[Blends-commit] [Git][blends-team/med][master] 2 commits: Standards-Version: 4.6.1; update dependencies
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Oct 14 09:18:23 BST 2022
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
16ee80e0 by Andreas Tille at 2022-10-14T10:16:42+02:00
Standards-Version: 4.6.1; update dependencies
- - - - -
9e8c07b7 by Andreas Tille at 2022-10-14T10:17:55+02:00
Cycle got a new maintainer and was uploaded to new
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/control.stub
- tasks/tools
Changes:
=====================================
debian/changelog
=====================================
@@ -4,6 +4,7 @@ debian-med (3.7.3) UNRELEASED; urgency=medium
Closes: #1012341
* dicompyler removed from Debian thus from oncology task
* zalign removed from Debian
+ * Standards-Version: 4.6.1
-- Andreas Tille <tille at debian.org> Fri, 03 Jun 2022 12:06:56 +0200
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Section: misc
Priority: optional
Build-Depends-Indep: blends-dev (>= 0.7.5~),
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
@@ -88,6 +88,7 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: abacas,
+ abpoa,
abyss,
acedb-other,
adapterremoval,
@@ -100,7 +101,6 @@ Recommends: abacas,
amap-align,
ampliconnoise,
andi,
- anfo,
aragorn,
arden,
ariba,
@@ -204,6 +204,7 @@ Recommends: abacas,
discosnp,
disulfinder,
dnaclust,
+ dnarrange,
dotter,
drop-seq-tools,
dssp,
@@ -230,6 +231,7 @@ Recommends: abacas,
fastlink,
fastml,
fastp,
+ fastq-pair,
fastqc,
fastqtl,
fasttree,
@@ -238,7 +240,6 @@ Recommends: abacas,
filtlong,
fitgcp,
flash,
- flexbar,
flye,
fml-asm,
freebayes,
@@ -280,7 +281,7 @@ Recommends: abacas,
hmmer2,
hyphy-mpi | hyphy-pt,
idba,
- igdiscover,
+ igblast,
igor,
igv,
indelible,
@@ -292,12 +293,12 @@ Recommends: abacas,
jaligner,
jalview,
jellyfish,
- jellyfish1,
jmodeltest,
jmol,
kalign,
kallisto,
kaptive,
+ khmer,
kineticstools,
king-probe,
kissplice,
@@ -306,10 +307,10 @@ Recommends: abacas,
kmc,
kmer,
kmerresistance,
- kraken,
kraken2,
lagan,
lamarc,
+ lamassemble,
lambda-align,
lambda-align2,
last-align,
@@ -344,7 +345,7 @@ Recommends: abacas,
melting,
meryl,
metabat,
- metaphlan2,
+ metaphlan,
metastudent,
mhap,
microbegps,
@@ -361,11 +362,9 @@ Recommends: abacas,
mlv-smile,
mmb,
mmseqs2,
- mosdepth,
mothur,
mptp,
mrbayes,
- msxpertsuite,
multiqc,
mummer,
murasaki | murasaki-mpi,
@@ -394,6 +393,7 @@ Recommends: abacas,
norsnet,
norsp,
ntcard,
+ nxtrim,
obitools,
openms,
optimir,
@@ -416,7 +416,6 @@ Recommends: abacas,
pftools,
phast,
phipack,
- phybin,
phylip,
phylonium,
phyml,
@@ -479,8 +478,10 @@ Recommends: abacas,
pscan-chip,
pscan-tfbs,
psortb,
+ pullseq,
pycoqc,
pycorrfit,
+ pyensembl,
pymol,
pyscanfcs,
python3-biomaj3-daemon,
@@ -493,7 +494,6 @@ Recommends: abacas,
python3-treetime,
pyvcf,
qcat,
- qcumber,
qiime,
qtltools,
quicktree,
@@ -513,6 +513,7 @@ Recommends: abacas,
r-bioc-htsfilter,
r-bioc-impute,
r-bioc-limma,
+ r-bioc-megadepth,
r-bioc-mergeomics,
r-bioc-metagenomeseq,
r-bioc-mofa,
@@ -615,6 +616,7 @@ Recommends: abacas,
sim4db,
simka,
simkamin,
+ ska,
skesa,
skewer,
smalt,
@@ -654,6 +656,7 @@ Recommends: abacas,
sumatra,
sumtrees,
surankco,
+ surpyvor,
survivor,
svim,
swarm,
@@ -661,6 +664,7 @@ Recommends: abacas,
t-coffee,
tabix,
tantan,
+ terraphast,
theseus,
thesias,
tiddit,
@@ -668,7 +672,6 @@ Recommends: abacas,
tipp,
tm-align,
tnseq-transit,
- toil,
tombo,
tophat-recondition,
topp,
@@ -686,16 +689,17 @@ Recommends: abacas,
trim-galore,
trimmomatic,
tvc,
+ twopaco,
uc-echo,
umis,
uncalled,
unicycler,
+ unikmer,
varna,
vcfanno,
vcftools,
velvet | velvet-long,
velvetoptimiser,
- vg,
virulencefinder,
vmatch,
vsearch,
@@ -703,15 +707,16 @@ Recommends: abacas,
wham-align,
wigeon,
wise,
+ xpore,
yaha,
yanagiba,
- yanosim,
- zalign
+ yanosim
Suggests: acacia,
adun.app,
agat,
amos-assembler,
amoscmp,
+ anfo,
annovar,
apollo,
arachne,
@@ -759,7 +764,6 @@ Suggests: acacia,
dendroscope,
diann,
dnapi,
- dnarrange,
e-hive,
ecell,
embassy-phylip,
@@ -773,11 +777,11 @@ Suggests: acacia,
exabayes,
exalt,
excavator,
- falcon,
ffp,
fieldbioinformatics,
figaro,
flappie,
+ flexbar,
forester,
forge,
galaxy,
@@ -788,6 +792,7 @@ Suggests: acacia,
genetrack,
genezilla,
genographer,
+ genomicsdb-tools,
gerp++,
getdata,
ghemical,
@@ -802,14 +807,14 @@ Suggests: acacia,
hts-nim-tools,
idefix,
idseq-bench,
- igblast,
+ igdiscover,
illustrate,
inspect,
jbrowse,
+ jellyfish1,
jigsaw,
kempbasu,
- khmer,
- lamassemble,
+ kraken,
libhdf5-dev,
libhnswlib-dev,
lofreq,
@@ -834,9 +839,11 @@ Suggests: acacia,
modeller,
molekel,
mosaik-aligner,
+ mosdepth,
mpsqed,
mrs,
msatfinder,
+ msxpertsuite,
mugsy,
mummergpu,
mview,
@@ -865,6 +872,7 @@ Suggests: acacia,
pfaat,
phagefinder,
phpphylotree,
+ phybin,
phylographer,
phylophlan,
phyloviz-core,
@@ -928,6 +936,7 @@ Suggests: acacia,
q2-vsearch,
q2cli,
q2templates,
+ qcumber,
qtlcart,
qtlreaper,
qualimap,
@@ -949,7 +958,6 @@ Suggests: acacia,
r-bioc-grohmm,
r-bioc-gviz,
r-bioc-isoformswitchanalyzer,
- r-bioc-megadepth,
r-bioc-mofa2,
r-bioc-org.hs.eg.db,
r-bioc-org.mm.eg.db,
@@ -1021,13 +1029,13 @@ Suggests: acacia,
tide,
tigr-glimmer-mg,
tn-seqexplorer,
+ toil,
tophat,
treebuilder3d,
trinityrnaseq,
tripal,
trnascan-se,
twain,
- twopaco,
ufasta,
ugene,
umap,
@@ -1037,6 +1045,7 @@ Suggests: acacia,
varmatch,
varscan,
vdjtools,
+ vg,
vienna-rna,
viewmol,
vmd,
@@ -1057,7 +1066,6 @@ Recommends: bio-tradis,
bioperl,
bioperl-run,
biosquid,
- cwltool,
gffread,
goby-java,
libace-perl,
@@ -1091,6 +1099,7 @@ Recommends: bio-tradis,
libbiococoa-dev,
libbiojava-java,
libbiojava4-java,
+ libbiojava5-java,
libbioparser-dev,
libblasr-dev,
libbpp-core-dev,
@@ -1158,7 +1167,9 @@ Recommends: bio-tradis,
librostlab3-dev,
libsbml5-dev,
libseqan2-dev,
+ libseqan3-dev,
libseqlib-dev,
+ libslow5-dev,
libsmithwaterman-dev,
libsnp-sites1-dev,
libsort-key-top-perl,
@@ -1178,10 +1189,7 @@ Recommends: bio-tradis,
libzerg-perl,
libzerg0-dev,
mcl,
- nim-hts-dev,
- nim-kexpr-dev,
- nim-lapper-dev,
- pyfai,
+ ont-fast5-api,
python3-airr,
python3-anndata,
python3-bcbio-gff,
@@ -1206,6 +1214,7 @@ Recommends: bio-tradis,
python3-freecontact,
python3-gfapy,
python3-gffutils,
+ python3-gtfparse,
python3-htseq,
python3-intervaltree-bio,
python3-kineticstools,
@@ -1219,7 +1228,9 @@ Recommends: bio-tradis,
python3-pbcore,
python3-peptidebuilder,
python3-presto,
+ python3-propka,
python3-py2bit,
+ python3-pyabpoa,
python3-pyani,
python3-pybedtools,
python3-pybel,
@@ -1228,14 +1239,18 @@ Recommends: bio-tradis,
python3-pymummer,
python3-pyranges,
python3-pysam,
+ python3-pyspoa,
python3-pyvcf,
python3-rdkit,
python3-ruffus,
python3-screed,
python3-shasta,
python3-skbio,
+ python3-slow5,
python3-sqt,
+ python3-streamz,
python3-tinyalign,
+ python3-torch,
python3-treetime,
python3-unifrac,
python3-wdlparse,
@@ -1267,18 +1282,20 @@ Recommends: bio-tradis,
r-cran-webgestaltr,
ruby-bio,
ruby-crb-blast,
- sbmltoolbox,
- snakemake,
- toil
+ sbmltoolbox
Suggests: bioclipse,
+ capsule-nextflow,
conda-package-handling,
ctdconverter,
cthreadpool-dev,
cwlformat,
+ cwltool,
libargs-dev,
libatomicqueue-dev,
libbam-dev,
libbbhash-dev,
+ libbiosoup-dev,
+ libcapsule-maven-nextflow-java,
libconcurrentqueue-dev,
libdisorder-dev,
libfast-perl,
@@ -1286,6 +1303,13 @@ Suggests: bioclipse,
libfreecontact-dev,
libfreecontact-doc,
libfreecontact-perl,
+ libgatk-bwamem-java,
+ libgatk-bwamem-jni,
+ libgatk-fermilite-java,
+ libgatk-fermilite-jni,
+ libgenomicsdb-dev,
+ libgenomicsdb-java,
+ libicb-utils-java,
libmaus2-dev,
libmilib-java,
libminimap-dev,
@@ -1297,17 +1321,23 @@ Suggests: bioclipse,
libroadrunner-dev,
librostlab-blast-doc,
librostlab-doc,
- libseqan3-dev,
libsuma-dev,
libsvmloc-dev,
libswarm2-dev,
+ libterraces-dev,
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-compclust,
@@ -1327,8 +1357,6 @@ Suggests: bioclipse,
python3-roadrunner,
python3-scanpy,
python3-seqcluster,
- python3-streamz,
- python3-torch,
q2-alignment,
q2-composition,
q2-cutadapt,
@@ -1462,6 +1490,8 @@ 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
@@ -1480,7 +1510,6 @@ Recommends: abyss,
altree,
amap-align,
ampliconnoise,
- anfo,
aragorn,
arden,
autodock,
@@ -1522,7 +1551,6 @@ Recommends: abyss,
fastqc,
fasttree,
fitgcp,
- flexbar,
freecontact,
gasic,
genometools,
@@ -1611,12 +1639,13 @@ Recommends: abyss,
tree-puzzle | tree-ppuzzle,
vcftools,
velvet,
- wise,
- zalign
-Suggests: bagpipe,
+ wise
+Suggests: anfo,
+ bagpipe,
blast2,
cufflinks,
embassy-phylip,
+ flexbar,
giira,
python3-cogent3
Description: Debian Med bioinformatics applications usable in cloud computing
@@ -1661,6 +1690,7 @@ Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
Recommends: python3-seirsplus,
+ python3-torch,
python3-treetime,
r-cran-covid19us,
r-cran-diagnosismed,
@@ -1684,7 +1714,6 @@ Suggests: chime,
netepi-analysis,
netepi-collection,
python3-epimodels,
- python3-torch,
r-cran-cmprsk,
r-cran-covid19,
r-cran-msm,
@@ -1759,7 +1788,6 @@ Recommends: aeskulap,
mricron,
mrtrix3,
nifti-bin,
- nifti2dicom,
odil,
odin,
openslide-tools,
@@ -1770,12 +1798,10 @@ Recommends: aeskulap,
python3-dipy,
python3-nibabel,
python3-nipy,
- python3-nipype,
python3-nitime,
python3-pydicom,
python3-pyxid,
python3-surfer,
- qnifti2dicom,
sigviewer,
teem-apps,
tifffile,
@@ -1816,6 +1842,7 @@ Suggests: afni,
fslview,
gimias,
ginkgocadx,
+ heudiconv,
hid,
illustrate,
imagemagick,
@@ -1843,6 +1870,7 @@ Suggests: afni,
mni-icbm152-nlin-2009,
mni-n3,
mrisim,
+ nifti2dicom,
omero,
opendicom.net,
openelectrophy,
@@ -1853,12 +1881,15 @@ Suggests: afni,
orthanc-gdcm,
orthanc-imagej,
orthanc-mysql,
+ orthanc-neuro,
orthanc-postgresql,
orthanc-webviewer,
paraview,
piano,
pngquant,
pymeg,
+ python3-nipype,
+ qnifti2dicom,
science-workflow,
slicer,
sofa-apps,
@@ -1927,6 +1958,7 @@ Recommends: cimg-dev,
odin,
python3-biosig,
python3-brian,
+ python3-dcmstack,
python3-dipy,
python3-gdcm,
python3-imageio,
@@ -1934,11 +1966,11 @@ 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,
@@ -1957,11 +1989,10 @@ Suggests: emokit,
libsimpleitk1-dev,
libvia-dev,
libvmtk-dev,
- libvtk7-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
@@ -1991,8 +2022,7 @@ Depends: ${misc:Depends},
med-tasks (= ${source:Version})
Recommends: orthanc-wsi,
simrisc
-Suggests: dicompyler,
- planunc,
+Suggests: planunc,
python3-dicompylercore,
uw-prism
Description: Debian Med packages for oncology
@@ -2086,16 +2116,17 @@ Architecture: all
Depends: ${misc:Depends},
med-config (= ${source:Version}),
med-tasks (= ${source:Version})
-Recommends: praat,
+Recommends: orthanc-neuro,
+ praat,
psignifit,
- psychopy,
r-cran-foreign,
r-cran-psy,
r-cran-psych,
r-cran-psychometric,
r-cran-psychotree,
r-cran-psyphy
-Suggests: python-pyepl,
+Suggests: psychopy,
+ python-pyepl,
python3-bids-validator,
python3-bmtk,
science-psychophysics
=====================================
debian/control.stub
=====================================
@@ -5,7 +5,7 @@ Section: misc
Priority: optional
Build-Depends-Indep: blends-dev (>= 0.7.5~),
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/blends-team/med
Vcs-Git: https://salsa.debian.org/blends-team/med.git
=====================================
tasks/tools
=====================================
@@ -5,10 +5,7 @@ Description: Debian Med several tools
Recommends: pcalendar
-Suggests: cycle
-Remark: Use pcalendar instead
- Please consider using pcalendar instead of cycle because cycle is outdated,
- not maintained any more and pcalendar simply overpasses it.
+Recommends: cycle
Suggests: mencal
Remark: Use pcalendar instead
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/57c82abd412b6e7c7894912a0465f10e55419b58...9e8c07b7091398d27c806b5ba58a43105c35b8f3
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/57c82abd412b6e7c7894912a0465f10e55419b58...9e8c07b7091398d27c806b5ba58a43105c35b8f3
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