[Blends-commit] [Git][blends-team/med][master] Update dependency relations
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Feb 8 08:41:51 GMT 2023
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
8452be90 by Andreas Tille at 2023-02-08T09:41:24+01:00
Update dependency relations
- - - - -
1 changed file:
- debian/control
Changes:
=====================================
debian/control
=====================================
@@ -101,6 +101,7 @@ Recommends: abacas,
amap-align,
ampliconnoise,
andi,
+ any2fasta,
aragorn,
arden,
ariba,
@@ -155,6 +156,7 @@ Recommends: abacas,
bppphyview,
bppsuite,
brig,
+ btllib-tools,
busco,
bustools,
bwa,
@@ -182,6 +184,7 @@ Recommends: abacas,
clustalx,
cnvkit,
codonw,
+ comet-ms,
concavity,
conservation-code,
covtobed,
@@ -257,11 +260,13 @@ Recommends: abacas,
genometester,
genomethreader,
genometools,
+ genomicsdb-tools,
gentle,
gff2aplot,
gff2ps,
gffread,
ggd-utils,
+ ghemical,
ghmm,
glam2,
gmap,
@@ -282,6 +287,7 @@ Recommends: abacas,
hyphy-mpi | hyphy-pt,
idba,
igblast,
+ igdiscover,
igor,
igv,
indelible,
@@ -293,6 +299,7 @@ Recommends: abacas,
jaligner,
jalview,
jellyfish,
+ jellyfish1,
jmodeltest,
jmol,
kalign,
@@ -307,6 +314,7 @@ Recommends: abacas,
kmc,
kmer,
kmerresistance,
+ kraken,
kraken2,
lagan,
lamarc,
@@ -336,6 +344,7 @@ Recommends: abacas,
maq,
maqview,
mash,
+ massxpert,
mauve-aligner,
mcaller,
mecat2,
@@ -362,6 +371,7 @@ Recommends: abacas,
mlv-smile,
mmb,
mmseqs2,
+ mosdepth,
mothur,
mptp,
mrbayes,
@@ -369,6 +379,7 @@ Recommends: abacas,
mummer,
murasaki | murasaki-mpi,
muscle,
+ muscle3,
mustang,
nanofilt,
nanolyse,
@@ -416,6 +427,7 @@ Recommends: abacas,
pftools,
phast,
phipack,
+ phybin,
phylip,
phylonium,
phyml,
@@ -424,6 +436,7 @@ Recommends: abacas,
phyx,
picard-tools,
picopore,
+ pigx-rnaseq,
piler,
pilercr,
pilon,
@@ -444,7 +457,6 @@ Recommends: abacas,
populations,
porechop,
poretools,
- pplacer,
prank,
predictnls,
presto,
@@ -482,9 +494,11 @@ Recommends: abacas,
pycoqc,
pycorrfit,
pyensembl,
+ pyfastx,
pymol,
pyscanfcs,
python3-biomaj3-daemon,
+ python3-cogent3,
python3-emperor,
python3-geneimpacts,
python3-gffutils,
@@ -494,6 +508,7 @@ Recommends: abacas,
python3-treetime,
pyvcf,
qcat,
+ qcumber,
qiime,
qtltools,
quicktree,
@@ -501,7 +516,6 @@ Recommends: abacas,
qutemol,
r-bioc-annotate,
r-bioc-biostrings,
- r-bioc-bitseq,
r-bioc-cner,
r-bioc-cummerbund,
r-bioc-deseq2,
@@ -587,10 +601,12 @@ Recommends: abacas,
runcircos-gui,
saint,
salmid,
+ salmon,
sambamba,
samblaster,
samclip,
samtools,
+ savvy-util,
scoary,
scrappie,
scrm,
@@ -598,8 +614,9 @@ Recommends: abacas,
seaview,
seer,
segemehl,
- sepp,
seqan-apps,
+ seqan-needle,
+ seqan-raptor,
seqkit,
seqmagick,
seqprep,
@@ -625,6 +642,7 @@ Recommends: abacas,
snap,
snap-aligner,
sniffles,
+ snippy,
snp-sites,
snpeff,
snpomatic,
@@ -669,9 +687,9 @@ Recommends: abacas,
thesias,
tiddit,
tigr-glimmer,
- tipp,
tm-align,
tnseq-transit,
+ toil,
tombo,
tophat-recondition,
topp,
@@ -691,6 +709,7 @@ Recommends: abacas,
tvc,
twopaco,
uc-echo,
+ umap-learn,
umis,
uncalled,
unicycler,
@@ -792,10 +811,8 @@ Suggests: acacia,
genetrack,
genezilla,
genographer,
- genomicsdb-tools,
gerp++,
getdata,
- ghemical,
glimmerhmm,
gmv,
gramalign,
@@ -807,14 +824,11 @@ Suggests: acacia,
hts-nim-tools,
idefix,
idseq-bench,
- igdiscover,
illustrate,
inspect,
jbrowse,
- jellyfish1,
jigsaw,
kempbasu,
- kraken,
libhdf5-dev,
libhnswlib-dev,
lofreq,
@@ -830,16 +844,17 @@ Suggests: acacia,
meme,
mesquite,
metabit,
+ metaeuk,
metarep,
metastudent-data,
metastudent-data-2,
migrate,
+ minexpert2,
minimus,
mirbase,
modeller,
molekel,
mosaik-aligner,
- mosdepth,
mpsqed,
mrs,
msatfinder,
@@ -871,16 +886,15 @@ Suggests: acacia,
pfaat,
phagefinder,
phpphylotree,
- phybin,
phylographer,
phylophlan,
phyloviz-core,
phylowin,
- pigx-rnaseq,
pigx-scrnaseq,
pipasic,
plato,
pomoxis,
+ pplacer,
profit,
profphd,
prot4est,
@@ -892,7 +906,6 @@ Suggests: acacia,
python3-alignlib,
python3-anndata,
python3-cgecore,
- python3-cogent3,
python3-cyvcf2,
python3-deeptools,
python3-deeptoolsintervals,
@@ -935,7 +948,6 @@ Suggests: acacia,
q2-vsearch,
q2cli,
q2templates,
- qcumber,
qtlcart,
qtlreaper,
qualimap,
@@ -945,6 +957,7 @@ Suggests: acacia,
r-bioc-beachmat,
r-bioc-biocneighbors,
r-bioc-biocsingular,
+ r-bioc-bitseq,
r-bioc-ctc,
r-bioc-dnacopy,
r-bioc-ensembldb,
@@ -998,13 +1011,12 @@ Suggests: acacia,
rose,
rsat,
sailfish,
- salmon,
sap,
science-workflow,
+ sepp,
seq-gen,
seq-seq-pan,
seqcluster,
- sequenceconverter.app,
seqwish,
sift,
signalalign,
@@ -1027,8 +1039,8 @@ Suggests: acacia,
tetra,
tide,
tigr-glimmer-mg,
+ tipp,
tn-seqexplorer,
- toil,
tophat,
treebuilder3d,
trinityrnaseq,
@@ -1038,7 +1050,6 @@ Suggests: acacia,
ufasta,
ugene,
umap,
- umap-learn,
unc-fish,
uniprime,
varmatch,
@@ -1065,6 +1076,7 @@ Recommends: bio-tradis,
bioperl,
bioperl-run,
biosquid,
+ cwltool,
gffread,
goby-java,
libace-perl,
@@ -1082,6 +1094,7 @@ Recommends: bio-tradis,
libbio-db-embl-perl,
libbio-db-hts-perl,
libbio-db-ncbihelper-perl,
+ libbio-db-seqfeature-perl,
libbio-eutilities-perl,
libbio-featureio-perl,
libbio-graphics-perl,
@@ -1098,7 +1111,7 @@ Recommends: bio-tradis,
libbiococoa-dev,
libbiojava-java,
libbiojava4-java,
- libbiojava5-java,
+ libbiojava6-java,
libbioparser-dev,
libblasr-dev,
libbpp-core-dev,
@@ -1138,13 +1151,11 @@ Recommends: bio-tradis,
libkmer-dev,
libmems-dev,
libminimap2-dev,
- libmmblib-dev,
libmuscle-dev,
libncbi-vdb-dev,
libncbi6-dev,
libncl-dev,
libngs-java,
- libngs-sdk-dev,
libnhgri-blastall-perl,
libopenmm-dev,
libopenms-dev,
@@ -1188,10 +1199,15 @@ Recommends: bio-tradis,
libzerg-perl,
libzerg0-dev,
mcl,
+ nim-hts-dev,
+ nim-kexpr-dev,
+ nim-lapper-dev,
ont-fast5-api,
+ pyfai,
python3-airr,
python3-anndata,
python3-bcbio-gff,
+ python3-bioframe,
python3-biom-format,
python3-biomaj3,
python3-biopython,
@@ -1200,6 +1216,8 @@ Recommends: bio-tradis,
python3-cgecore,
python3-cigar,
python3-cobra,
+ python3-cogent3,
+ python3-cooler,
python3-corepywrap,
python3-csb,
python3-cutadapt,
@@ -1217,10 +1235,12 @@ Recommends: bio-tradis,
python3-htseq,
python3-intervaltree-bio,
python3-kineticstools,
+ python3-loompy,
python3-mirtop,
python3-nanoget,
python3-ngs,
python3-pairix,
+ python3-pangolearn,
python3-parasail,
python3-pbcommand,
python3-pbconsensuscore,
@@ -1235,6 +1255,7 @@ Recommends: bio-tradis,
python3-pybel,
python3-pybigwig,
python3-pyfaidx,
+ python3-pyfastx,
python3-pymummer,
python3-pyranges,
python3-pysam,
@@ -1247,7 +1268,6 @@ Recommends: bio-tradis,
python3-skbio,
python3-slow5,
python3-sqt,
- python3-streamz,
python3-tinyalign,
python3-torch,
python3-treetime,
@@ -1281,19 +1301,21 @@ Recommends: bio-tradis,
r-cran-webgestaltr,
ruby-bio,
ruby-crb-blast,
- sbmltoolbox
+ sbmltoolbox,
+ snakemake,
+ toil
Suggests: bioclipse,
capsule-nextflow,
conda-package-handling,
ctdconverter,
cthreadpool-dev,
cwlformat,
- cwltool,
libargs-dev,
libatomicqueue-dev,
libbam-dev,
libbbhash-dev,
libbiosoup-dev,
+ libbtllib-dev,
libcapsule-maven-nextflow-java,
libconcurrentqueue-dev,
libdisorder-dev,
@@ -1306,20 +1328,24 @@ Suggests: bioclipse,
libgatk-bwamem-jni,
libgatk-fermilite-java,
libgatk-fermilite-jni,
+ libgatk-native-bindings-java,
libgenomicsdb-dev,
libgenomicsdb-java,
libicb-utils-java,
libmaus2-dev,
libmilib-java,
libminimap-dev,
+ libmmblib-dev,
libmodhmm-dev,
libnexml-java,
+ libngs-sdk-dev,
libpbcopper-dev,
libqcpp-dev,
librelion-dev,
libroadrunner-dev,
librostlab-blast-doc,
librostlab-doc,
+ libsavvy-dev,
libsuma-dev,
libsvmloc-dev,
libswarm2-dev,
@@ -1327,35 +1353,30 @@ Suggests: bioclipse,
libtfbs-perl,
libvbz-hdf-plugin-dev,
libxxsds-dynamic-dev,
- nim-hts-dev,
- nim-kexpr-dev,
- nim-lapper-dev,
octace-bioinfo,
- pyfai,
python-biopython-doc,
python3-alignlib,
python3-bcbio,
python3-bel-resources,
python3-bioblend,
python3-biopython-sql,
- python3-cogent3,
+ python3-cgelib,
python3-compclust,
+ python3-conda-package-streaming,
python3-consensuscore2,
- python3-cooler,
python3-ctdopts,
python3-galaxy-lib,
python3-intake,
python3-joypy,
- python3-loompy,
python3-misopy,
python3-ncls,
python3-networkx,
- python3-pangolearn,
python3-pycosat,
python3-pyflow,
python3-roadrunner,
python3-scanpy,
python3-seqcluster,
+ python3-streamz,
q2-alignment,
q2-composition,
q2-cutadapt,
@@ -1489,8 +1510,6 @@ Suggests: bioclipse,
r-cran-venndiagram,
r-other-apmswapp,
ruby-rgfa,
- snakemake,
- toil,
vdjtools
Description: Debian Med packages for development of bioinformatics applications
This metapackage will install Debian packages which might be helpful
@@ -1582,6 +1601,7 @@ Recommends: abyss,
mrbayes,
mummer,
muscle,
+ muscle3,
mustang,
ncbi-epcr,
ncbi-tools-bin,
@@ -1607,6 +1627,7 @@ Recommends: abyss,
prodigal,
python3-biomaj3-cli,
python3-biopython,
+ python3-cogent3,
qiime,
r-bioc-edger,
r-bioc-hilbertvis,
@@ -1645,8 +1666,7 @@ Suggests: anfo,
cufflinks,
embassy-phylip,
flexbar,
- giira,
- python3-cogent3
+ 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
@@ -1764,7 +1784,6 @@ Recommends: aeskulap,
bart,
bart-view,
biosig-tools,
- camitk-imp,
ctn,
ctsim,
dcm2niix,
@@ -1774,7 +1793,9 @@ Recommends: aeskulap,
dicomscope,
gdf-tools,
gwyddion,
+ heudiconv,
imagej,
+ invesalius,
ismrmrd-tools,
king,
libgdcm-tools,
@@ -1797,6 +1818,7 @@ Recommends: aeskulap,
python3-dipy,
python3-nibabel,
python3-nipy,
+ python3-nipype,
python3-nitime,
python3-pydicom,
python3-pyxid,
@@ -1814,6 +1836,7 @@ Suggests: afni,
bioimagexd,
blox,
brainvisa,
+ camitk-imp,
caret,
cdmedicpacs,
cellprofiler,
@@ -1841,7 +1864,6 @@ Suggests: afni,
fslview,
gimias,
ginkgocadx,
- heudiconv,
hid,
illustrate,
imagemagick,
@@ -1849,7 +1871,6 @@ Suggests: afni,
imview,
incf-nidash-oneclick-clients,
insightapplications,
- invesalius,
isis,
itksnap,
jemris,
@@ -1869,7 +1890,6 @@ Suggests: afni,
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
- nifti2dicom,
omero,
opendicom.net,
openelectrophy,
@@ -1887,8 +1907,6 @@ Suggests: afni,
piano,
pngquant,
pymeg,
- python3-nipype,
- qnifti2dicom,
science-workflow,
slicer,
sofa-apps,
@@ -1924,7 +1942,6 @@ Recommends: cimg-dev,
gmic,
libbart-dev,
libbiosig-dev,
- libcamitk-dev,
libcifti-dev,
libedf-dev,
libgdf-dev,
@@ -1956,6 +1973,7 @@ Recommends: cimg-dev,
octave-gdf,
odin,
python3-biosig,
+ python3-bioxtasraw,
python3-brian,
python3-dcmstack,
python3-dipy,
@@ -1965,15 +1983,16 @@ Recommends: cimg-dev,
python3-mne,
python3-nibabel,
python3-nipy,
+ python3-nipype,
python3-nitime,
python3-openslide,
python3-pydicom,
python3-pyxnat,
- python3-torchvision,
python3-vigra,
r-cran-rniftilib
Suggests: emokit,
libbio-formats-java,
+ libcamitk-dev,
libcamp-dev,
libctk-dev,
libeegdev-dev,
@@ -1985,13 +2004,11 @@ Suggests: emokit,
libnifti-doc,
libopenmeeg-dev,
libopenslide-java,
- libsimpleitk1-dev,
libvia-dev,
libvmtk-dev,
libxdffileio-dev,
python-vmtk,
- python3-nipype,
- python3-simpleitk,
+ python3-torchvision,
tifffile
Description: Debian Med image processing and visualization packages development
This metapackage will install Debian packages which might be useful
@@ -2118,6 +2135,7 @@ Depends: ${misc:Depends},
Recommends: orthanc-neuro,
praat,
psignifit,
+ python3-bioxtasraw,
r-cran-foreign,
r-cran-psy,
r-cran-psych,
@@ -2176,6 +2194,7 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: cronometer,
+ cycle,
edfbrowser,
galileo,
hunspell-de-med,
@@ -2188,8 +2207,7 @@ Recommends: cronometer,
r-cran-fitcoach,
wgerman-medical,
workrave
-Suggests: cycle,
- entangle,
+Suggests: entangle,
goldencheetah,
mencal,
mssstest,
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/8452be90140637c279c7b7d54b690e9efd33d032
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View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/8452be90140637c279c7b7d54b690e9efd33d032
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