Author: tbooth-guest Date: 2011-08-11 12:59:52 +0000 (Thu, 11 Aug 2011) New Revision: 7424
Modified: trunk/packages/velvet/trunk/debian/changelog trunk/packages/velvet/trunk/debian/copyright trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch trunk/packages/velvet/trunk/debian/patches/series trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch trunk/packages/velvet/trunk/debian/rules Log: New upstream, now uses system Zlib by default, so removed one unneedded patch. I was having trouble with the get-orig-source and the modified tarball. After reading #561433 I decided it was easier to modify the build to work on a pristine tarball and add the short Copyright statement from /usr/share/doc/zlib1g/copyright to the copyright file. Only tested to compile on Ubuntu Lucid Modified: trunk/packages/velvet/trunk/debian/changelog =================================================================== --- trunk/packages/velvet/trunk/debian/changelog 2011-08-10 08:09:04 UTC (rev 7423) +++ trunk/packages/velvet/trunk/debian/changelog 2011-08-11 12:59:52 UTC (rev 7424) @@ -1,3 +1,11 @@ +velvet (1.1.05-1ubuntu2) lucid; urgency=low + + * New upstream. Still includes a copy of Zlib but the default + is now to use the system version, so removed relevant patch. + * Modified build to work on unmodified upstream. + + -- Tim Booth <[email protected]> Thu, 11 Aug 2011 13:34:46 +0100 + velvet (1.1.02~nozlibcopy-1) unstable; urgency=low * New upstream version Modified: trunk/packages/velvet/trunk/debian/copyright =================================================================== --- trunk/packages/velvet/trunk/debian/copyright 2011-08-10 08:09:04 UTC (rev 7423) +++ trunk/packages/velvet/trunk/debian/copyright 2011-08-11 12:59:52 UTC (rev 7424) @@ -37,7 +37,7 @@ Copyright 2007, 2008 Daniel Zerbino ([email protected]) This file is part of Velvet. - + Velvet 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 2 of the License, or @@ -110,3 +110,24 @@ Copyright: 2008-2009 Charles Plessy <[email protected]> 2008-2009 Andreas Tille <[email protected]>, License: Same as velvet + +Files: third-party/zlib* +Copyright: 1995-1998 Jean-loup Gailly and Mark Adler +License: + + This software is provided 'as-is', without any express or implied + warranty. In no event will the authors be held liable for any damages + arising from the use of this software. + + Permission is granted to anyone to use this software for any purpose, + including commercial applications, and to alter it and redistribute it + freely, subject to the following restrictions: + + 1. The origin of this software must not be misrepresented; you must not + claim that you wrote the original software. If you use this software + in a product, an acknowledgment in the product documentation would be + appreciated but is not required. + 2. Altered source versions must be plainly marked as such, and must not be + misrepresented as being the original software. + 3. This notice may not be removed or altered from any source distribution. + Modified: trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch =================================================================== --- trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch 2011-08-10 08:09:04 UTC (rev 7423) +++ trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch 2011-08-11 12:59:52 UTC (rev 7424) @@ -1,8 +1,8 @@ Description: s?/usr/local/perl?/usr/perl? Author: Andreas Tille <[email protected]> Forwarded: No ---- velvet_1.1.02~nozlibcopy.orig/contrib/select_paired/select_paired.pl -+++ velvet_1.1.02~nozlibcopy/contrib/select_paired/select_paired.pl +--- a/contrib/select_paired/select_paired.pl ++++ b/contrib/select_paired/select_paired.pl @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/perl -w Modified: trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch =================================================================== --- trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch 2011-08-10 08:09:04 UTC (rev 7423) +++ trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch 2011-08-11 12:59:52 UTC (rev 7424) @@ -1,10 +1,10 @@ Description: Use the zlib distributed by Debian, not the one in third-party/zlib-1.2.3/. Author: Charles Plessy <[email protected]> Forwarded: no ---- velvet_1.1.02~nozlibcopy.orig/src/readSet.c -+++ velvet_1.1.02~nozlibcopy/src/readSet.c -@@ -33,7 +33,7 @@ - #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32) +--- a/src/readSet.c ++++ b/src/readSet.c +@@ -35,7 +35,7 @@ + #elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32) #include "../third-party/zlib-1.2.3/Win32/include/zlib.h" #else -#include "../third-party/zlib-1.2.3/zlib.h" Modified: trunk/packages/velvet/trunk/debian/patches/series =================================================================== --- trunk/packages/velvet/trunk/debian/patches/series 2011-08-10 08:09:04 UTC (rev 7423) +++ trunk/packages/velvet/trunk/debian/patches/series 2011-08-11 12:59:52 UTC (rev 7424) @@ -1,4 +1,3 @@ include_debians_zlib.patch shuffleSequences_fasta.patch fix-perl-path.patch -ld-as-needed.patch Modified: trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch =================================================================== --- trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch 2011-08-10 08:09:04 UTC (rev 7423) +++ trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch 2011-08-11 12:59:52 UTC (rev 7424) @@ -1,8 +1,8 @@ Description: Scripts need to specify interpreter in the first line Author: Andreas Tille <[email protected]> Forwarded: not yet ---- velvet_1.1.02~nozlibcopy.orig/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py -+++ velvet_1.1.02~nozlibcopy/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py +--- a/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py ++++ b/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py @@ -1,3 +1,4 @@ +#!/usr/bin/python import sys Modified: trunk/packages/velvet/trunk/debian/rules =================================================================== --- trunk/packages/velvet/trunk/debian/rules 2011-08-10 08:09:04 UTC (rev 7423) +++ trunk/packages/velvet/trunk/debian/rules 2011-08-11 12:59:52 UTC (rev 7424) @@ -14,7 +14,7 @@ pkg=velvet -DEB_MAKE_BUILD_TARGET = obj velveth velvetg LIBS='-lm -lz' OPT='' +DEB_MAKE_BUILD_TARGET = obj velveth velvetg LDFLAGS='-lm -lz' OPT='' build/velvet:: make color CFLAGS='$(CFLAGS)' LIBS='-lm -lz' OPT='' @@ -30,6 +30,11 @@ --name="de Bruijn graph construction, error removal and repeat resolution (colorspace version)" \ $(CURDIR)/velvetg_de > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg_de.1 +#If the taball is not being scrubbed we need this. +binary-install/velvet:: + find $(CURDIR)/debian/$(pkg) -name '.DS_Store' -exec rm {} \; + rm -rf $(CURDIR)/debian/$(pkg)/usr/share/velvet/contrib/MetaVelvet* + get-orig-source: . debian/get-orig-source _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
