bugBAM MDS plot - Bugs: bug #45393, Won't plot because it can't find...

 
 

bug #45393: Won't plot because it can't find bammds_plot.r

Submitted by:  None
Submitted on:  Wed 24 Jun 2015 03:36:17 PM UTC  
 
Category: NoneSeverity: 3 - Normal
Item Group: NoneStatus: None
Privacy: PublicAssigned to: None
Open/Closed: Open

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Wed 24 Jun 2015 03:36:17 PM UTC, original submission:

Can't exec "bammds_plot.r": No such file or directory at /gpfs/hpchome/cls83/bammds-20140602/src/bammds line 4807.

# bammds_plot.r tmp/Han_700000reads_hg19,HanPop.HanIndv_70000,Wollstein.hg19.chr21.chr22.one_allele.30.20.asd tmp/Han_700000reads_hg19,HanPop.HanIndv_70000,Wollstein.hg19.chr21.chr22.one_allele.legend.filled.csv tmp/Han_700000reads_hg19,HanPop.HanIndv_70000,Wollstein.hg19.chr21.chr22.one_allele.30.20.pdf
command_in_path_or_exit("bammds_plot.r");
my $mds = $opt::mds ? "T" : "F";
my $pca = $opt::pca ? "T" : "F";
my $sum = $opt::nosum ? "F" : "T";
if(not $opt::pca and not $opt::mds) {
$mds = "T";
}
my $tmp = $ENV{'TMPDIR'};
# When installing local packages $TMPDIR must be /tmp (donno why)
$ENV{'TMPDIR'} = undef;
debug("bammds_plot.r $asd_file $legend $legend_filled $plot_file $xvector $yvector $mds $pca $sum\n");
print `bammds_plot.r $asd_file $legend $legend_filled $plot_file $xvector $yvector $mds $pca $sum`;
$ENV{'TMPDIR'} = $tmp;
}

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