Re: [galaxy-dev] Script not working in Galaxy

2012-06-24 Thread Ciara Ledero 
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.
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Re: [galaxy-dev] Script not working in Galaxy

2012-06-23 Thread Thon Deboer 
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=perlexec_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 
 21`;
 
 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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[galaxy-dev] Script not working in Galaxy

2012-06-21 Thread Ciara Ledero 
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=perlexec_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 21`;

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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