This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository biceps.
commit 0e7a0311574dbda78f2962784ef67918e097eccb Author: Andreas Tille <[email protected]> Date: Sun Feb 9 00:46:08 2014 +0100 Add initial debian/ dir --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 30 ++++++++++++++++++++++++++++++ debian/copyright | 32 ++++++++++++++++++++++++++++++++ debian/get-orig-source | 19 +++++++++++++++++++ debian/rules | 23 +++++++++++++++++++++++ debian/source/format | 1 + debian/upstream | 12 ++++++++++++ debian/watch | 2 ++ 9 files changed, 125 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..c8d2260 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +biceps (0.0.201401-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + + -- Andreas Tille <[email protected]> Sat, 08 Feb 2014 23:33:13 +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..9f4aa99 --- /dev/null +++ b/debian/control @@ -0,0 +1,30 @@ +Source: biceps +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9), + cmake, + libboost-filesystem-dev, + libboost-system-dev, + libboost-regex-dev, + libboost-program-options-dev, + libboost-iostreams-dev, + libboost-serialization-dev, + libboost-thread-dev, + zlib1g-dev +Standards-Version: 3.9.5 +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/biceps.git +Vcs-Git: git://anonscm.debian.org/debian-med/biceps.git +Homepage: http://hci.iwr.uni-heidelberg.de/MIP/Software/biceps.php + +Package: biceps +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: error-tolerant peptide identification + BICEPS is tool for the error-tolerant identification of peptides based + on a statistical regularization scheme. It balances possible + improvements in peptide-spectrum-matches by allowing substitutions + against the increased risk of false positives. BICEPS can identify + peptides containing two or more substitutions as occuring e.g. in + cross-species searches. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..f8f7fb0 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,32 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: BICEPS +Ustream-Contact: Buote Xu <[email protected]> +Source: https://github.com/buotex/BICEPS + +Files: * +Copyright: 2012-2014 Buote Xu <[email protected]> +License: BSDlike + +Files: debian/* +Copyright: 2014 Andreas Tille <[email protected]> +License: BSDlike + +License: BSDlike + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + . + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. + diff --git a/debian/get-orig-source b/debian/get-orig-source new file mode 100755 index 0000000..04ab55e --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,19 @@ +#!/bin/sh +# get source for biceps since the releases are not tagged + +set -e +# set -x +NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +COMPRESSION=xz +VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` + +mkdir -p ../tarballs +cd ../tarballs +TARDIR=${NAME}-${VERSION} + +# fetch source from SVN +git clone https://github.com/buotex/BICEPS.git $TARDIR +rm -rf $TARDIR/.git + +GZIP="--best --no-name" XZ_OPT="-6v" tar --owner=root --group=root --mode=a+rX -a -cf ${NAME}_${VERSION}.orig.tar.${COMPRESSION} ${TARDIR} +rm -rf ${TARDIR} diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..7c47e34 --- /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 $@ --buildsystem=cmake + +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..8d690c5 --- /dev/null +++ b/debian/upstream @@ -0,0 +1,12 @@ +Reference: + Author: Bernhard Y. Renard‡and Buote Xu and Marc Kirchner and Franziska Zickmann‡and Dominic Winter and Simone Korten‡and Norbert W. Brattig‡and Amit Tzur and Fred A. Hamprecht and Hanno Steen + Title: "Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)" + Journal: Mol Cell Proteomics + Year: 2012 + Volume: ;11 + Number: 7 + Pages: M111.014167 + DOI: 10.1074/mcp.M111.014167 + PMID: 22493179 + URL: http://www.mcponline.org/content/11/7/M111.014167.abstract + eprint: http://www.mcponline.org/content/11/7/M111.014167.full.pdf+html diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..f0ef894 --- /dev/null +++ b/debian/watch @@ -0,0 +1,2 @@ +version=3 +#https://github.com/buotex/BICEPS/releases .*/(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz)) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/biceps.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
