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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]>, + Charles Plessy <[email protected]> +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 <[email protected]>, Heng Li <[email protected]>, + Mengyao Zhao <[email protected]> +Source : http://sourceforge.net/projects/maq/files/ + +License: GPL2 +Copyright: 2007-2008, Jue Ruan <[email protected]> + + 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 <[email protected]> +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 + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
