Discussion :

[karaudrey88]

Bonjour je lance un qsub depuis un script perl
Voici le script

Code :

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#generate qsub file and launch it
my $qsuboutfile3 = "summary_$chr.qsub";
open (QSUB,">summary_chr/$chr/$qsuboutfile3")or die "\nError : $qsuboutfile3 file could not be created: $!\n";
print QSUB qq(#!/bin/bash
#\$ -S /bin/bash
#\$ -V
#\$ -M $users{$user}
#\$ -m e
#\$ -o $qsuboutfile3.out
#\$ -e $qsuboutfile3.err
#\$ -cwd
#\$ -q long.q
#\$ -pe thread 3
# command(s):
hostname >&2
 
for sample in $(ls *_rmdup_$chr/_find_CNV.txt)
	do cat $sample > summary_$chr.txt
done
sort -t: -k 3,3 -n  summary_$chr.txt  | uniq -c - > summary_$chr/_sorted.txt
 
);
close QSUB;
#launch qsub job if asked
my $jobid;
if ($submit eq "yes") {
	my $dependencies = "-hold_jid ".join(",",@compare_samples_jobs);
	my $instruction = "cd summary_chr/$chr;qsub $dependencies $qsuboutfile3 | awk '{print \$3}'";
	$jobid=qx{$instruction};
	chomp $jobid;
	$summary_samples_jobs{$chr}=$jobid;
	print STDERR ".";
	}

Et quand je fais tourner le script voici ce qu'il me dit

Global symbol "$sample" requires explicit package name at /projet/gabi/save/kbarrilliot/bin/sge_CNVcapt_FINAL_essai.pl line 284.

Et ce $sample doit etre compris dans le script bash et non dans le perl.
Merci de votre aide

[djibril]

Code :

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#generate qsub file and launch it
my $qsuboutfile3 = "summary_$chr.qsub";
open( QSUB, '>', "summary_chr/$chr/$qsuboutfile3" )
  or die "\nError : $qsuboutfile3 file could not be created: $!\n";
print QSUB <<'PROG';
#!/bin/bash
#\$ -S /bin/bash
#\$ -V
#\$ -M $users{$user}
#\$ -m e
#\$ -o $qsuboutfile3.out
#\$ -e $qsuboutfile3.err
#\$ -cwd
#\$ -q long.q
#\$ -pe thread 3
# command(s):
hostname >&2
 
for sample in $(ls *_rmdup_$chr/_find_CNV.txt)
	do cat $sample > summary_$chr.txt
done
sort -t: -k 3,3 -n  summary_$chr.txt  | uniq -c - > summary_$chr/_sorted.txt
 
PROG
close QSUB;
 
#launch qsub job if asked
my $jobid;
if ( $submit eq "yes" ) {
  my $dependencies = "-hold_jid " . join( ",", @compare_samples_jobs );
  my $instruction = "cd summary_chr/$chr;qsub $dependencies $qsuboutfile3 | awk '{print \$3}'";
  $jobid = qx{$instruction};
  chomp $jobid;
  $summary_samples_jobs{$chr} = $jobid;
  print STDERR ".";
}

Au moins, cela évite les interpolations.