[med-svn] r2765 - in trunk/packages/euler2/trunk/debian: . patches

[tille at alioth.debian.org]

Author: tille
Date: 2008-12-09 21:34:28 +0000 (Tue, 09 Dec 2008)
New Revision: 2765

Added:
   trunk/packages/euler2/trunk/debian/patches/10_euler2_path_on_debian.patch
Modified:
   trunk/packages/euler2/trunk/debian/install
   trunk/packages/euler2/trunk/debian/patches/series
   trunk/packages/euler2/trunk/debian/rules
Log:
Patch perl scripts and install them also to /usr/lib/euler2


Modified: trunk/packages/euler2/trunk/debian/install
===================================================================
--- trunk/packages/euler2/trunk/debian/install	2008-12-09 20:29:06 UTC (rev 2764)
+++ trunk/packages/euler2/trunk/debian/install	2008-12-09 21:34:28 UTC (rev 2765)
@@ -1,22 +1,22 @@
-euler_db           usr/bin
-euler_et           usr/bin
-euler_cons         usr/bin
-over-repeat-new    usr/bin
-over-repeat-end    usr/bin
-over-repeat-end-po usr/bin
-po-prod            usr/bin
-over-align-phrap   usr/bin
-overlapper-all     usr/bin
-over-align-all     usr/bin
-errcorr_pair_mem   usr/bin
-trans_qual         usr/bin
-trimseq_qual       usr/bin
-pairreads          usr/bin
-pairreads_file     usr/bin
-pairreads1         usr/bin
-pairreads2         usr/bin
-pairreads3         usr/bin
-errcorr_fin_mem    usr/bin
-makeintv           usr/bin
-makealn            usr/bin
-
+euler_db           usr/lib/euler2
+euler_et           usr/lib/euler2
+euler_cons         usr/lib/euler2
+over-repeat-new    usr/lib/euler2
+over-repeat-end    usr/lib/euler2
+over-repeat-end-po usr/lib/euler2
+po-prod            usr/lib/euler2
+over-align-phrap   usr/lib/euler2
+overlapper-all     usr/lib/euler2
+over-align-all     usr/lib/euler2
+errcorr_pair_mem   usr/lib/euler2
+trans_qual         usr/lib/euler2
+trimseq_qual       usr/lib/euler2
+pairreads          usr/lib/euler2
+pairreads_file     usr/lib/euler2
+pairreads1         usr/lib/euler2
+pairreads2         usr/lib/euler2
+pairreads3         usr/lib/euler2
+errcorr_fin_mem    usr/lib/euler2
+makeintv           usr/lib/euler2
+makealn            usr/lib/euler2
+*.pl               usr/lib/euler2

Added: trunk/packages/euler2/trunk/debian/patches/10_euler2_path_on_debian.patch
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/10_euler2_path_on_debian.patch	                        (rev 0)
+++ trunk/packages/euler2/trunk/debian/patches/10_euler2_path_on_debian.patch	2008-12-09 21:34:28 UTC (rev 2765)
@@ -0,0 +1,37 @@
+--- euler-2.0.orig/eubatch.pl
++++ euler-2.0/eubatch.pl
+@@ -16,8 +16,8 @@
+ use Data::Dumper;
+ 
+ sub init_globals {
+-#    $pgms::bin = "/usr/local/apps/euler";
+-    $pgms::bin = getbindir();
++    $pgms::bin = "/usr/lib/euler2";
++#    $pgms::bin = getbindir();
+ }
+ 
+ sub print_usage {
+--- euler-2.0.orig/consens.pl
++++ euler-2.0/consens.pl
+@@ -11,7 +11,7 @@
+ # See file LICENSE for details.
+ #**************************************************************************/
+ 
+-my $RAHOME=$ENV{'EULERBIN'};
++my $RAHOME='/usr/lib/euler2';
+ 
+ `$RAHOME/create_alignment.pl $ARGV[0] $ARGV[1] 80 3 realigner.inp`;
+ `$RAHOME/realigner/converter -hV < realigner.inp| $RAHOME/realigner/ReAligner | $RAHOME/realigner/converter -vHC > realigner.out`;
+--- euler-2.0.orig/euindex.pl
++++ euler-2.0/euindex.pl
+@@ -17,8 +17,8 @@
+ #use Data::Dumper;
+ 
+ sub init_globals {
+-#    $pgms::bin = "/usr/local/apps/euler";
+-    $pgms::bin = getbindir();
++    $pgms::bin = "/usr/lib/euler2";
++#    $pgms::bin = getbindir();
+ 
+     my $bin = $pgms::bin ? $pgms::bin : ".";
+     $pgms::FASTASTAT = "${bin}/seqcount.pl";

Modified: trunk/packages/euler2/trunk/debian/patches/series
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/series	2008-12-09 20:29:06 UTC (rev 2764)
+++ trunk/packages/euler2/trunk/debian/patches/series	2008-12-09 21:34:28 UTC (rev 2765)
@@ -1,2 +1,3 @@
 20_warnings.patch
 20_gcc4_static.patch
+10_euler2_path_on_debian.patch

Modified: trunk/packages/euler2/trunk/debian/rules
===================================================================
--- trunk/packages/euler2/trunk/debian/rules	2008-12-09 20:29:06 UTC (rev 2764)
+++ trunk/packages/euler2/trunk/debian/rules	2008-12-09 21:34:28 UTC (rev 2765)
@@ -12,4 +12,4 @@
 	echo "You have to gegister to obtain the upstream source"
 
 clean::
-	rm -f `sed 's?[[:space:]]\+usr/bin??' debian/install`
+	rm -f `grep -v '^*\.pl' debian/install | sed 's?[[:space:]]\+usr/[a-z0-9/]\+??'`