[med-svn] [biceps] 01/01: Add initial debian/ dir
Andreas Tille
tille at debian.org
Sat Feb 8 23:46:23 UTC 2014
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 <tille at debian.org>
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <buote.xu at gmail.com>
+Source: https://github.com/buotex/BICEPS
+
+Files: *
+Copyright: 2012-2014 Buote Xu <buote.xu at gmail.com>
+License: BSDlike
+
+Files: debian/*
+Copyright: 2014 Andreas Tille <tille at debian.org>
+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))
--
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