Hi all,

 

I have integrated a script that runs rsem in Galaxy and the following is the .xml that shows it in Galaxy:

 

<tool id="sixthStep" name="RESM">
 <description></description>
 <command interpreter="perl">exec_rrsem.pl $input1 $input2 $input3 $output1 $output2
 </command>
 <inputs>
  <param name="input1" format="fasta" type="data" label="Transcript from OASES"/>
  <param name="input2" format="fastq" type="data" label="Left read: " />
  <param name="input3" format="fastq" type="data" label="Right read: "/> 
 </inputs>
 <outputs>
  <data name="output1" format="text" />
  <data name="output2" format="text" />
 </outputs>
</tool>

 

And here is exec_rrsem.pl, the file that accepts the parameters and sets everything up:

 

$genes = $ARGV[3];
$isoforms = $ARGV[4];

$trans = $ARGV[0];
$left = $ARGV[1];
$right = $ARGV[2];

 

$directory = "/home/applications/galaxy-dist/tools/VELVET-OASES";

 

$transcript = "$directory/trans.fa";
$left_read = "$directory/left_read.fastq";
$right_read = "$directory/right_read.fastq";

 

symlink $trans, $transcript;
symlink $left, $left_read;
symlink $right, $right_read;

 

@out = `perl /home/applications/galaxy-dist/tools/VELVET-OASES/run_rsem.pl 2>&1`;

run_rsem.pl is the actual script that runs the rsem programs. I'm wondering though, why Galaxy isn't executing the command properly. This is the same pattern I've used in other programs that I've integrated with Galaxy, so it came as a surprise to me when this one didn't run. Is there something wrong with my script? By the way, when I run exec_rrsem.pl from the konsole, it works just fine. Any insights on this?

 

Thanks a lot!

 

CL