[med-svn] r9762 - trunk/packages/sift/trunk/debian/patches

[H. Soon Gweon]

Author: soonio-guest
Date: 2012-02-23 13:39:12 +0000 (Thu, 23 Feb 2012)
New Revision: 9762

Modified:
   trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
   trunk/packages/sift/trunk/debian/patches/series
Log:
Further changes to perl path

Modified: trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path
===================================================================
--- trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path	2012-02-23 13:05:53 UTC (rev 9761)
+++ trunk/packages/sift/trunk/debian/patches/fix_perl_interpreter_and_lib_path	2012-02-23 13:39:12 UTC (rev 9762)
@@ -2713,3 +2713,43 @@
  use Class::Struct;
  
  #
+--- a/bin/SIFT_exome_indels.pl
++++ b/bin/SIFT_exome_indels.pl
+@@ -14,7 +14,7 @@
+ use Tie::IxHash;
+ use File::Copy;
+ use Getopt::Std;
+-$ENV{'SIFT_HOME'} = '/usr/share/sift';
++$ENV{'SIFT_HOME'} = '/usr/lib/sift';
+ $SIFT_HOME = $ENV{'SIFT_HOME'};
+ use vars qw($opt_i $opt_c $opt_d $opt_o);
+ getopts("i:c:d:o:");
+@@ -40,7 +40,7 @@
+ system("umask 006");
+ my $bin             = "$SIFT_HOME/bin";
+ my $pid             = $$;
+-my $tmp = defined($opt_o) ? "$opt_o/$pid" : "$SIFT_HOME/tmp/$pid";
++my $tmp = defined($opt_o) ? "$opt_o/$pid" : "/tmp/sift_$pid";
+ require "$bin/SIFT_subroutines.pm";
+ mkdir $tmp;
+ chmod 0777, $tmp;
+--- a/bin/SIFT_exome_nssnvs.pl
++++ b/bin/SIFT_exome_nssnvs.pl
+@@ -16,7 +16,7 @@
+ 
+ $| = 1;
+ system("umask 006");
+-$ENV{'SIFT_HOME'} = '/usr/local/projects/SIFT/sift4.0.2/';
++$ENV{'SIFT_HOME'} = '/usr/lib/sift/';
+ my $SIFT_HOME = $ENV{'SIFT_HOME'};
+ use vars qw($opt_i $opt_d $opt_o $opt_A $opt_B $opt_C $opt_D $opt_E $opt_F $opt_G $opt_H $opt_I $opt_J $opt_K $opt_L);
+ getopts("i:d:o:A:B:C:D:E:F:G:H:I:J:K:L:");
+@@ -66,7 +66,7 @@
+ my $oo12 = defined($opt_L) ? 1:0;
+ my $pid             = $$;
+ my $bin             = "$SIFT_HOME/bin";
+-my $tmp = defined($opt_o) ? "$opt_o/$pid" : "$SIFT_HOME/tmp/$pid";
++my $tmp = defined($opt_o) ? "$opt_o/$pid" : "/tmp/sift_$pid";
+ my $Variation_db_dir = $opt_d;
+ mkdir $tmp;
+ my $num_coords_per_split = 1000;

Modified: trunk/packages/sift/trunk/debian/patches/series
===================================================================
--- trunk/packages/sift/trunk/debian/patches/series	2012-02-23 13:05:53 UTC (rev 9761)
+++ trunk/packages/sift/trunk/debian/patches/series	2012-02-23 13:39:12 UTC (rev 9762)
@@ -1,2 +1 @@
 fix_perl_interpreter_and_lib_path
-fix_perl_path