[med-svn] [Git][med-team/multiqc][master] 4 commits: wrap-and-sort -ast
Alexandre Detiste (@detiste-guest)
gitlab at salsa.debian.org
Sun Nov 16 11:27:41 GMT 2025
Alexandre Detiste pushed to branch master at Debian Med / multiqc
Commits:
3e145c8e by Alexandre Detiste at 2025-11-16T12:25:02+01:00
wrap-and-sort -ast
- - - - -
64d7a83b by Alexandre Detiste at 2025-11-16T12:25:45+01:00
rewrite d/rules in short syntax
- - - - -
438a05e8 by Alexandre Detiste at 2025-11-16T12:26:14+01:00
bump Standards-Version to 4.7.2
- - - - -
8dba3711 by Alexandre Detiste at 2025-11-16T12:26:36+01:00
drop "Rules-Requires-Root: no": it is the default now
- - - - -
4 changed files:
- debian/control
- debian/multiqc.links
- debian/rules
- debian/tests/control
Changes:
=====================================
debian/control
=====================================
@@ -1,151 +1,155 @@
Source: multiqc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Steffen Moeller <moeller at debian.org>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
+ Steffen Moeller <moeller at debian.org>,
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 13),
- python3-all,
- dh-sequence-python3,
- python3-setuptools,
- python3-click,
- python3-lzstring,
- python3-jinja2,
- python3-matplotlib,
- python3-markdown,
- python3-numpy,
- python3-yaml,
- python3-requests,
- python3-spectra,
- python3-coloredlogs <!nocheck>,
- python3-humanfriendly <!nocheck>,
- python3-humanize <!nocheck>,
- python3-importlib-metadata <!nocheck>,
- python3-plotly <!nocheck>,
- python3-pyaml-env <!nocheck>,
- python3-rich <!nocheck>,
- python3-rich-click <!nocheck>
-Standards-Version: 4.6.2
+Build-Depends:
+ debhelper-compat (= 13),
+ dh-sequence-python3,
+ python3-all,
+ python3-click,
+ python3-coloredlogs <!nocheck>,
+ python3-humanfriendly <!nocheck>,
+ python3-humanize <!nocheck>,
+ python3-importlib-metadata <!nocheck>,
+ python3-jinja2,
+ python3-lzstring,
+ python3-markdown,
+ python3-matplotlib,
+ python3-numpy,
+ python3-plotly <!nocheck>,
+ python3-pyaml-env <!nocheck>,
+ python3-requests,
+ python3-rich <!nocheck>,
+ python3-rich-click <!nocheck>,
+ python3-setuptools,
+ python3-spectra,
+ python3-yaml,
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/multiqc
Vcs-Git: https://salsa.debian.org/med-team/multiqc.git
Homepage: https://multiqc.info/
-Rules-Requires-Root: no
Package: multiqc
Architecture: all
-Depends: ${python3:Depends},
- ${misc:Depends},
- python3-click,
- python3-lzstring,
- python3-jinja2,
- python3-matplotlib,
- python3-markdown,
- python3-numpy,
- python3-yaml,
- python3-requests,
- python3-spectra,
- python3-coloredlogs,
- python3-humanfriendly,
- python3-rich,
- fonts-glyphicons-halflings,
- libjs-bootstrap,
- libjs-jquery,
- libjs-jquery-tablesorter,
- libjs-jquery-ui
-Recommends: node-clipboard,
- libjs-filesaver,
- pandoc,
- texlive-xetex
-Enhances: adapterremoval,
- afterqc,
- bamtools,
- bbmap,
- bcftools,
- bcl2fastq,
- biobambam2,
- biobloomtools,
- biscuit,
- bismark,
- bowtie,
- bowtie2,
- busco,
- clipandmerge,
- clusterflow,
- conpair,
- cutadapt,
- damageprofiler,
- dedup,
- deeptools,
- disambiguate,
- dragen,
- fastp,
- fastq-screen,
- fastqc,
- featurecounts,
- fgbio,
- flash,
- flexbar,
- gatk,
- goleft-indexcov,
- happy,
- hicexplorer,
- hicpro,
- hicup,
- hisat2,
- homer,
- htseq,
- interop,
- ivar,
- jellyfish,
- kaiju,
- kallisto,
- kat,
- kraken,
- leehom,
- longranger,
- macs2,
- malt,
- methylqa,
- minionqc,
- mirtop,
- mirtrace,
- mosdepth,
- mtnucratio,
- multivcfanalyzer,
- peddy,
- phantompeakqualtools,
- picard-tools,
- preseq,
- prokka,
- pycoqc,
- qorts,
- qualimap,
- quast,
- rna-seqc,
- rockhopper,
- rsem,
- rseqc,
- salmon,
- samblaster,
- samtools,
- sargasso,
- seqyclean,
- sexdeterrmine,
- sickle,
- skewer,
- slamdunk,
- snpeff,
- snpsplit,
- somalier,
- sortmerna,
- stacks,
- rna-star,
- supernova,
- theta2,
- trimmomatic,
- varscan2,
- vcftools,
- verifybamid
+Depends:
+ fonts-glyphicons-halflings,
+ libjs-bootstrap,
+ libjs-jquery,
+ libjs-jquery-tablesorter,
+ libjs-jquery-ui,
+ python3-click,
+ python3-coloredlogs,
+ python3-humanfriendly,
+ python3-jinja2,
+ python3-lzstring,
+ python3-markdown,
+ python3-matplotlib,
+ python3-numpy,
+ python3-requests,
+ python3-rich,
+ python3-spectra,
+ python3-yaml,
+ ${misc:Depends},
+ ${python3:Depends},
+Recommends:
+ libjs-filesaver,
+ node-clipboard,
+ pandoc,
+ texlive-xetex,
+Enhances:
+ adapterremoval,
+ afterqc,
+ bamtools,
+ bbmap,
+ bcftools,
+ bcl2fastq,
+ biobambam2,
+ biobloomtools,
+ biscuit,
+ bismark,
+ bowtie,
+ bowtie2,
+ busco,
+ clipandmerge,
+ clusterflow,
+ conpair,
+ cutadapt,
+ damageprofiler,
+ dedup,
+ deeptools,
+ disambiguate,
+ dragen,
+ fastp,
+ fastq-screen,
+ fastqc,
+ featurecounts,
+ fgbio,
+ flash,
+ flexbar,
+ gatk,
+ goleft-indexcov,
+ happy,
+ hicexplorer,
+ hicpro,
+ hicup,
+ hisat2,
+ homer,
+ htseq,
+ interop,
+ ivar,
+ jellyfish,
+ kaiju,
+ kallisto,
+ kat,
+ kraken,
+ leehom,
+ longranger,
+ macs2,
+ malt,
+ methylqa,
+ minionqc,
+ mirtop,
+ mirtrace,
+ mosdepth,
+ mtnucratio,
+ multivcfanalyzer,
+ peddy,
+ phantompeakqualtools,
+ picard-tools,
+ preseq,
+ prokka,
+ pycoqc,
+ qorts,
+ qualimap,
+ quast,
+ rna-seqc,
+ rna-star,
+ rockhopper,
+ rsem,
+ rseqc,
+ salmon,
+ samblaster,
+ samtools,
+ sargasso,
+ seqyclean,
+ sexdeterrmine,
+ sickle,
+ skewer,
+ slamdunk,
+ snpeff,
+ snpsplit,
+ somalier,
+ sortmerna,
+ stacks,
+ supernova,
+ theta2,
+ trimmomatic,
+ varscan2,
+ vcftools,
+ verifybamid,
Description: output integration for RNA sequencing across tools and samples
The sequencing of DNA or RNA with current high-throughput technologies
involves an array of tools and these are applied over a range of samples.
=====================================
debian/multiqc.links
=====================================
@@ -1,19 +1,15 @@
+/usr/share/javascript/bootstrap/css/bootstrap.min.css usr/lib/python3/dist-packages/multiqc/templates/default/assets/css/bootstrap.min.css
+# bootstrap
+/usr/share/javascript/bootstrap/js/bootstrap.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/bootstrap.min.js
# Fonts from the fonts-glyphicons-halflings package
usr/share/fonts-glyphicons/glyphicons-halflings-regular.eot usr/lib/python3/dist-packages/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.eot
usr/share/fonts-glyphicons/glyphicons-halflings-regular.svg usr/lib/python3/dist-packages/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.svg
usr/share/fonts-glyphicons/glyphicons-halflings-regular.ttf usr/lib/python3/dist-packages/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.ttf
usr/share/fonts-glyphicons/glyphicons-halflings-regular.woff usr/lib/python3/dist-packages/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.woff
usr/share/fonts-glyphicons/glyphicons-halflings-regular.woff2 usr/lib/python3/dist-packages/multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.woff2
-
-# JS from the libjs-jquery package
-usr/share/javascript/jquery/jquery.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
-
-# JS from the libjs-jquery-ui package
-usr/share/javascript/jquery-ui/jquery-ui.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery-ui.min.js
-
# JS from the libjs-jquery-tablesorter package
usr/share/javascript/jquery-tablesorter/jquery.tablesorter.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
-
-# bootstrap
-/usr/share/javascript/bootstrap/js/bootstrap.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/bootstrap.min.js
-/usr/share/javascript/bootstrap/css/bootstrap.min.css usr/lib/python3/dist-packages/multiqc/templates/default/assets/css/bootstrap.min.css
+# JS from the libjs-jquery-ui package
+usr/share/javascript/jquery-ui/jquery-ui.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery-ui.min.js
+# JS from the libjs-jquery package
+usr/share/javascript/jquery/jquery.min.js usr/lib/python3/dist-packages/multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
=====================================
debian/rules
=====================================
@@ -14,17 +14,14 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) dh_auto_test
endif
-override_dh_auto_clean:
- dh_auto_clean
+execute_after_dh_auto_clean:
rm -rf multiqc.egg-info/
-override_dh_install:
- dh_install
+execute_after_dh_install:
mkdir -p debian/$(PYBUILD_NAME)/usr/lib/python3/dist-packages/multiqc/templates/default/assets/css/
cp -a debian/missing-sources/jquery-toast-plugin/jquery.toast.min.css debian/$(PYBUILD_NAME)/usr/lib/python3/dist-packages/multiqc/templates/default/assets/css/jquery.toast.css
-override_dh_installdocs:
- dh_installdocs
+execute_after_dh_installdocs:
for html in `find debian -name "*.html"` ; do \
sed -i \
-e 's#https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/[^/]*/clipboard.min.js#file:///usr/share/javascript/clipboard.js#g' \
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,6 @@
-Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr
+Tests:
+ run-unit-test,
+Depends:
+ @,
+Restrictions:
+ allow-stderr,
View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/compare/7ce1b73d76c5d8631cdbdfb8e5899724e8e59345...8dba3711703487b1f393b73a3e02633e8186883d
--
View it on GitLab: https://salsa.debian.org/med-team/multiqc/-/compare/7ce1b73d76c5d8631cdbdfb8e5899724e8e59345...8dba3711703487b1f393b73a3e02633e8186883d
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