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

Submitter:  None
Submitted:  Wed 24 Jun 2015 03:36:17 PM UTC
   
 
Category:  None Severity:  3 - Normal
Item Group:  None Status:  None
Privacy:  Public Assigned to:  None
Open/Closed:  Open
* Mandatory Fields

Add a New Comment Rich Markup
   

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;
}


Anonymous

 

(Note: upload size limit is set to 16384 kB, after insertion of the required escape characters.)

Attach Files:
   
   
Comment:
   

No files currently attached

 

Depends on the following items: None found

Items that depend on this one: None found

 

CC list is empty

 

There are 0 votes so far. Votes easily highlight which items people would like to see resolved in priority, independently of the priority of the item set by tracker managers.

Only logged-in users can vote.

 

No changes have been made to this item

Back to the top

Powered by Savane 3.13-02a9.
Corresponding source code