Script not working in Galaxy
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 <#@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
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 thondeboer@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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Thanks for the reply! Weird enough though, the problem went away before I read this message. Still, thanks for the reply. We could use it for future reference.
participants (2)
-
Ciara Ledero -
Thon Deboer