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stat-lab · Jun 28, 2023 · 87e61a7 · 87e61a7
1 parent 64dc1c5
commit 87e61a7
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Showing 3 changed files with 12 additions and 1 deletion.
diff --git a/scripts/run_SVcallers/run_batch_LSF.pl b/scripts/run_SVcallers/run_batch_LSF.pl
@@ -53,6 +53,10 @@ =head1 SYNOPSIS
 my $non_human = 0;
 my $run_svcaller_dir = '';
 
+my $script_dir = '';
+$script_dir = $1 if ($0 =~ /(.+)\//);
+$run_svcaller_dir = $script_dir;
+
 my @tools;
 
 my %tool_opt;

diff --git a/scripts/run_SVcallers/run_batch_slurm.pl b/scripts/run_SVcallers/run_batch_slurm.pl
@@ -70,6 +70,10 @@ =head1 SYNOPSIS
 my $non_human = 0;
 my $run_svcaller_dir = '';
 
+my $script_dir = '';
+$script_dir = $1 if ($0 =~ /(.+)\//);
+$run_svcaller_dir = $script_dir;
+
 my @tools;
 
 my %tool_opt;

diff --git a/scripts/run_SVcallers/run_single.pl b/scripts/run_SVcallers/run_single.pl
@@ -33,6 +33,9 @@ =head1 SYNOPSIS
 die "bam is not specified:\n" if ($bam eq '');
 die "config file is not specified:\n" if ($config eq '');
 
+my $script_dir = '';
+$script_dir = $1 if ($0 =~ /(.+)\//);
+
 my $bam_base = basename ($bam);
 my $sample_name = $sample_dir_name if ($sample_dir_name ne '');
 $sample_name = $1 if ($sample_dir_name eq '') and ($bam_base =~ /(.+?)\./);
@@ -43,7 +46,7 @@ =head1 SYNOPSIS
 my $ref = '';
 my $target_chr = 'ALL';
 my $non_human = 0;
-my $run_svcaller_dir = '';
+my $run_svcaller_dir = $script_dir;
 
 my @tools;