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...
Thon de Boer, Ph.D.
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">
> <command interpreter="perl">exec_rrsem.pl $input1 $input2 $input3 $output1
> <param name="input1" format="fasta" type="data" label="Transcript from
> <param name="input2" format="fastq" type="data" label="Left read: " />
> <param name="input3" format="fastq" type="data" label="Right read: "/>
> <data name="output1" format="text" />
> <data name="output2" format="text" />
> And here is exec_rrsem.pl, the file that accepts the parameters and sets
> everything up:
> $genes = $ARGV;
> $isoforms = $ARGV;
> $trans = $ARGV;
> $left = $ARGV;
> $right = $ARGV;
> $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
> 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!
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