This is an automated email from the git hooks/post-receive script. lckarssen-guest pushed a commit to branch master in repository probabel.
commit 5bbc713e96609b80d2e835a648a53390ec467765 Author: L.C. Karssen <[email protected]> Date: Sun Dec 8 23:09:50 2013 +0100 Initial commit of debian packaging files. Based on what I already had in place for the Ubuntu PPA package I created before. --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 19 +++++++++++++++++++ debian/copyright | 28 ++++++++++++++++++++++++++++ debian/get-orig-source | 45 +++++++++++++++++++++++++++++++++++++++++++++ debian/rules | 23 +++++++++++++++++++++++ debian/source/format | 1 + debian/upstream | 12 ++++++++++++ debian/watch | 23 +++++++++++++++++++++++ 9 files changed, 157 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..f2440cc --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +probabel (0.4.1-1) unstable; urgency=low + + * Initial release (Closes: #<bug>) + + -- DMPT <[email protected]> Sun, 08 Dec 2013 16:06:13 +0100 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..2486359 --- /dev/null +++ b/debian/control @@ -0,0 +1,19 @@ +Source: probabel +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9), autotools-dev, texlive-latex-base, texlive-latex-extra, latex-xcolor, libeigen3-dev +Standards-Version: 3.9.4 +Homepage: http://www.genabel.org +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/probabel.git +Vcs-Git: git://anonscm.debian.org/debian-med/probabel.git + +Package: probabel +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Recommends: ${perl:Depends} +Description: Toolset for Genome-Wide Association Analysis + The ProbABEL package is part of the GenABEL project for analysis of genome-wide + data. ProbABEL is used to run GWAS. Using files in filevector/DatABEL format + even allows for running GWAS on computers with only a few GB of RAM. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..a252698 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,28 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: probabel +Source: http://www.genabel.org/sites/default/files/software/probabel-0.4.1.tar.gz + +Files: * +Copyright: © 2009-2013 The GenABEL team +License: GPL-2.0+ + +Files: debian/* +Copyright: © 2013 L.C. Karssen <[email protected]> +License: GPL-2.0+ + +License: GPL-2.0+ + This package is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + . + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/> + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". diff --git a/debian/get-orig-source b/debian/get-orig-source new file mode 100755 index 0000000..e486809 --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,45 @@ +#!/bin/sh +# if you need to repack for whatever reason you can +# use this script via uscan or directly +# +# FIXME: currently the code is not conform to Debian Policy +# http://www.debian.org/doc/debian-policy/ch-source.html +# "get-orig-source (optional)" +# This target may be invoked in any directory, ... +# --> currently it is assumed the script is called in the +# source directory featuring the debian/ dir + +COMPRESS=xz + +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/'` + uscan --force-download +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 + +TARDIR=${NAME}-${VERSION} +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 * +tar -xaf ../${TARDIR}.tar.gz + +UPSTREAMTARDIR=`find . -mindepth 1 -maxdepth 1 -type d` +if [ "${UPSTREAMTARDIR}" != "${TARDIR}" ] ; then + mv "${UPSTREAMTARDIR}" "${TARDIR}" +fi + +# Remove useless binaries +# ... do something which needs to be done ... + +GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}" +rm -rf ${TARDIR} diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..514459b --- /dev/null +++ b/debian/rules @@ -0,0 +1,23 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +# some helpful variables +# 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 $@ --parallel + +#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 b/debian/upstream new file mode 100644 index 0000000..6f40ab9 --- /dev/null +++ b/debian/upstream @@ -0,0 +1,12 @@ +Reference: + Author: Yurii S Aulchenko and Maksim V Struchalin and Cornelia M van Duijn + Title: ProbABEL package for genome-wide association analysis of imputed data. + Journal: BMC Bioinformatics + Year: 2010 + Volume: 11 + Number: + Pages: 134 + DOI: 10.1186/1471-2105-11-134 + PMID: 20233392 + URL: http://www.biomedcentral.com/1471-2105/11/134 + eprint: diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..4f75db0 --- /dev/null +++ b/debian/watch @@ -0,0 +1,23 @@ +version=3 + +# Uncomment to examine a Webpage +# <Webpage URL> <string match> +#http://www.example.com/downloads.php #PACKAGE#-(.*)\.tar\.gz +http://www.genabel.org/sites/default/files/software/ #PACKAGE#-(.*)\.tar\.gz + +# Uncomment to examine a Webserver directory +#http://www.example.com/pub/#PACKAGE#-(.*)\.tar\.gz + +# Uncommment to examine a FTP server +#ftp://ftp.example.com/pub/#PACKAGE#-(.*)\.tar\.gz debian uupdate + +# Uncomment to find new files on sourceforge +# http://sf.net/#PACKAGE#/#PACKAGE#-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) + +# Uncomment to find new files on GooglePages +# http://code.google.com/p/#PACKAGE#/downloads/list?can=1 \ +# .*/#PACKAGE#-([-.\d]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip) + +# if tweaking of source is needed +# \ +# debian debian/get-orig-source -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/probabel.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
