This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository mugsy.
commit 1bc4beb5d5b9bb02ed6e58a0c4c4becb16eef3e2 Author: Andreas Tille <[email protected]> Date: Mon Apr 13 20:54:38 2015 +0200 Initial Debian packaging --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 21 +++++++++++++++++++++ debian/copyright | 11 +++++++++++ debian/get-orig-source | 44 ++++++++++++++++++++++++++++++++++++++++++++ debian/rules | 23 +++++++++++++++++++++++ debian/source/format | 1 + debian/upstream/metadata | 12 ++++++++++++ debian/watch | 5 +++++ 9 files changed, 123 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..f731860 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +mugsy (1r2.3+dfsg-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + + -- Andreas Tille <[email protected]> Mon, 13 Apr 2015 15:21:26 +0200 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..e05237c --- /dev/null +++ b/debian/control @@ -0,0 +1,21 @@ +Source: mugsy +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.6 +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/mugsy.git +Vcs-Git: git://anonscm.debian.org/debian-med/mugsy.git +Homepage: http://mugsy.sourceforge.net/ + +Package: mugsy +Architecture: any +Depends: ${misc:Depends}, ${shlibs:Depends} +Description: multiple whole genome alignment tool + Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for + pairwise alignment, a custom graph based segmentation procedure for + identifying collinear regions, and the segment-based progressive + multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft + genomes in the form of multi-FASTA files and does not require a + reference genome. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..c76e73d --- /dev/null +++ b/debian/copyright @@ -0,0 +1,11 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: <pkg> +Source: <path_to_download> + +Files: * +Copyright: © 20xx-20yy <upstream> +License: <license> + +Files: debian/* +Copyright: © 2014 maintainername <[email protected]> +License: <license> diff --git a/debian/get-orig-source b/debian/get-orig-source new file mode 100755 index 0000000..8d3ba11 --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,44 @@ +#!/bin/sh +# get source for mugsy from SVN because there is no source tarball distribution + +set -e +NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` + +if ! echo $@ | grep -q upstream-version ; then + VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` +else + VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"` + if echo "$VERSION" | grep -q "upstream-version" ; then + echo "Unable to parse version number" + exit + fi +fi + +SVNTAG=`echo ${VERSION} | sed 's/\./_/g'` +rm -f ../${ORIGNAME}_release_${SVNTAG} +RELEASE=${ORIGNAME}_release_${SVNTAG} +TARDIR=${NAME}-${VERSION} + +mkdir -p ../tarballs +cd ../tarballs +# svn export conserves time stamps of the files, checkout does not +LC_ALL=C svn export svn://svn.code.sf.net/p/${NAME}/code/trunk ${TARDIR} >/dev/null 2>/dev/null + +cd ${TARDIR} +rm -rf MUMmer* +# rm -rf *seqan* +rm -rf mugsy-seqan/projects/library/apps/mugsy/gcc/mugsy +rm -rf mugsy-seqan/projects/library/apps/mugsy/libmaf.a +rm -rf mugsy-seqan/projects/library/apps/seqan_tcoffee +for seqandir in cmake demos lib extra seqan CMakeLists.txt seqan.h ; do + rm -rf mugsy-seqan/projects/library/$seqandir +done +rm -rf mugsy-seqan/projects/tests +for seqandir in docs misc platforms visual_studio Makefile ; do + rm -rf mugsy-seqan/$seqandir +done +rm -rf chaining/synchain-mugsy +cd .. + +tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.xz "${TARDIR}" +rm -rf "${NAME}"-"$VERSION" diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..58ec00b --- /dev/null +++ b/debian/rules @@ -0,0 +1,23 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +# some helpful variables - uncomment them if needed +# shamelessly stolen from http://jmtd.net/log/awk/ +#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}') +#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//') +#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}') +#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') +#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf) +#GIT_TAG := $(subst ~,_,$(VERSION)) + +# alternatively to manually set those variables you can +# include /usr/share/cdbs/1/rules/buildvars.mk +# and use what is set there. Any hint whether dh might set variables in +# a similar manner are welcome. + +%: + dh $@ + +#get-orig-source: +# . debian/get-orig-source diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..888c4d2 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: Samuel V. Angiuoli and Steven L. Salzberg + Title: "Mugsy: fast multiple alignment of closely related whole genomes" + Journal: Bioinformatics + Year: 2011 + Volume: 27 + Number: 3 + Pages: 334-342 + DOI: 10.1093/bioinformatics/btq665 + PMID: 21148543 + URL: http://bioinformatics.oxfordjournals.org/content/27/3/334 + eprint: http://bioinformatics.oxfordjournals.org/content/27/3/334.full.pdf+html diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..3cbbe5e --- /dev/null +++ b/debian/watch @@ -0,0 +1,5 @@ +version=3 + +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \ +http://sf.net/mugsy/mugsy_.*-v(\d[r\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) \ + debian debian/get-orig-source -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mugsy.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
