[med-svn] r5453 - in trunk/packages: . maqview maqview/trunk maqview/trunk/debian
Andreas Tille
tille at alioth.debian.org
Fri Nov 19 21:20:49 UTC 2010
Author: tille
Date: 2010-11-19 21:20:48 +0000 (Fri, 19 Nov 2010)
New Revision: 5453
Added:
trunk/packages/maqview/
trunk/packages/maqview/trunk/
trunk/packages/maqview/trunk/debian/
trunk/packages/maqview/trunk/debian/README.source
trunk/packages/maqview/trunk/debian/changelog
trunk/packages/maqview/trunk/debian/compat
trunk/packages/maqview/trunk/debian/control
trunk/packages/maqview/trunk/debian/copyright
trunk/packages/maqview/trunk/debian/get-orig-source
trunk/packages/maqview/trunk/debian/install
trunk/packages/maqview/trunk/debian/rules
trunk/packages/maqview/trunk/debian/watch
Log:
Inject maqview which I will probably package because it might be here. Removed parts of zlib from the code so it will not build currently without patches.
Added: trunk/packages/maqview/trunk/debian/README.source
===================================================================
--- trunk/packages/maqview/trunk/debian/README.source (rev 0)
+++ trunk/packages/maqview/trunk/debian/README.source 2010-11-19 21:20:48 UTC (rev 5453)
@@ -0,0 +1,4 @@
+This packages uses the quilt patch system. Please read
+/usr/share/doc/quilt/README.source for more information.
+
+ -- Andreas Tille <tille at debian.org> Mon, 31 Aug 2009 14:50:19 +0200
Added: trunk/packages/maqview/trunk/debian/changelog
===================================================================
--- trunk/packages/maqview/trunk/debian/changelog (rev 0)
+++ trunk/packages/maqview/trunk/debian/changelog 2010-11-19 21:20:48 UTC (rev 5453)
@@ -0,0 +1,5 @@
+maqview (0.2.5-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Andreas Tille <tille at debian.org> Wed, 16 Jul 2008 12:01:33 +0200
Added: trunk/packages/maqview/trunk/debian/compat
===================================================================
--- trunk/packages/maqview/trunk/debian/compat (rev 0)
+++ trunk/packages/maqview/trunk/debian/compat 2010-11-19 21:20:48 UTC (rev 5453)
@@ -0,0 +1 @@
+7
Added: trunk/packages/maqview/trunk/debian/control
===================================================================
--- trunk/packages/maqview/trunk/debian/control (rev 0)
+++ trunk/packages/maqview/trunk/debian/control 2010-11-19 21:20:48 UTC (rev 5453)
@@ -0,0 +1,34 @@
+Source: maqview
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>,
+ Charles Plessy <plessy at debian.org>
+Build-Depends: debhelper (>= 7), quilt, autotools-dev, automake, freeglut3-dev
+Standards-Version: 3.9.1
+Homepage: http://maq.sourceforge.net/maqview.shtml
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maqview/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maqview/trunk/
+
+Package: maqview
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: graphical read alignment viewer for short gene sequences
+ Maqview is graphical read alignment viewer. It is specifically designed
+ for the Maq alignment file and allows you to see the mismatches, base
+ qualities and mapping qualities. Maqview is nothing fancy as Consed or
+ GAP, but just a simple viewer for you to see what happens in a
+ particular region.
+ .
+ In comparison to tgap-maq, the text-based read alignment viewer writen
+ by James Bonfield, Maqview is faster and takes up much less memory and
+ disk space in indexing. This is possibly because tgap aims to be a
+ general-purpose viewer but Maqview fully makes use of the fact that a
+ Maq alignment file has already been sorted. Maqview is also efficient in
+ viewing and provides a command-line tool to quickly retrieve any region
+ in an Maq alignment file.
+ .
+ Maqview is based on OpenGL. Installing OpenGL on your system is the
+ trade-off of getting a better feel and look. The following screenshots
+ show the two viewing modes of Maqview.
Added: trunk/packages/maqview/trunk/debian/copyright
===================================================================
--- trunk/packages/maqview/trunk/debian/copyright (rev 0)
+++ trunk/packages/maqview/trunk/debian/copyright 2010-11-19 21:20:48 UTC (rev 5453)
@@ -0,0 +1,30 @@
+Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+
+Name : MaqView: Mapping and Assembly with Qualities
+Contact : Jue Ruan <ruanjue at genomics.org.cn>, Heng Li <lh3 at sanger.ac.uk>,
+ Mengyao Zhao <zhaomengyao at gmail.com>
+Source : http://sourceforge.net/projects/maq/files/
+
+License: GPL2
+Copyright: 2007-2008, Jue Ruan <ruanjue at genomics.org.cn>
+
+ This program 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 3 of the License, or
+ (at your option) any later version.
+
+ This program 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’.
+
+Files: debian/*
+Copyright: 2010, Andreas Tille <tille at debian.org>
+License: Same as MaqView itelf
+ (see above)
Added: trunk/packages/maqview/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/maqview/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/maqview/trunk/debian/get-orig-source 2010-11-19 21:20:48 UTC (rev 5453)
@@ -0,0 +1,28 @@
+#!/bin/sh
+# script to download and repack source package of maqview
+# this is needed to remove a copy of zlib
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download | \
+ grep "Newest version on remote site is .* local version is .*" | \
+ head -n 1 | \
+ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+UTAR="${PKG}-${VERSION}.tar.gz"
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+cd $PKG
+# remove all files belonging to zlib
+rm -rf zutil.[ch] zlib.h zconf.h uncompr.c trees.[ch] inftrees.[ch] inflate.[ch] inffixed.h inffast.[ch] infback.c gzio.c deflate.[ch] crc32.[ch] compress.c adler32.c
+# remove useless SVN dir
+rm -rf .svn
+cd ..
+
+mv ${PKG} ${PKG}-${VERSION}~nozlibcopy
+
+GZIP=-9 tar -czf "$PKG"_"$VERSION~nozlibcopy".orig.tar.gz "${PKG}-${VERSION}~nozlibcopy"
+rm -rf "${PKG}-${VERSION}~nozlibcopy"
Added: trunk/packages/maqview/trunk/debian/install
===================================================================
--- trunk/packages/maqview/trunk/debian/install (rev 0)
+++ trunk/packages/maqview/trunk/debian/install 2010-11-19 21:20:48 UTC (rev 5453)
@@ -0,0 +1,4 @@
+maqindex usr/bin
+maqindex_socks usr/bin
+maqview usr/bin
+zrio usr/bin
Added: trunk/packages/maqview/trunk/debian/rules
===================================================================
--- trunk/packages/maqview/trunk/debian/rules (rev 0)
+++ trunk/packages/maqview/trunk/debian/rules 2010-11-19 21:20:48 UTC (rev 5453)
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+# debian/rules file for maqview
+# (C) Andreas Tille
+# GPL
+
+%:
+ dh $@ # --with quilt
+
+override_dh_auto_configure:
+ ./autogen.sh
+ dh_auto_configure
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f maqindex maqindex_socks maqview zrio
+ rm -f config.h config.log config.status Makefile stamp-h1
+ rm -f aclocal.m4 config.guess config.h.in config.sub configure depcomp install-sh Makefile.in missing
+
+get-orig-source:
+ . debian/get-orig-source
Property changes on: trunk/packages/maqview/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/maqview/trunk/debian/watch
===================================================================
--- trunk/packages/maqview/trunk/debian/watch (rev 0)
+++ trunk/packages/maqview/trunk/debian/watch 2010-11-19 21:20:48 UTC (rev 5453)
@@ -0,0 +1,4 @@
+version=3
+
+http://sf.net/maq/maqview-([\d\.]+)\.tar\.gz
+
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