabel,
- mgltools-vision,
+ libtfbs-perl,
octace-bioinfo,
- pyfai,
python-biopython-doc,
- python-cogent,
- python-corepywrap,
- python-kineticstools,
- python-pbcommand,
- python-pbcore,
- python-pbh5tools,
python3-alignlib,
+ python3-anndata,
+ python3-bcbio,
+ python3-bel-resources,
python3-biopython-sql,
+ python3-cogent3,
python3-consensuscore2,
python3-ctdopts,
- python3-deeptools,
- python3-deeptoolsintervals,
- python3-ete3,
+ python3-galaxy-lib,
python3-hyphy,
- python3-intervaltree-bio,
- python3-loompy,
- python3-mirtop,
+ python3-intake,
python3-misopy,
- python3-pyani,
+ python3-ncls,
+ python3-networkx,
+ python3-pairix,
python3-pycosat,
python3-pyflow,
+ python3-pyranges,
python3-roadrunner,
python3-seqcluster,
- python3-skbio,
+ python3-torch,
+ python3-unifrac,
r-bioc-affy,
r-bioc-affyio,
r-bioc-altcdfenvs,
@@ -1121,13 +1260,18 @@ Suggests: biobambam2,
r-bioc-biostrings,
r-bioc-biovizbase,
r-bioc-bitseq,
+ r-bioc-bridgedbr,
r-bioc-bsgenome,
r-bioc-cner,
+ r-bioc-complexheatmap,
+ r-bioc-ctc,
r-bioc-cummerbund,
r-bioc-dada2,
+ r-bioc-deseq,
r-bioc-deseq2,
r-bioc-dnacopy,
r-bioc-ebseq,
+ r-bioc-enrichedheatmap,
r-bioc-ensembldb,
r-bioc-genefilter,
r-bioc-geneplotter,
@@ -1148,6 +1292,8 @@ Suggests: biobambam2,
r-bioc-metagenomeseq,
r-bioc-mofa,
r-bioc-multiassayexperiment,
+ r-bioc-nanostringqcpro,
+ r-bioc-org.hs.eg.db,
r-bioc-pcamethods,
r-bioc-phyloseq,
r-bioc-preprocesscore,
@@ -1163,24 +1309,36 @@ Suggests: biobambam2,
r-bioc-tximport,
r-bioc-variantannotation,
r-bioc-xvector,
- r-cran-corrplot,
+ r-cran-adegenet,
+ r-cran-adephylo,
+ r-cran-amap,
+ r-cran-biwt,
r-cran-drinsight,
r-cran-dt,
r-cran-dynamictreecut,
+ r-cran-fastcluster,
r-cran-future.apply,
r-cran-future.batchtools,
r-cran-ica,
+ r-cran-itertools,
r-cran-kaos,
r-cran-metap,
+ r-cran-minerva,
r-cran-natserv,
+ r-cran-nmf,
+ r-cran-optimalcutpoints,
+ r-cran-parmigene,
r-cran-pcapp,
r-cran-proc,
r-cran-rann,
+ r-cran-robustrankaggreg,
r-cran-rocr,
+ r-cran-rook,
+ r-cran-rsgcc,
r-cran-rsvd,
- r-cran-sctransform,
- r-cran-seurat,
- r-cran-tsne,
+ r-cran-shazam,
+ r-cran-sitmo,
+ r-cran-venndiagram,
r-other-apmswapp,
ruby-rgfa,
vdjtools
@@ -1212,12 +1370,10 @@ Recommends: abyss,
bioperl,
bioperl-run,
biosquid,
- blast2,
bowtie,
bowtie2,
boxshade,
bwa,
- cain,
cassiopee,
cd-hit,
cdbfasta,
@@ -1231,6 +1387,7 @@ Recommends: abyss,
datamash,
dialign,
dialign-tx,
+ discosnp,
disulfinder,
dnaclust,
dssp,
@@ -1250,8 +1407,8 @@ Recommends: abyss,
genometools,
gff2aplot,
gff2ps,
- giira,
glam2,
+ gmap,
grinder,
gromacs,
hhsuite,
@@ -1284,6 +1441,7 @@ Recommends: abyss,
neobio,
paraclu,
parsinsert,
+ pdb2pqr,
perm,
phyml,
phyutility,
@@ -1300,7 +1458,9 @@ Recommends: abyss,
pynast,
python3-biomaj3-cli,
python3-biopython,
+ python3-cogent3,
qiime,
+ r-bioc-edger,
r-bioc-hilbertvis,
r-cran-pvclust,
r-cran-qtl,
@@ -1333,12 +1493,10 @@ Recommends: abyss,
wise,
zalign
Suggests: bagpipe,
+ blast2,
cufflinks,
- discosnp,
embassy-phylip,
- gmap,
- pdb2pqr,
- python-cogent
+ giira
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
@@ -1355,8 +1513,7 @@ Recommends: python3-hl7
Suggests: drugref.org,
freediams,
freemedforms-freedata,
- oscar,
- sleepyhead
+ oscar
Description: Debian Med drug databases
This metapackage will install free drug databases and related
applications. The database can be accessed by any EMR using
@@ -1382,22 +1539,29 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: epigrass,
+ python3-seirsplus,
python3-treetime,
+ r-cran-covid19us,
r-cran-diagnosismed,
r-cran-epi,
r-cran-epibasix,
r-cran-epicalc,
+ r-cran-epiestim,
r-cran-epir,
r-cran-epitools,
+ r-cran-incidence,
r-cran-lexrankr,
r-cran-seroincidence,
r-cran-sf,
r-cran-sjplot,
r-cran-surveillance
-Suggests: epifire,
+Suggests: chime,
+ epifire,
netepi-analysis,
netepi-collection,
+ python3-torch,
r-cran-cmprsk,
+ r-cran-covid19,
r-cran-msm,
repast,
shiny-server,
@@ -1444,8 +1608,11 @@ Depends: ${misc:Depends},
med-tasks (= ${source:Version})
Recommends: aeskulap,
amide,
+ ants,
bart,
bart-view,
+ biosig-tools,
+ camitk-imp,
ctn,
ctsim,
dcm2niix,
@@ -1454,10 +1621,12 @@ Recommends: aeskulap,
dicomnifti,
dicomscope,
gdf-tools,
+ ginkgocadx,
gwyddion,
imagej,
invesalius,
ismrmrd-tools,
+ itksnap,
king,
libgdcm-tools,
medcon,
@@ -1467,26 +1636,33 @@ Recommends: aeskulap,
minc-tools,
mriconvert,
mricron,
- mrtrix,
+ mrtrix3,
nifti-bin,
odil,
+ odin,
openslide-tools,
orthanc,
orthanc-wsi,
pixelmed-apps,
- python3-dicom,
+ plastimatch,
python3-nibabel,
+ python3-nipy,
+ python3-nitime,
+ python3-pydicom,
+ python3-pyxid,
+ python3-surfer,
+ sigviewer,
+ sofa-apps,
+ teem-apps,
tifffile,
+ vrrender,
vtk-dicom-tools,
xmedcon
Suggests: afni,
- ants,
bioimagesuite,
bioimagexd,
- biosig-tools,
blox,
brainvisa,
- camitk-imp,
caret,
cdmedicpacs,
cellprofiler,
@@ -1512,9 +1688,7 @@ Suggests: afni,
freesurfer,
fsl,
fslview,
- fw4spl,
gimias,
- ginkgocadx,
hid,
imagemagick,
imagevis3d,
@@ -1522,7 +1696,6 @@ Suggests: afni,
incf-nidash-oneclick-clients,
insightapplications,
isis,
- itksnap,
jemris,
jist,
kradview,
@@ -1540,8 +1713,6 @@ Suggests: afni,
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
- mrtrix3,
- odin,
omero,
opendicom.net,
openelectrophy,
@@ -1555,23 +1726,15 @@ Suggests: afni,
orthanc-webviewer,
paraview,
piano,
- plastimatch,
pngquant,
pymeg,
python-dipy,
- python-nipy,
python-nipype,
- python-nitime,
- python-pyxid,
python3-mvpa2,
- python3-surfer,
science-workflow,
- sigviewer,
slicer,
- sofa-apps,
stabilitycalc,
stir,
- teem-apps,
tempo,
trimage,
via-bin,
@@ -1601,8 +1764,11 @@ Recommends: cimg-dev,
ctn-dev,
gmic,
libbart-dev,
+ libbiosig-dev,
+ libcamitk-dev,
libcifti-dev,
libedf-dev,
+ libgdcm2-dev,
libgdf-dev,
libgiftiio-dev,
libinsighttoolkit4-dev,
@@ -1617,7 +1783,11 @@ Recommends: cimg-dev,
libodil-dev,
libopenigtlink-dev,
libopenslide-dev,
+ libopensurgsim-dev,
libpapyrus3-dev,
+ libsight-dev,
+ libsimpleitk1-dev,
+ libteem-dev,
libvigraimpex-dev,
libvistaio-dev,
libvolpack1-dev,
@@ -1627,49 +1797,43 @@ Recommends: cimg-dev,
octave-bart,
octave-dicom,
octave-gdf,
- python3-dicom,
+ odin,
+ python3-biosig,
python3-gdcm,
python3-imageio,
python3-mia,
+ python3-mne,
python3-nibabel,
+ python3-nipy,
+ python3-nitime,
python3-openslide,
+ python3-pydicom,
+ python3-pyxnat,
+ python3-simpleitk,
r-cran-rniftilib
Suggests: emokit,
libbio-formats-java,
- libbiosig-dev,
- libcamitk-dev,
libcamp-dev,
libctk-dev,
libcv-dev,
libeegdev-dev,
libfreeimage-dev,
- libgdcm2-dev,
libics-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-cfflib,
python-dipy,
- python-nipy,
python-nipype,
- python-nitime,
- python-pyxnat,
python-vigra,
python-vmtk,
- python3-biosig,
- python3-mne,
python3-mvpa2,
- python3-simpleitk,
+ pytorch-vision,
tifffile
Description: Debian Med image processing and visualization packages development
This metapackage will install Debian packages which might be useful
@@ -1682,9 +1846,9 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: orthanc-wsi
+Recommends: opencfu,
+ orthanc-wsi
Suggests: catissuesuite,
- opencfu,
openelis,
openfreezer
Description: Debian Med suggestions for medical laboratories
@@ -1726,13 +1890,13 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: gdf-tools,
+Recommends: biosig-tools,
+ gdf-tools,
octave,
paw,
paw++,
r-base
-Suggests: biosig-tools,
- gate,
+Suggests: gate,
libbiosig-dev,
octave-biosig,
openvibe,
@@ -1752,13 +1916,15 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: entangle,
+ ginkgocadx,
+ gnumed-client,
gnumed-server,
libchipcard-tools,
orthanc,
orthanc-wsi,
+ oscar,
qrisk2,
- r-cran-medadherence,
- sleepyhead
+ r-cran-medadherence
Suggests: clearhealth,
elementalclinic,
elexis,
@@ -1767,8 +1933,6 @@ Suggests: clearhealth,
freemed,
freemedforms-emr,
freeshim,
- ginkgocadx,
- gnumed-client,
libctapimkt1,
medintux,
mirrormed,
@@ -1776,7 +1940,6 @@ Suggests: clearhealth,
openemr,
openpms,
openrep,
- oscar,
proteus,
remitt,
resmedicinae,
@@ -1795,14 +1958,14 @@ Depends: ${misc:Depends},
med-tasks (= ${source:Version})
Recommends: praat,
psignifit,
+ psychopy,
r-cran-foreign,
r-cran-psy,
- r-cran-psych
-Suggests: psychopy,
- python-pyepl,
- r-cran-psychometric,
- r-cran-psychotree,
- r-cran-psyphy,
+ r-cran-psych,
+ r-cran-psychometric,
+ r-cran-psychotree,
+ r-cran-psyphy
+Suggests: python-pyepl,
science-psychophysics
Description: Debian Med packages for psychology
This metapackage contains dependencies for a collection of software
@@ -1826,7 +1989,8 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: r-bioc-limma,
+Recommends: r-bioc-edger,
+ r-bioc-limma,
r-bioc-multtest,
r-bioc-qvalue,
r-cran-ade4,
@@ -1870,8 +2034,7 @@ Suggests: cycle,
nut-nutrition,
oscar,
pesco,
- pondus,
- sleepyhead
+ pondus
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care..
Currently it contains some simple programs for Personal Health.
=====================================
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~),
-Build-Depends: debhelper-compat (= 12)
-Standards-Version: 4.4.1
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
@@ -17,4 +17,3 @@ Description: Debian Med tasks for tasksel
.
These tasks are described in detail at
https://blends.debian.org/med/tasks/
-
=====================================
dependency_data/debian-med_3.6.json
=====================================
@@ -0,0 +1 @@
+{"bio-dev": {"depends": [], "suggests": ["conda-package-handling", "python3-biopython-sql", "python-biopython-doc", "python3-cogent3", "python3-ncls", "python3-pycosat", "libtfbs-perl", "libfreecontact-dev", "libfreecontact-perl", "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-bridgedbr", "r-bioc-bsgenome", "r-bioc-cner", "r-bioc-complexheatmap", "r-bioc-cummerbund", "r-bioc-ctc", "r-bioc-dada2", "r-bioc-deseq", "r-bioc-deseq2", "r-bioc-dnacopy", "r-bioc-ebseq", "r-bioc-enrichedheatmap", "r-bioc-ensembldb", "r-bioc-genefilter", "r-bioc-geneplotter", "r-bioc-genomeinfodb", "r-bioc-genomicalignments", "r-bioc-genomicfeatures", "r-bioc-genomicranges", "r-bioc-geoquery", "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-nanostringqcpro", "r-bioc-org.hs.eg.db", "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-adegenet", "r-cran-adephylo", "r-cran-amap", "r-cran-biwt", "r-cran-dt", "r-cran-dynamictreecut", "r-cran-fastcluster", "r-cran-future.apply", "r-cran-future.batchtools", "r-cran-ica", "r-cran-itertools", "r-cran-kaos", "r-cran-metap", "r-cran-minerva", "r-cran-natserv", "r-cran-nmf", "r-cran-optimalcutpoints", "r-cran-parmigene", "r-cran-pcapp", "r-cran-proc", "r-cran-rann", "r-cran-rsgcc", "r-cran-robustrankaggreg", "r-cran-rocr", "r-cran-rook", "r-cran-rsvd", "r-cran-shazam", "r-cran-sitmo", "r-cran-venndiagram", "ruby-rgfa", "librostlab-doc", "librostlab-blast-doc", "libswarm2-dev", "python3-networkx", "libbam-dev", "libfast-perl", "libpbcopper-dev", "libminimap-dev", "libdisorder-dev", "cthreadpool-dev", "python3-pyflow", "libmilib-java", "vdjtools", "python3-alignlib", "python3-ctdopts", "ctdconverter", "libmodhmm-dev", "libsvmloc-dev", "python3-bel-resources", "libmaus2-dev", "libbbhash-dev", "python3-intake"], "recommends": ["bioperl", "bioperl-run", "libncbi6-dev", "mcl", "biosquid", "cwltool", "snakemake", "libvibrant6-dev", "python3-biopython", "python3-screed", "python3-cutadapt", "python3-dnaio", "python3-tinyalign", "ruby-bio", "libbiojava-java", "libbiojava4-java", "libgenome-dev", "libmuscle-dev", "libmems-dev", "libhtsjdk-java", "libai-fann-perl", "libbio-mage-perl", "libnhgri-blastall-perl", "libhdf5-dev", "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", "python3-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-boolnet", "r-cran-corrplot", "r-cran-distory", "r-cran-drinsight", "r-cran-forecast", "r-cran-fitdistrplus", "r-cran-genetics", "r-cran-gprofiler", "r-cran-haplo.stats", "r-cran-metamix", "r-cran-phangorn", "r-cran-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-sctransform", "r-cran-seurat", "r-cran-seqinr", "r-cran-tsne", "r-cran-vegan", "r-cran-webgestaltr", "r-other-hms-dbmi-spp", "r-other-apmswapp", "r-bioc-biobase", "libffindex0-dev", "librostlab3-dev", "librostlab-blast0-dev", "librg-blast-parser-perl", "libsort-key-top-perl", "libhmsbeagle-dev", "libforester-java", "libbambamc-dev", "libbamtools-dev", "libpbbam-dev", "libbigwig-dev", "libbio-das-lite-perl", "libopenms-dev", "libgenometools0-dev", "librdp-taxonomy-tree-java", "python3-biom-format", "python3-rdkit", "libgenome-perl", "libgenome-model-tools-music-perl", "pyfai", "libhts-dev", "python3-htseq", "python3-intervaltree-bio", "python3-csb", "python3-misopy", "python3-freecontact", "python3-pymummer", "libkmer-dev", "libsnp-sites1-dev", "libssm-dev", "librelion-dev", "libdivsufsort-dev", "bioclipse", "libgff-dev", "python3-pysam", "python3-pbcore", "python3-cobra", "libtabixpp-dev", "python3-ruffus", "python3-hyphy", "python3-dendropy", "python3-skbio", "libparasail-dev", "python3-parasail", "python3-pbconsensuscore", "python3-consensuscore2", "libconsensuscore-dev", "python3-pbcommand", "python3-pyvcf", "python3-pyfaidx", "python3-sqt", "python3-kineticstools", "libqes-dev", "libfast5-dev", "python3-fast5", "libpbseq-dev", "libpbdata-dev", "libpbihdf-dev", "libblasr-dev", "libminimap2-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", "libssw-dev", "libssw-java", "libfml-dev", "libgkarrays-dev", "libjloda-java", "libvcflib-dev", "libswiss-perl", "python3-pybedtools", "python3-gffutils", "python3-bx", "toil", "python3-galaxy-lib", "libbio-eutilities-perl", "libseqlib-dev", "libroadrunner-dev", "python3-roadrunner", "python3-biotools", "bio-tradis", "python3-biomaj3", "libbiod-dev", "python3-ete3", "python3-gfapy", "libgoby-java", "python3-seqcluster", "python3-cyvcf2", "libgatbcore-dev", "python3-airr", "python3-presto", "python3-bcbio", "libpll-dev", "libstatgen-dev", "python3-pyani", "python3-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-dev", "biobambam2", "libcdk-java", "libhtscodecs-dev", "python3-torch", "python3-anndata", "python3-cooler", "python3-pairix", "python3-pyranges", "python3-streamz", "libssu-dev", "python3-unifrac", "python3-nanoget", "libopenmm-dev", "libmmblib-dev"], "ignore": ["golang-github-biogo-hts-dev"], "avoid": []}, "oncology": {"depends": [], "suggests": [], "recommends": ["uw-prism", "orthanc-wsi", "planunc", "dicompyler"], "ignore": [], "avoid": []}, "bio-ngs": {"depends": [], "suggests": ["python3-anndata", "graphmap2", "nanolyse", "nanoplot"], "recommends": ["bedtools", "bwa", "bowtie", "blasr", "daligner", "mhap", "last-align", "wham-align", "maq", "picard-tools", "r-bioc-edger", "r-bioc-hilbertvis", "r-bioc-rsubread", "rna-star", "samtools", "sra-toolkit", "ssake", "tabix", "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", "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", "pbjelly", "pbhoney", "pirs", "pizzly", "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", "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", "flexbar", "picard-tools", "samtools", "tabix", "vcftools", "anfo", "cufflinks", "bowtie", "bowtie2", "bwa", "last-align", "maq", "perm", "hisat2", "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", "readseq", "tigr-glimmer", "seqan-apps", "staden-io-lib-utils", "python3-cogent3", "aevol", "python3-biomaj3-cli", "bioperl", "bioperl-run", "clonalframe", "circos", "datamash", "prodigal", "python3-biopython", "qiime", "r-bioc-edger", "r-cran-pvclust", "r-cran-vegan"], "ignore": [], "avoid": []}, "bio": {"depends": [], "suggests": ["conda-package-handling", "dascrubber", "emboss-explorer", "dnapi", "q2-cutadapt", "q2-demux", "q2-feature-classifier", "q2-feature-table", "q2-metadata", "q2-quality-filter", "q2-types", "q2cli", "q2templates", "q2-taxa", "q2-alignment", "q2-emperor", "q2-composition", "q2-sample-classifier", "q2-vsearch", "q2-dada2", "q2-deblur", "q2-diversity", "q2-gneiss", "q2-longitudinal", "q2-phylogeny", "q2-quality-control", "q2-fragment-insertion", "python3-intake", "python3-ncls", "python3-pychopper", "python3-pyrle", "python3-pyranges", "python3-anndata", "adun.app", "science-workflow", "getdata", "epigrass", "idseq-bench", "libhdf5-dev", "metastudent-data", "metastudent-data-2", "mrs", "python3-alignlib", "python3-cgecore", "python3-cyvcf2", "python3-deeptools", "python3-deeptoolsintervals", "python3-htseq", "python3-loompy", "python3-nanomath", "python3-pybel", "python3-pyfaidx", "python3-pyflow", "python3-py2bit", "python3-pysam", "python3-tinyalign", "r-bioc-annotationhub", "r-bioc-aroma.light", "r-bioc-biosingular", "r-bioc-ctc", "r-bioc-dnacopy", "r-bioc-ensembldb", "r-bioc-experimenthub", "r-bioc-geneplotter", "r-bioc-go.db", "r-bioc-grohmm", "r-bioc-gviz", "r-bioc-qusage", "r-bioc-tximport", "r-cran-amap", "r-cran-biwt", "r-cran-corrplot", "r-cran-dynamictreecut", "r-cran-epir", "r-cran-forecast", "r-cran-gprofiler", "r-cran-fitdistrplus", "r-cran-qqman", "r-cran-rentrez", "r-cran-boolnet", "r-cran-minerva", "r-cran-optimalcutpoints", "r-cran-parmigene", "r-cran-pheatmap", "r-cran-rsgcc", "r-bioc-savr", "r-cran-sctransform", "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", "gff2aplot", "muscle", "sim4", "sibsim4", "tabix", "wise", "maqview", "blasr", "daligner", "mhap", "bwa", "megahit", "metabat", "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", "bustools", "last-align", "maq", "ssake", "velvet | velvet-long", "qiime", "scoary", "tophat", "tophat-recondition", "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", "mustang", "probabel", "theseus", "staden-io-lib-utils", "samtools", "bedtools", "datamash", "gassst", "hinge", "r-bioc-hilbertvis", "r-other-mott-happy.hbrem", "seq-gen", "snp-sites", "mira-assembler", "alien-hunter", "seqan-apps", "ncoils", "gentle", "gmap", "igv", "picard-tools", "acedb-other", "blixem", "dotter", "belvu", "paml", "velvetoptimiser", "ensembl", "mrbayes", "pdb2pqr", "squizz", "clonalframe", "clonalframeml", "dssp", "jellyfish", "jellyfish1", "ballview", "pynast", "pizzly", "raxml", "mlv-smile", "cd-hit", "cufflinks", "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", "trim-galore", "saint", "rtax", "rate4site", "rna-star", "sailfish", "topp", "openms", "scythe", "sickle", "skewer", "kmc", "king-probe", "ncl-tools", "tvc", "libvcflib-tools", "bppsuite", "bppphyview", "acacia", "adapterremoval", "aegean", "andi", "arden", "artfastqgenerator", "art-nextgen-simulation-tools", "assemblytics", "ataqv", "augustus", "baitfisher", "bandage", "bbmap", "bcalm", "beagle", "bedops", "biceps", "cnvkit", "csb", "diamond-aligner", "python3-emperor", "euler2", "euler-sr", "fitgcp", "gasic", "ipig", "aevol", "alter-sequence-alignment", "amos-assembler", "hawkeye", "anfo", "apollo", "aragorn", "ariba", "arvados", "assembly-stats", "atac", "atropos", "augur", "axe-demultiplexer", "axparafit", "axpcoords", "bali-phy", "bamkit", "bamtools", "bagpipe", "barrnap", "bax2bam", "bcbio", "bcftools", "bigsdb", "bio-eagle", "bio-tradis", "biobambam2", "biosyntax", "bismark", "bitseq", "blat", "blobology", "bio-rainbow", "braker", "busco", "card-rgi", "cassiopee", "cat-bat", "ccs", "cdbfasta", "centrifuge", "cellprofiler", "chromhmm", "cgview", "brig", "cct", "cinema", "circlator", "clearcut", "clonalorigin", "cluster3", "chromimpute", "codonw", "condetri", "contrafold", "covtobed", "crac", "crossbow", "crux-toolkit", "cutadapt", "cytoscape", "damapper", "dawg", "dazzdb", "dazzle", "deepbinner", "dextractor", "delly", "deepnano", "dendroscope", "dindel", "drop-seq-tools", "dwgsim", "ea-utils", "ecell", "ecopcr", "edtsurf", "emmax", "ensembl-vep", "examl", "raxml-ng", "exabayes", "berkeley-express", "falcon", "fasta3", "fasttree", "fastahack", "fastaq", "fastml", "fastp", "fastqc", "fastqtl", "flappie", "flash", "flye", "ffp", "fieldbioinformatics", "filtlong", "unc-fish", "fml-asm", "forester", "freecontact", "freebayes", "fsa", "fsm-lite", "garli", "gatb-core", "gatk", "genometester", "genomethreader", "genometools", "gerp++", "gffread", "grabix", "graphbin", "graphlan", "graphmap2", "gwama", "gubbins", "haploview-cran-amap", "harvest-tools", "hilive", "hisat2", "hmmer2", "htqc", "idba", "idefix", "igdiscover", "indelible", "insilicoseq", "iqtree", "iva", "jaligner", "jbrowse", "jmodeltest", "kaptive", "kleborate", "kempbasu", "kineticstools", "kissplice", "kma", "kmerresistance", "kraken", "kraken2", "lagan", "lambda-align", "lambda-align2", "lastz", "leaff", "ltrsift", "lofreq", "kallisto", "khmer", "kmer", "radiant", "lefse", "lighter", "lumpy-sv", "mach-haplotyper", "macs", "macsyfinder", "maffilter", "mage2tab", "tab2mage", "malt", "manta", "mapdamage", "marginphase", "martj", "mash", "progressivemauve", "mauve-aligner", "mecat2", "medaka", "meme", "meryl", "metabit", "metaphlan2", "metastudent", "microbegps", "mindthegap", "miniasm", "minimac4", "minimap", "minimap2", "mirtop", "mmb", "molekel", "mosaik-aligner", "mosdepth", "mmseqs2", "mpsqed", "mptp", "mugsy", "multiqc", "murasaki | murasaki-mpi", "mview", "nanocall", "nanook", "nanopolish", "nanolyse", "nanofilt", "nanoplot", "nanosv", "ncbi-acc-download", "ncbi-entrez-direct", "ncbi-magicblast", "ncbi-seg", "nextsv", "ngila", "ngmlr", "ngsqctoolkit", "nw-align", "oases", "obitools", "oncofuse", "optimir", "optitype", "paipline", "pal2nal", "paleomix", "paraclu", "parasail", "parsinsert", "parsnp", "partitionfinder", "patman", "patristic", "pbdagcon", "pbsuite", "pbgenomicconsensus", "pbjelly", "pbhoney", "pbsim", "pcma", "perm", "pftools", "phast", "phipack", "phybin", "phylophlan", "phyloviz-core", "phyutility", "phyx", "physamp", "picopore", "piler", "pilercr", "pilon", "pipasic", "inspect", "tide", "pique", "pirs", "placnet", "plasmidid", "plasmidseeker", "plato", "plip", "pomoxis", "poretools", "porechop", "pplacer", "prank", "predictprotein", "prinseq-lite", "proalign", "prodigal", "prokka", "proteinortho", "prottest", "psortb", "pscan-tfbs", "pscan-chip", "psipred", "pssh2", "pufferfish", "pycorrfit", "pyscanfcs", "python3-cogent", "python3-geneimpacts", "python3-gffutils", "python3-pairtools", "python3-pybedtools", "python3-sqt", "qtlreaper", "python3-treetime", "purple", "pycoqc", "qcat", "qcumber", "quicktree", "qtltools", "qualimap", "quast", "quorum", "ragout", "rambo-k", "rapmap", "r-bioc-annotate", "r-bioc-biostrings", "r-bioc-bitseq", "r-bioc-cummerbund", "r-bioc-deseq2", "r-bioc-edger", "r-bioc-genefilter", "r-bioc-geoquery", "r-bioc-htsfilter", "r-bioc-impute", "r-bioc-limma", "r-bioc-mergeomics", "r-bioc-metagenomeseq", "r-bioc-phyloseq", "r-bioc-mofa", "r-bioc-multiassayexperiment", "r-bioc-mutationalpatterns", "r-bioc-pcamethods", "r-bioc-rtracklayer", "r-cran-samr", "r-bioc-ebseq", "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-cran-spp", "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-cran-wgcna", "r-other-ascat", "readucks", "recan", "relion-bin+gui | relion-bin+mpi+gui", "relion-bin | relion-bin+mpi", "rdp-alignment", "rdp-readseq", "rdp-classifier", "reapr", "repeatmasker-recon", "repeatmasker", "resfinder", "roadtrips", "roary", "roguenarok", "rosa", "rsat", "rsem", "sambamba", "samblaster", "salmon", "samclip", "sap", "scrappie", "scrm", "seer", "segemehl", "sepp", "seq-seq-pan", "seqkit", "seqmagick", "seqprep", "seqsero", "seqtk", "sequenceconverter.app", "seqwish", "sga", "shovill", "signalalign", "sibelia", "sina", "sistr", "situs", "sim4db", "skesa", "smalt", "smithwaterman", "smrtanalysis", "snpeff", "snpomatic", "solvate", "sortmerna", "snap-aligner", "sniffles", "sourmash", "spaced", "spades", "spaln", "sparta", "sprai", "srst2", "ssaha", "sspace", "ssw-align", "staden", "stacks", "strap", "strap-base", "strelka", "stringtie", "subread", "suitename", "sumatra", "sumaclust", "sumtrees", "surankco", "swarm", "tacg", "tantan", "thesias", "tiddit", "toppred", "transdecoder", "tnseq-transit", "tn-seqexplorer", "toil", "tombo", "tracetuner", "transrate-tools", "treeview", "trf", "trinityrnaseq", "uc-echo", "ufasta", "umap-learn", "umis", "unanimity", "unicycler", "varna", "varmatch", "varscan", "vcfanno", "vdjtools", "vg", "vienna-rna", "virulencefinder", "vmatch", "vmd", "vsearch", "vt", "yaha", "yanagiba", "yanosim", "canu", "zalign", "zodiac-zeden", "discosnp", "mapsembler2", "dnaclust", "r-cran-tcr", "r-cran-tigger", "r-cran-alakazam", "r-cran-shazam", "igor", "r-cran-sdmtools", "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", "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", "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", "python-nipype", "emokit", "python-dipy", "libeegdev-dev", "libxdffileio-dev", "tifffile", "python-vmtk", "python-vigra", "libcamp-dev"], "recommends": ["ctn-dev", "cimg-dev", "libminc-dev", "libmdc2-dev", "libvtk7-dev", "libnifti-dev", "libinsighttoolkit4-dev", "libvolpack1-dev", "libgdcm2-dev", "python3-gdcm", "libopensurgsim-dev", "libmaxflow-dev", "python3-mvpa2", "python3-nipy", "python3-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-pydicom", "libopenmeeg-dev", "python3-nibabel", "libgdf-dev", "octave-gdf", "python3-pyxnat", "libbiosig-dev", "python3-biosig", "libctk-dev", "libopenslide-dev", "python3-openslide", "libopenslide-java", "libbio-formats-java", "octave-dicom", "libcamitk-dev", "libpapyrus3-dev", "python3-mne", "libvmtk-dev", "libvigraimpex-dev", "libvtk-dicom-dev", "libedf-dev", "python3-imageio", "libismrmrd-dev", "libodil-dev", "libbart-dev", "octave-bart", "libcifti-dev", "libxdf-dev", "libsimpleitk1-dev", "python3-simpleitk", "pytorch-vision", "libsight-dev"], "ignore": [], "avoid": []}, "research": {"depends": [], "suggests": [], "recommends": ["r-cran-rpact", "openclinica"], "ignore": [], "avoid": []}, "statistics": {"depends": [], "suggests": ["science-statistics"], "recommends": ["r-bioc-edger", "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", "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", "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", "python-pyepl"], "recommends": ["praat", "r-cran-foreign", "psignifit", "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", "pplacer", "quicktree"], "ignore": [], "avoid": []}, "imaging": {"depends": [], "suggests": ["imagemagick", "pngquant", "imview", "trimage", "python-nipype", "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-dipy", "dtitk", "openwalnut-qt4", "miview", "cmtk", "freesurfer", "isis", "pymeg", "stabilitycalc", "hid", "incf-nidash-oneclick-clients", "science-workflow"], "recommends": ["amide", "ctsim", "ctn", "dicomnifti", "imagej", "minc-tools", "medcon", "python3-nibabel", "python3-pydicom", "xmedcon", "dcmtk", "nifti-bin", "aeskulap", "fsl", "fslview", "via-bin", "gwyddion", "sofa-apps", "python3-mvpa2", "python3-nipy", "python3-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", "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", "python3-pyxid", "plastimatch", "medisnap", "gimias", "mayam", "xnat", "biosig-tools", "python3-surfer", "dicoogle", "cellprofiler", "bioimagexd", "omero", "king", "vtk-dicom-tools", "gdf-tools", "vrrender", "bart", "bart-view", "dcm2niix", "orthanc-wsi", "odil"], "ignore": [], "avoid": []}, "covid-19": {"depends": [], "suggests": ["python3-anndata", "r-bioc-rsubread", "libsimde-dev", "python3-mmtf"], "recommends": ["cwltool", "snakemake", "arvados", "augur", "auspice", "blat", "chip-seq", "fieldbioinformatics", "megahit", "idseq-dag", "nextstrain-ncov", "parasail", "r-bioc-htsfilter", "r-bioc-mutationalpatterns", "r-bioc-rcpi", "r-bioc-rgsepd", "r-bioc-pwmenrich", "r-bioc-tcgabiolinks", "r-cran-mediana", "r-cran-spp", "recan", "trinculo", "vadr", "wtdbg2", "pigx-rnaseq", "bowtie2", "minimap2", "bwa", "nanoseq", "guppy", "chiron", "qcat", "pycoqc", "nanoplot", "fastqc", "graphmap2", "samtools", "bedtools", "multiqc", "artic", "viralrecon", "parallel-fastq-dump", "fastp", "picard-tools", "ivar", "varscan", "snpeff", "snpsift", "bcftools", "cutadapt", "kraken2", "spades", "unicycler", "minia", "vg", "ncbi-blast+", "abacas", "quast", "bustools", "kallisto", "salmon", "rna-star", "allelecount", "r-other-ascat", "freebayes", "manta", "qualimap", "strelka", "tiddit", "umap-learn", "ensembl-vep", "busco", "cat-bat", "centrifuge", "dextractor", "drop-seq-tools", "filtlong", "mecat2", "metabat", "nanolyse", "porechop", "changeo", "muscle", "plasmidid", "pplacer", "presto", "python3-cooler", "python3-pairix", "r-cran-alakazam", "r-cran-shazam", "r-cran-tigger", "rosa", "sepp", "seqwish", "signalalign", "tombo", "vsearch", "assembly-stats", "bamkit", "libbbhash-dev", "flappie", "flash", "flye", "lastz", "lighter", "lumpy-sv", "medaka", "ncbi-magicblast", "nanofilt", "python3-nanomath", "nanopolish", "nanook", "nanosv", "ngmlr", "oncofuse", "optitype", "python3-nanoget", "python3-pairtools", "python3-pauvre", "picopore", "pomoxis", "poretools", "prinseq-lite", "pybedtools-bin", "python3-pychopper", "pyomo", "python3-biopython", "python3-vcf", "r-bioc-rsamtools", "readucks", "sailfish", "samclip", "scrappie", "python3-seqcluster", "seqkit", "shovill", "python3-streamz", "tophat-recondition", "vienna-rna", "vt", "python3-toolz", "python3-tornado", "yanagiba", "yanosim", "ufasta", "epigrass", "r-cran-covid19", "r-cran-covid19us", "r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi", "r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "r-cran-seroincidence", "shiny-server", "r-cran-lexrankr", "r-cran-sf", "r-cran-sjplot", "python3-treetime", "chime", "aeskulap", "conquest-common", "dcmtk", "ginkgocadx", "imagej", "libgdcm-tools", "orthanc", "orthanc-wsi", "orthanc-python", "streamlit", "libtensorflow-framework2", "abyss", "bbmap", "bcalm", "bcbio", "biobambam2", "clonalframeml", "python3-cyvcf2", "delly", "diamond-aligner", "discosnp", "python3-drmaa", "fasta3", "genometools", "gffread", "gnumed-client", "gnumed-server", "gromacs", "gubbins", "libhtscodecs-dev", "python3-htseq", "kalign", "libchipcard-dev", "libgclib-dev", "libics-dev", "libmaus2-dev", "libmilib-java", "mmseqs2", "odil", "orthanc-dicomweb", "paleomix", "plink1.9", "plip", "prokka", "proteinortho", "python3-pydicom", "python3-pynn", "python3-biom-format", "python3-bx", "python3-cgecore", "python3-cogent3", "python3-depinfo", "python3-etelemetry", "python3-gffutils", "python3-pbcommand", "python3-pbcore", "python3-pyani", "python3-pyfaidx", "python3-pysam", "python3-questplus", "python3-scitrack", "python3-screed", "python3-tinyalign", "python3-typed-ast", "q2-cutadapt", "q2-feature-table", "q2-quality-filter", "r-bioc-limma", "r-cran-hms", "r-cran-msm", "r-cran-qtl", "r-cran-stringi", "ragout", "rsem", "ruby-bio", "samblaster", "libseqan3-dev", "seqmagick", "shapeit4", "smrtanalysis", "spaln", "staden-io-lib-utils", "stringtie", "sumaclust", "texlive-science", "thesias", "tnseq-transit", "toil", "umis", "workrave", "python3-torch", "nextflow", "quicktree", "r-cran-incidence", "r-cran-epiestim", "python3-seirsplus", "mmb"], "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": ["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-covid19", "r-cran-covid19us", "r-cran-epibasix", "r-cran-epitools", "r-cran-surveillance", "r-cran-epi", "r-cran-diagnosismed", "r-cran-epicalc", "r-cran-epir", "r-cran-seroincidence", "r-cran-incidence", "r-cran-epiestim", "ushahidi", "r-cran-lexrankr", "r-cran-sf", "r-cran-sjplot", "python3-treetime", "python3-torch", "python3-seirsplus", "chime", "netepi-analysis", "netepi-collection", "epifire"], "ignore": [], "avoid": []}}
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/459e5a4d40345e5e8db161dc28271761588b1ed6...06f895d8725a1edbb52d046b8d46427d4effd58d
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/459e5a4d40345e5e8db161dc28271761588b1ed6...06f895d8725a1edbb52d046b8d46427d4effd58d
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/blends-commit/attachments/20200814/a4ac97d2/attachment-0001.html>
More information about the Blends-commit
mailing list