[med-svn] [Git][med-team/metabit][master] 13 commits: Use git mode in watch file
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 11 09:49:21 BST 2019
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 <tille at debian.org> Mon, 25 Jul 2016 14:09:29 +0200
+ -- Andreas Tille <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
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
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