Check the Paster.log file...You probably will see an error there when it tries 
to load your file and it will be a clue how to fix it...
Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839
thondeb...@me.com
LinkedIn Profile




On Jun 21, 2012, at 5:55 PM, Ciara Ledero wrote:

> 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
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