comparison runNGSplot.pl @ 1:4dd92ce61a5c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'3611708386b2a2495ac9daee71a32cd990f2aa16\n'

0:3ca58369469c

my $randfile = rand(100)."\.config\.txt";
my $randfile2 = $randfile;
$randfile2 =~ s/config\.txt/logfile/gm;

my $outfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile");
open(FILE,">$outfile");

for (my $i=1;$i<=$numsamples;$i++) {
   my $bamfile=shift(@inputs);
   my $reffile=shift(@inputs);

if ($GO eq 'km') {
   $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS";
}

my $logfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile2");
open(FILE2,">>$logfile");
my $cmd5="pwd >> $logfile 2>&1";
system($cmd5);
my $NGSPLOT = $ENV{"NGSPLOT"};
my $cmd='';

}

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);

close(FILE2);

1:4dd92ce61a5c

my $randfile = rand(100)."\.config\.txt";
my $randfile2 = $randfile;
$randfile2 =~ s/config\.txt/logfile/gm;

my $outfile = File::Spec->catfile($ENV{"PWD"},"ngsplot.config.txt");
open(FILE,">$outfile");

for (my $i=1;$i<=$numsamples;$i++) {
   my $bamfile=shift(@inputs);
   my $reffile=shift(@inputs);

if ($GO eq 'km') {
   $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS";
}

my $logfile = File::Spec->catfile($ENV{"PWD"},"ngsplot.log");
open(FILE2,">>$logfile");
my $cmd5="pwd >> $logfile 2>&1";
system($cmd5);
my $NGSPLOT = $ENV{"NGSPLOT"};
my $cmd='';

}

print("$cmd\n");
my $cmd2="cp data.zip $O";
my $cmd3="rm $outfile";
syswrite(FILE2, "\n$cmd\n");
syswrite(FILE2, "\n$cmd2\n");
syswrite(FILE2, "\n$cmd3\n");

# print STDERR "cmd: $cmd\n";
system($cmd);
system($cmd2);
system($cmd3);

close(FILE2);