Mercurial > repos > artbio > ngsplot
diff runNGSplot.pl @ 1:4dd92ce61a5c draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'3611708386b2a2495ac9daee71a32cd990f2aa16\n'
author | artbio |
---|---|
date | Fri, 08 Dec 2017 09:25:05 -0500 |
parents | 3ca58369469c |
children | de27d4172d19 |
line wrap: on
line diff
--- a/runNGSplot.pl Wed Dec 06 19:01:53 2017 -0500 +++ b/runNGSplot.pl Fri Dec 08 09:25:05 2017 -0500 @@ -22,7 +22,7 @@ my $randfile2 = $randfile; $randfile2 =~ s/config\.txt/logfile/gm; -my $outfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile"); +my $outfile = File::Spec->catfile($ENV{"PWD"},"ngsplot.config.txt"); open(FILE,">$outfile"); for (my $i=1;$i<=$numsamples;$i++) { @@ -87,7 +87,7 @@ $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS"; } -my $logfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile2"); +my $logfile = File::Spec->catfile($ENV{"PWD"},"ngsplot.log"); open(FILE2,">>$logfile"); my $cmd5="pwd >> $logfile 2>&1"; system($cmd5); @@ -112,17 +112,14 @@ print("$cmd\n"); my $cmd2="cp data.zip $O"; my $cmd3="rm $outfile"; -my $cmd4="rm $logfile"; syswrite(FILE2, "\n$cmd\n"); syswrite(FILE2, "\n$cmd2\n"); syswrite(FILE2, "\n$cmd3\n"); -syswrite(FILE2, "\n$cmd4\n\n"); # print STDERR "cmd: $cmd\n"; system($cmd); system($cmd2); -#system($cmd3); -#system($cmd4); +system($cmd3); close(FILE2);