[med-svn] r20194 - in trunk/packages/crux-toolkit: . trunk trunk/debian trunk/debian/source trunk/debian/upstream
Andreas Tille
tille at moszumanska.debian.org
Mon Oct 5 12:44:48 UTC 2015
Author: tille
Date: 2015-10-05 12:44:47 +0000 (Mon, 05 Oct 2015)
New Revision: 20194
Added:
trunk/packages/crux-toolkit/trunk/
trunk/packages/crux-toolkit/trunk/debian/
trunk/packages/crux-toolkit/trunk/debian/changelog
trunk/packages/crux-toolkit/trunk/debian/compat
trunk/packages/crux-toolkit/trunk/debian/control
trunk/packages/crux-toolkit/trunk/debian/copyright
trunk/packages/crux-toolkit/trunk/debian/get-orig-source
trunk/packages/crux-toolkit/trunk/debian/rules
trunk/packages/crux-toolkit/trunk/debian/source/
trunk/packages/crux-toolkit/trunk/debian/source/format
trunk/packages/crux-toolkit/trunk/debian/upstream/
trunk/packages/crux-toolkit/trunk/debian/upstream/metadata
trunk/packages/crux-toolkit/trunk/debian/watch
Log:
Really add crux-toolkit packaging - feel free to continue packaging
Added: trunk/packages/crux-toolkit/trunk/debian/changelog
===================================================================
--- trunk/packages/crux-toolkit/trunk/debian/changelog (rev 0)
+++ trunk/packages/crux-toolkit/trunk/debian/changelog 2015-10-05 12:44:47 UTC (rev 20194)
@@ -0,0 +1,5 @@
+crux-toolkit (0.0.r16826-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 29 Sep 2015 15:21:50 +0200
Added: trunk/packages/crux-toolkit/trunk/debian/compat
===================================================================
--- trunk/packages/crux-toolkit/trunk/debian/compat (rev 0)
+++ trunk/packages/crux-toolkit/trunk/debian/compat 2015-10-05 12:44:47 UTC (rev 20194)
@@ -0,0 +1 @@
+9
Added: trunk/packages/crux-toolkit/trunk/debian/control
===================================================================
--- trunk/packages/crux-toolkit/trunk/debian/control (rev 0)
+++ trunk/packages/crux-toolkit/trunk/debian/control 2015-10-05 12:44:47 UTC (rev 20194)
@@ -0,0 +1,18 @@
+Source: crux-toolkit
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/crux-toolkit/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/crux-toolkit/trunk/
+Homepage: http://cruxtoolkit.sourceforge.net/
+
+Package: crux-toolkit
+Architecture: any
+Depends: ${misc:Depends},
+ ${shlibs:Depends}
+Description: toolkit for tandem mass spectrometry analysis
+ Crux is a software toolkit for tandem mass spectrometry analysis, with a
+ focus on peptide identification.
Added: trunk/packages/crux-toolkit/trunk/debian/copyright
===================================================================
--- trunk/packages/crux-toolkit/trunk/debian/copyright (rev 0)
+++ trunk/packages/crux-toolkit/trunk/debian/copyright 2015-10-05 12:44:47 UTC (rev 20194)
@@ -0,0 +1,18 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: crux-toolkit
+Source: http://sourceforge.net/p/cruxtoolkit/code/HEAD/tree/crux-toolkit/
+
+Files: *
+Copyright: 2008-2014
+License: Apache-2.0
+Comment: License is specified at Sourceforge page
+ http://sourceforge.net/projects/cruxtoolkit/
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: Apache-2.0
+
+License: Apache-2.0
+ On Debian systems you can find the full text of the Apache License V2.0
+ at /usr/share/common-licenses/Apache-2.0
+
Added: trunk/packages/crux-toolkit/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/crux-toolkit/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/crux-toolkit/trunk/debian/get-orig-source 2015-10-05 12:44:47 UTC (rev 20194)
@@ -0,0 +1,34 @@
+#!/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
+set -x
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+
+## NO tags no branches
+SVNURI="svn://svn.code.sf.net/p/cruxtoolkit/code/crux/trunk/"
+revision=`LANG=C svn info ${SVNURI} | grep "^Last Changed Rev:" | sed 's/Last Changed Rev: *//'`
+VERSION=`echo ${VERSION}| sed "s/.r[0-9]\+$//"`.r${revision}
+
+TARDIR=${NAME}-${VERSION}
+
+mkdir -p ../tarballs
+cd ../tarballs
+# svn export conserves time stamps of the files, checkout does not
+LC_ALL=C svn export ${SVNURI} ${TARDIR} >/dev/null 2>/dev/null || true
+
+find ${TARDIR} -name .svnignore -delete
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
Property changes on: trunk/packages/crux-toolkit/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/crux-toolkit/trunk/debian/rules
===================================================================
--- trunk/packages/crux-toolkit/trunk/debian/rules (rev 0)
+++ trunk/packages/crux-toolkit/trunk/debian/rules 2015-10-05 12:44:47 UTC (rev 20194)
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@
+
+get-orig-source:
+ sh debian/get-orig-source
Property changes on: trunk/packages/crux-toolkit/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/crux-toolkit/trunk/debian/source/format
===================================================================
--- trunk/packages/crux-toolkit/trunk/debian/source/format (rev 0)
+++ trunk/packages/crux-toolkit/trunk/debian/source/format 2015-10-05 12:44:47 UTC (rev 20194)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/crux-toolkit/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/crux-toolkit/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/crux-toolkit/trunk/debian/upstream/metadata 2015-10-05 12:44:47 UTC (rev 20194)
@@ -0,0 +1,21 @@
+Reference:
+ - Author: Sean McIlwain and Kaipo Tamura and Attila Kertesz-Farkas and Charles E. Grant and Benjamin Diament and Barbara Frewen and J. Jeffry Howbert and Michael R. Hoopmann and Lukas Käll and Jimmy K. Eng and Michael J. MacCoss and William Stafford Noble
+ Title: "Crux: rapid open source protein tandem mass spectrometry analysis"
+ Journal: 2014
+ Year: Journal of Proteome Research
+ Volume: 13
+ Number: 10
+ Pages: 4488-4491
+ DOI: 10.1021/pr500741y
+ PMID: 25182276
+ URL: http://pubs.acs.org/doi/abs/10.1021/pr500741y
+ - Author: Christopher Y. Park and Aaron A. Klammer and Lukas Kall and Michael MacCoss and William Stafford Noble
+ Title: Rapid and accurate peptide identification from tandem mass spectra
+ Journal: Journal of Proteome Research
+ Year: 2008
+ Volume: 7
+ Number: 7
+ Pages: 3022-3027
+ DOI: 10.1021/pr800127y
+ PMID: 18505281
+ URL: http://pubs.acs.org/doi/abs/10.1021/pr800127y
Added: trunk/packages/crux-toolkit/trunk/debian/watch
===================================================================
--- trunk/packages/crux-toolkit/trunk/debian/watch (rev 0)
+++ trunk/packages/crux-toolkit/trunk/debian/watch 2015-10-05 12:44:47 UTC (rev 20194)
@@ -0,0 +1 @@
+# There is no tarball download location, this software is only available in SVN
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