[med-svn] r2766 - in trunk/packages/euler2/trunk/debian: . patches

[tille at alioth.debian.org]

Author: tille
Date: 2008-12-10 12:38:53 +0000 (Wed, 10 Dec 2008)
New Revision: 2766

Added:
   trunk/packages/euler2/trunk/debian/eubatch
   trunk/packages/euler2/trunk/debian/patches/20_perl_warnings.patch
Modified:
   trunk/packages/euler2/trunk/debian/compat
   trunk/packages/euler2/trunk/debian/control
   trunk/packages/euler2/trunk/debian/install
   trunk/packages/euler2/trunk/debian/patches/series
   trunk/packages/euler2/trunk/debian/rules
Log:
Wrapper script, -w in all perl scripts


Modified: trunk/packages/euler2/trunk/debian/compat
===================================================================
--- trunk/packages/euler2/trunk/debian/compat	2008-12-09 21:34:28 UTC (rev 2765)
+++ trunk/packages/euler2/trunk/debian/compat	2008-12-10 12:38:53 UTC (rev 2766)
@@ -1 +1 @@
-7
+5

Modified: trunk/packages/euler2/trunk/debian/control
===================================================================
--- trunk/packages/euler2/trunk/debian/control	2008-12-09 21:34:28 UTC (rev 2765)
+++ trunk/packages/euler2/trunk/debian/control	2008-12-10 12:38:53 UTC (rev 2766)
@@ -13,6 +13,6 @@
 Package: euler2
 Architecture: any
 Section: science
-Depends: ${shlibs:Depends}
+Depends: ${shlibs:Depends}, graphviz
 Description: short description
  long description

Added: trunk/packages/euler2/trunk/debian/eubatch
===================================================================
--- trunk/packages/euler2/trunk/debian/eubatch	                        (rev 0)
+++ trunk/packages/euler2/trunk/debian/eubatch	2008-12-10 12:38:53 UTC (rev 2766)
@@ -0,0 +1,3 @@
+#!/bin/sh -e
+export EULERBIN=/usr/lib/euler2
+${EULERBIN}/eubatch.pl $@

Modified: trunk/packages/euler2/trunk/debian/install
===================================================================
--- trunk/packages/euler2/trunk/debian/install	2008-12-09 21:34:28 UTC (rev 2765)
+++ trunk/packages/euler2/trunk/debian/install	2008-12-10 12:38:53 UTC (rev 2766)
@@ -20,3 +20,4 @@
 makeintv           usr/lib/euler2
 makealn            usr/lib/euler2
 *.pl               usr/lib/euler2
+debian/eubatch     usr/bin

Added: trunk/packages/euler2/trunk/debian/patches/20_perl_warnings.patch
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/20_perl_warnings.patch	                        (rev 0)
+++ trunk/packages/euler2/trunk/debian/patches/20_perl_warnings.patch	2008-12-10 12:38:53 UTC (rev 2766)
@@ -0,0 +1,25 @@
+--- euler-2.0.orig/consens.pl
++++ euler-2.0/consens.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#! /usr/bin/perl -w
+ 
+ #***************************************************************************
+ # Title:          consens.pl
+--- euler-2.0.orig/errcorr-lapper-pair-mem.pl
++++ euler-2.0/errcorr-lapper-pair-mem.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#! /usr/bin/perl -w
+ 
+ #***************************************************************************
+ # Title:          errcorr-lapper-pair-mem.pl
+@@ -50,7 +50,7 @@
+ }
+ $i = 1;
+ while($i <= $allsteps)	{
+-	system("mv reads.tmp reads.txt");
++	system("mv reads.tmp reads.txt") || die "Unable to find file reads.tmp\n.";
+ 	system("mv reads.tmp.score reads.txt.score");
+ 	system("$MYHOME/overlapper-all -i reads.txt -q reads.txt.score -o reads.aln -l $overlen -p 200 -d $min_id -H");
+ 	$i = $i + 1;

Modified: trunk/packages/euler2/trunk/debian/patches/series
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/series	2008-12-09 21:34:28 UTC (rev 2765)
+++ trunk/packages/euler2/trunk/debian/patches/series	2008-12-10 12:38:53 UTC (rev 2766)
@@ -1,3 +1,4 @@
 20_warnings.patch
 20_gcc4_static.patch
 10_euler2_path_on_debian.patch
+20_perl_warnings.patch

Modified: trunk/packages/euler2/trunk/debian/rules
===================================================================
--- trunk/packages/euler2/trunk/debian/rules	2008-12-09 21:34:28 UTC (rev 2765)
+++ trunk/packages/euler2/trunk/debian/rules	2008-12-10 12:38:53 UTC (rev 2766)
@@ -12,4 +12,4 @@
 	echo "You have to gegister to obtain the upstream source"
 
 clean::
-	rm -f `grep -v '^*\.pl' debian/install | sed 's?[[:space:]]\+usr/[a-z0-9/]\+??'`
+	rm -f `grep -v -e '^*\.pl' -e '^debian/' debian/install | sed 's?[[:space:]]\+usr/[a-z0-9/]\+??'`