Author: Alastair McKinstry <mckinstry@debian.org>
Description: Don't use /usr/bin/env in Debian - call directly
Last-Updated: 2018-12-26
Forwarded: not-needed

Index: cctools-7.0.9/apps/wq_maker/wq_maker
===================================================================
--- cctools-7.0.9.orig/apps/wq_maker/wq_maker
+++ cctools-7.0.9/apps/wq_maker/wq_maker
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # wq_maker
 # 
Index: cctools-7.0.9/chirp/src/perl/chirp_jobs_perl_example.pl
===================================================================
--- cctools-7.0.9.orig/chirp/src/perl/chirp_jobs_perl_example.pl
+++ cctools-7.0.9/chirp/src/perl/chirp_jobs_perl_example.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 use v5.8.8;
 
Index: cctools-7.0.9/chirp/src/perl/chirp_perl_example.pl
===================================================================
--- cctools-7.0.9.orig/chirp/src/perl/chirp_perl_example.pl
+++ cctools-7.0.9/chirp/src/perl/chirp_perl_example.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 use v5.8.8;
 
Index: cctools-7.0.9/sand/src/sand_runCA_5.4
===================================================================
--- cctools-7.0.9.orig/sand/src/sand_runCA_5.4
+++ cctools-7.0.9/sand/src/sand_runCA_5.4
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # This file is a modified version of the runCA script distributed
 # with the Whole Genome Shotgun Assembler (wgs-assembler), which is
@@ -980,7 +980,7 @@ sub submitScript ($) {
     print F "hostname\n";
     print F "echo \$bin\n";
 
-    print F "/usr/bin/env perl \$bin/runCA $commandLineOptions\n";
+    print F "/usr/bin/perl \$bin/runCA $commandLineOptions\n";
     close(F);
 
     system("chmod +x $script");
@@ -1877,7 +1877,7 @@ sub createOverlapJobs($) {
     open(F, "> $wrk/$outDir/overlap.sh") or caFailure("can't open '$wrk/$outDir/overlap.sh'", undef);
     print F "#!" . getGlobal("shell") . "\n";
     print F "\n";
-    print F "perl='/usr/bin/env perl'\n";
+    print F "perl='/usr/bin/perl'\n";
     print F "\n";
     print F "jobid=\$SGE_TASK_ID\n";
     print F "if [ x\$jobid = x -o x\$jobid = xundefined ]; then\n";
@@ -1980,7 +1980,7 @@ sub createOverlapJobs($) {
     }
 
     open(SUB, "> $wrk/$outDir/ovlopts.pl") or caFailure("failed to open '$wrk/$outDir/ovlopts.pl'", undef);
-    print SUB "#!/usr/bin/env perl\n";
+    print SUB "#!/usr/bin/perl\n";
     print SUB "use strict;\n";
     print SUB "my \@bat = (\n";  foreach my $b (@bat) { print SUB "\"$b\",\n"; }  print SUB ");\n";
     print SUB "my \@job = (\n";  foreach my $b (@job) { print SUB "\"$b\",\n"; }  print SUB ");\n";
@@ -4046,7 +4046,7 @@ sub terminate ($) {
     $cgwDir = "$wrk/7-CGW" if (!defined($cgwDir));
 
     my $bin  = getBinDirectory();
-    my $perl = "/usr/bin/env perl";
+    my $perl = "/usr/bin/perl";
 
     my $termDir = "$wrk/9-terminator";
     system("mkdir $termDir") if (! -e "$termDir");
Index: cctools-7.0.9/sand/src/sand_runCA_6.1
===================================================================
--- cctools-7.0.9.orig/sand/src/sand_runCA_6.1
+++ cctools-7.0.9/sand/src/sand_runCA_6.1
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 use strict;
 use Config;  #  for @signame
@@ -1084,7 +1084,7 @@ sub submitScript ($) {
     #print F "hostname\n";
     #print F "echo \$bin\n";
 
-    print F "/usr/bin/env perl \$bin/runCA $commandLineOptions\n";
+    print F "/usr/bin/perl \$bin/runCA $commandLineOptions\n";
     close(F);
 
     system("chmod +x $script");
@@ -2121,7 +2121,7 @@ sub createOverlapJobs($) {
     open(F, "> $wrk/$outDir/overlap.sh") or caFailure("can't open '$wrk/$outDir/overlap.sh'", undef);
     print F "#!" . getGlobal("shell") . "\n";
     print F "\n";
-    print F "perl='/usr/bin/env perl'\n";
+    print F "perl='/usr/bin/perl'\n";
     print F "\n";
     print F "jobid=\$SGE_TASK_ID\n";
     print F "if [ x\$jobid = x -o x\$jobid = xundefined ]; then\n";
@@ -2229,7 +2229,7 @@ sub createOverlapJobs($) {
     }
 
     open(SUB, "> $wrk/$outDir/ovlopts.pl") or caFailure("failed to open '$wrk/$outDir/ovlopts.pl'", undef);
-    print SUB "#!/usr/bin/env perl\n";
+    print SUB "#!/usr/bin/perl\n";
     print SUB "use strict;\n";
     print SUB "my \@bat = (\n";  foreach my $b (@bat) { print SUB "\"$b\",\n"; }  print SUB ");\n";
     print SUB "my \@job = (\n";  foreach my $b (@job) { print SUB "\"$b\",\n"; }  print SUB ");\n";
@@ -4352,7 +4352,7 @@ sub summarizeConsensusStatistics ($) {
 
 sub terminate () {
     my $bin  = getBinDirectory();
-    my $perl = "/usr/bin/env perl";
+    my $perl = "/usr/bin/perl";
 
     my $termDir = "$wrk/9-terminator";
     system("mkdir $termDir") if (! -e "$termDir");
Index: cctools-7.0.9/sand/src/sand_runCA_7.0
===================================================================
--- cctools-7.0.9.orig/sand/src/sand_runCA_7.0
+++ cctools-7.0.9/sand/src/sand_runCA_7.0
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 use strict;
 
@@ -1205,7 +1205,7 @@ sub submitScript ($) {
 
     print F getBinDirectoryShellCode();
 
-    print F "/usr/bin/env perl \$bin/runCA $commandLineOptions\n";
+    print F "/usr/bin/perl \$bin/runCA $commandLineOptions\n";
     close(F);
 
     system("chmod +x $script");
@@ -2759,7 +2759,7 @@ sub merTrim {
         open(F, "> $wrk/0-mertrim/mertrim.sh") or caFailure("can't open '$wrk/0-mertrim/mertrim.sh'", undef);
         print F "#!" . getGlobal("shell") . "\n";
         print F "\n";
-        print F "perl='/usr/bin/env perl'\n";
+        print F "perl='/usr/bin/perl'\n";
         print F "\n";
         print F "jobid=\$SGE_TASK_ID\n";
         print F "if [ x\$jobid = x -o x\$jobid = xundefined ]; then\n";
@@ -3367,7 +3367,7 @@ sub createOverlapJobs($) {
     open(F, "> $wrk/$outDir/overlap.sh") or caFailure("can't open '$wrk/$outDir/overlap.sh'", undef);
     print F "#!" . getGlobal("shell") . "\n";
     print F "\n";
-    print F "perl='/usr/bin/env perl'\n";
+    print F "perl='/usr/bin/perl'\n";
     print F "\n";
     print F "jobid=\$SGE_TASK_ID\n";
     print F "if [ x\$jobid = x -o x\$jobid = xundefined ]; then\n";
@@ -5295,7 +5295,7 @@ sub summarizeConsensusStatistics ($) {
 
 
 sub terminate () {
-    my $perl = "/usr/bin/env perl";
+    my $perl = "/usr/bin/perl";
 
     my $termDir = "$wrk/9-terminator";
     system("mkdir $termDir") if (! -e "$termDir");
Index: cctools-7.0.9/work_queue/src/perl/work_queue_example.pl
===================================================================
--- cctools-7.0.9.orig/work_queue/src/perl/work_queue_example.pl
+++ cctools-7.0.9/work_queue/src/perl/work_queue_example.pl
@@ -1,4 +1,4 @@
-#! /usr/bin/env perl
+#! /usr/bin/perl
 
 # Copyright (c) 2010- The University of Notre Dame.
 # This software is distributed under the GNU General Public License.
Index: cctools-7.0.9/makeflow/src/makeflow_linker_perl_driver
===================================================================
--- cctools-7.0.9.orig/makeflow/src/makeflow_linker_perl_driver
+++ cctools-7.0.9/makeflow/src/makeflow_linker_perl_driver
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Copyright (C) 2013- The University of Notre Dame
 # This software is distributed under the GNU General Public License.
