[med-svn] r5486 - in trunk/packages/velvet/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2010-11-24 14:59:49 +0000 (Wed, 24 Nov 2010)
New Revision: 5486

Added:
   trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch
   trunk/packages/velvet/trunk/debian/patches/series
   trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch
Modified:
   trunk/packages/velvet/trunk/debian/changelog
   trunk/packages/velvet/trunk/debian/control
   trunk/packages/velvet/trunk/debian/get-orig-source
Log:
New upstream source


Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog	2010-11-24 13:35:59 UTC (rev 5485)
+++ trunk/packages/velvet/trunk/debian/changelog	2010-11-24 14:59:49 UTC (rev 5486)
@@ -1,3 +1,13 @@
+velvet (1.0.15~nozlibcopy-1) unstable; urgency=low
+
+  * New upstream source
+  * Standards-Version: 3.9.1 (no changes needed)
+  * debian/get-upstream-source: Remove precompiled *.o files and
+    .DS_Store files once we are repackaging anyway
+  * debian/patches/fix-perl-path.patch: Fix Perl path
+
+ -- Andreas Tille <tille at debian.org>  Wed, 24 Nov 2010 15:42:33 +0100
+
 velvet (1.0.02~nozlibcopy-1) unstable; urgency=low
 
   * New upstream version

Modified: trunk/packages/velvet/trunk/debian/control
===================================================================
--- trunk/packages/velvet/trunk/debian/control	2010-11-24 13:35:59 UTC (rev 5485)
+++ trunk/packages/velvet/trunk/debian/control	2010-11-24 14:59:49 UTC (rev 5486)
@@ -6,7 +6,7 @@
 Uploaders: Charles Plessy <plessy at debian.org>,
  Andreas Tille <tille at debian.org>
 Build-Depends: cdbs, debhelper (>= 7.1), zlib1g-dev, help2man, quilt
-Standards-Version: 3.8.4
+Standards-Version: 3.9.1
 Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/velvet/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/velvet/trunk/

Modified: trunk/packages/velvet/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/velvet/trunk/debian/get-orig-source	2010-11-24 13:35:59 UTC (rev 5485)
+++ trunk/packages/velvet/trunk/debian/get-orig-source	2010-11-24 14:59:49 UTC (rev 5486)
@@ -15,6 +15,14 @@
 mv ../${UPSTREAMDIR}.tgz .
 tar -xzf ${UPSTREAMDIR}.tgz
 rm -rf ${UPSTREAMDIR}/third-party
+
+## Deletue useless binaries once we are changing the original tarball anyway
+# delete precompiled object files
+# rm -f ${UPSTREAMDIR}/obj/*.o
+find ${UPSTREAMDIR} -name "*.o" -exec rm -f \{\} \;
+# delete .DS_Store files
+find ${UPSTREAMDIR} -name .DS_Store -exec rm -f \{\} \;
+
 mv ${UPSTREAMDIR} ${UPSTREAMDIR}~nozlibcopy
 
 GZIP=-9 tar -czf "$PKG"_"$VERSION~nozlibcopy".orig.tar.gz "${UPSTREAMDIR}~nozlibcopy"

Added: trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch	2010-11-24 14:59:49 UTC (rev 5486)
@@ -0,0 +1,11 @@
+Description: s?/usr/local/perl?/usr/perl?
+Author: Andreas Tille <tille at debian.org>
+Forwarded: No
+--- velvet_1.0.15~nozlibcopy.orig/contrib/select_paired/select_paired.pl
++++ velvet_1.0.15~nozlibcopy/contrib/select_paired/select_paired.pl
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+ # Konrad Paszkiewicz, University of Exeter UK.
+ # k.h.paszkiewicz at exeter.ac.uk
+ 

Added: trunk/packages/velvet/trunk/debian/patches/series
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/patches/series	2010-11-24 14:59:49 UTC (rev 5486)
@@ -0,0 +1,3 @@
+include_debians_zlib.patch
+shuffleSequences_fasta.patch
+fix-perl-path.patch

Added: trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch	2010-11-24 14:59:49 UTC (rev 5486)
@@ -0,0 +1,10 @@
+Description: Scripts need to specify interpreter in the first line
+Author: Andreas Tille <tille at debian.org>
+Forwarded: not yet
+--- velvet_1.0.02~nozlibcopy.orig/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
++++ velvet_1.0.02~nozlibcopy/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python
+ import sys
+ from Bio import SeqIO
+ def interleave(iter1, iter2) :