[med-svn] r7424 - in trunk/packages/velvet/trunk/debian: . patches

Timothy Booth tbooth-guest at alioth.debian.org
Thu Aug 11 12:59:52 UTC 2011 

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 <tbooth at ceh.ac.uk>  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 (zerbino at ebi.ac.uk)
  
  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 <plessy at debian.org>
            2008-2009 Andreas Tille <tille at debian.org>,
 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 <tille at debian.org>
 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 <plessy at debian.org>
 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 <tille at debian.org>
 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

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