Andreas Tille pushed to branch master at Debian Med / metabit
Commits: ab3427bf by Andreas Tille at 2019-09-11T08:39:21Z Use git mode in watch file - - - - - 237d1f95 by Andreas Tille at 2019-09-11T08:40:52Z Drop get-orig-source, use +dfsg suffix - - - - - fa3649ec by Andreas Tille at 2019-09-11T08:41:48Z Use markdown instead of python-markdown - - - - - 77692713 by Andreas Tille at 2019-09-11T08:43:49Z New upstream version 0.0+git20170725.24cb3ee+dfsg - - - - - a60267e0 by Andreas Tille at 2019-09-11T08:43:49Z New upstream version - - - - - fe61fbb3 by Andreas Tille at 2019-09-11T08:43:59Z Update upstream source from tag 'upstream/0.0+git20170725.24cb3ee+dfsg' Update to upstream version '0.0+git20170725.24cb3ee+dfsg' with Debian dir c7f197377f3a030faebc8c3f845d2bacd442866c - - - - - dedf2433 by Andreas Tille at 2019-09-11T08:44:00Z debhelper-compat 12 - - - - - 34881017 by Andreas Tille at 2019-09-11T08:44:19Z Point Vcs fields to salsa.debian.org - - - - - d3d983c6 by Andreas Tille at 2019-09-11T08:44:19Z Standards-Version: 4.4.0 - - - - - 0679ad05 by Andreas Tille at 2019-09-11T08:44:20Z Secure URI in copyright format - - - - - 40ab580d by Andreas Tille at 2019-09-11T08:44:47Z Do not parse d/changelog - - - - - 6b545856 by Andreas Tille at 2019-09-11T08:46:25Z Upload to unstable - - - - - d0e6a060 by Andreas Tille at 2019-09-11T08:48:29Z Cleanup changelog from automatic changes - - - - - 9 changed files: - + .gitignore - debian/changelog - − debian/compat - debian/control - debian/copyright - − debian/get-orig-source - debian/rules - debian/watch - metaBIT.py Changes: ===================================== .gitignore ===================================== @@ -0,0 +1 @@ +*.pyc ===================================== debian/changelog ===================================== @@ -1,5 +1,5 @@ -metabit (0.0+20170220-1) UNRELEASED; urgency=medium +metabit (0.0+git20170725.24cb3ee+dfsg-1) UNRELEASED; urgency=medium * Initial release (Closes: #<bug>) - -- Andreas Tille <[email protected]> Mon, 25 Jul 2016 14:09:29 +0200 + -- Andreas Tille <[email protected]> Wed, 11 Sep 2019 10:44:49 +0200 ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -9 ===================================== debian/control ===================================== @@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 9), +Build-Depends: debhelper-compat (= 12), python-all, dh-python, - python-markdown, + markdown, bowtie2 -Standards-Version: 3.9.8 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/metabit.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/metabit.git +Standards-Version: 4.4.0 +Vcs-Browser: https://salsa.debian.org/med-team/metabit +Vcs-Git: https://salsa.debian.org/med-team/metabit.git Homepage: https://bitbucket.org/Glouvel/metabit/wiki/ Package: metabit @@ -21,7 +21,7 @@ Depends: ${python:Depends}, r-base-core, metaphlan2, python-pysam, - libpicard-java (>= 1.138+dfsg.1), + libpicard-java, samtools, radiant, bedtools, @@ -43,7 +43,7 @@ Description: analysing microbial profiles from high-throughput sequencing shotgu Package: metabit-examples Architecture: all -Depends: ${misc:Depends}, +Depends: ${misc:Depends} Recommends: metabit Description: example data for MetaBIT pipeline for high-throughput sequencing data MetaBIT is an integrative and automated metagenomic pipeline for ===================================== debian/copyright ===================================== @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: metaBIT Source: https://bitbucket.org/Glouvel/metabit/downloads Files-Excluded: */pypeline/yaml ===================================== debian/get-orig-source deleted ===================================== @@ -1,25 +0,0 @@ -#!/bin/sh -e - -COMPRESS=xz - -NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` -MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'` - -mkdir -p ../tarballs -cd ../tarballs -# need to clean up the tarballs dir first because upstream tarball might -# contain a directory with unpredictable name -rm -rf * -git clone --quiet https://bitbucket.org/Glouvel/metabit.git -cd $NAME -VERSION=${MVERSION}+`date -d @$(git show --format="%at" | head -n1) +%Y%m%d` -# for esthetical reasons set file timestamps (if git-restore-mtime is installed) -git restore-mtime || true -cd .. -TARDIR=${NAME}-${VERSION} -mv ${NAME} ${TARDIR} -rm -rf ${TARDIR}/.git* -find ${TARDIR} -path */pypeline/yaml | xargs rm -rf - -GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}" -rm -rf ${TARDIR} ===================================== debian/rules ===================================== @@ -3,19 +3,19 @@ # DH_VERBOSE := 1 export LC_ALL=C.UTF-8 -DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') -RDIR := debian/$(DEBPKGNAME)/usr/lib/R/site-library/metabit +include /usr/share/dpkg/default.mk +RDIR := debian/$(DEB_SOURCE)/usr/lib/R/site-library/metabit %: dh $@ --with python2 override_dh_auto_build: dh_auto_build - markdown_py -f README.html README.md + markdown README.md > README.html override_dh_link: dh_link mkdir -p $(RDIR) - for r in debian/$(DEBPKGNAME)/usr/share/metabit/nodes/tools/statax_Rmodule/*.R ; do \ + for r in debian/$(DEB_SOURCE)/usr/share/metabit/nodes/tools/statax_Rmodule/*.R ; do \ ln -s `echo $$r | sed 's:.*/usr:../../../..:'` $(RDIR) ; \ done ===================================== debian/watch ===================================== @@ -1,3 +1,4 @@ -# version=3 -# upstream has not proper versioning +version=4 +opts="mode=git,pretty=0.0+git%cd.%h,repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \ + https://bitbucket.org/Glouvel/metabit.git HEAD ===================================== metaBIT.py ===================================== @@ -36,7 +36,8 @@ _tools = {"filterMetaphlan": ["nodes", "tools", "filterMetaphlan.py"], "doPcoa": ["nodes", "tools", "statax_Rmodule", "doPcoa.R"], "doClust": ["nodes", "tools", "statax_Rmodule", "doClust.R"], "doDiv": ["nodes", "tools", "statax_Rmodule", "doDiv.R"], - "doHeatmap": ["nodes", "tools", "statax_Rmodule", "doHeatmap.R"]} + "doHeatmap": ["nodes", "tools", "statax_Rmodule", "doHeatmap.R"], + "doBarplot": ["nodes", "tools", "statax_Rmodule", "doBarplot.R"]} def run(config, args): View it on GitLab: https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69 -- View it on GitLab: https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69 You're receiving this email because of your account on salsa.debian.org.
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