canu should use the perl it is run with

[EricDeveaud]

Hello,

canu may be set to. use a specific perl via sheebang edition, or launched using a specific perl not in user path.

when run canu check for perl in user path via Execution.pm using which perl that may return incorrect result.
eg

rpm_maker:canu/2.2 > which perl
/usr/bin/perl
rpm_maker:canu/2.2 > /opt/gensoft/adm/bin/perl /opt/gensoft/exe/canu/2.2/bin/canu -p ecoli      -d ecoli-pacbio      genomeSize=4.8m      -pacbio ../../datas/canu/pacbio.fastq

but canu will found and use /usr/bin/perl

see

Found perl:
   /usr/bin/perl
   This is perl 5, version 26, subversion 3 (v5.26.3) built for x86_64-linux-thread-multi

and will generate some perl scripts using this one.

won't it be more logical, as canu knows the perl interpreter it was run with using $^X see: https://perldoc.perl.org/perlvar#$EXECUTABLE_NAME

to modifiy Execution.pm to. use. this predefined variable, this way.

--- lib/perl5/canu/Execution.pm.orig	2023-03-18 10:28:23.392717937 +0000
+++ lib/perl5/canu/Execution.pm	2023-03-18 10:30:01.344031609 +0000
@@ -440,9 +440,9 @@
     $string .= "#  Report paths.\n";
     $string .= "\n";
     $string .= "echo \"\"\n";
-    $string .= "echo \"Found perl:\"\n";
-    $string .= "echo \"  \" `which perl`\n";
-    $string .= "echo \"  \" `perl --version | grep version`\n";
+    $string .= "echo \"using perl:\"\n";
+    $string .= "echo \"  \" $^X\n";
+    $string .= "echo \"  \" `$^X --version | grep version`\n";
     $string .= "echo \"\"\n";
     $string .= "echo \"Found java:\"\n";
     $string .= "echo \"  \" `which $javaPath`\n";
@@ -686,7 +686,7 @@
     print F "rm -f canu.out\n";
     print F "ln -s $scriptOut canu.out\n";
     print F "\n";
-    print F "/usr/bin/env perl \\\n";
+    print F "$^X \\\n";
     print F "\$bin/" . basename($0) . " " . getCommandLineOptions() . " canuIteration=" . getGlobal("canuIteration") . "\n";
     close(F);

regards

Eric