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Question: How to integrate and run SoftSearch tool in galaxy.
0
gravatar for Shirish
4.6 years ago by
Shirish • 20
India
Shirish • 20 wrote:

Hi,

I am Shirish, I installed SoftSearch tool in my system, I run successfully it on command prompt but when I run it from GUI using Galaxy then it will produce output with error  "write:Broken pipe ", for the execution of SoftSearch I refer  this link " https://code.google.com/p/softsearch/ ".

     Please can anyone help me how to resolve this error.

 

Thanks..
rna-seq tool galaxy samtools bam • 1.7k views
ADD COMMENT • link •
modified 4.6 years ago by Martin Čech ♦♦ 4.9k • written 4.6 years ago by Shirish • 20

Hi,

can you point us to the wrappers your are using?

ADD REPLY • link written 4.6 years ago by Bjoern Gruening ♦ 5.1k

hi,

For running SoftSearch in Galaxy I wrote command in xml file, like this..

<command interpreter="perl">/home/plus91/2.4/src/ samtools index Small_test.bam ; /home/plus91/2.4/src/SoftSearch.pl -b /home/plus91/2.4/src/Small_test.bam -f /home/plus91/2.4/src/chr1.small.fa $out_file1

</command> 

and i follow this link for integrate  the softsearch tool in galaxy.

 

"https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial".

can you please tell me I am correct or not.?

 

 

ADD REPLY • link modified 4.6 years ago by Martin Čech ♦♦ 4.9k • written 4.6 years ago by Shirish • 20

You are on the right way, yes. But we can't help you without having a look into the complete XML file. For example there is a white space before samtools? That seems to be wrong.

ADD REPLY • link written 4.6 years ago by Bjoern Gruening ♦ 5.1k

Thanks Bjoern,

here is my xml code: 

<tool id="SoftSearch" name="SoftSearch">
      <description>for Structure Variation</description>
       <command interpreter="perl">/home/plus91/2.4/src/ samtools index Small_test.bam ; /home/plus91/2.4/src/SoftSearch.pl -b /home/plus91/2.4/src/Small_test.bam -f /home/plus91/2.4/src/chr1.small.fa $out_file1</command>  
  <outputs>
    <data format="fasta" name="out_file1" />
  </outputs>    
 <help>
</help>
</tool>
      

ADD REPLY • link modified 4.6 years ago by Martin Čech ♦♦ 4.9k • written 4.6 years ago by Shirish • 20
1
gravatar for Bjoern Gruening
4.6 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

you are running it via the perl interpreter, but samtools is not perl. remove the 'interpreter' from your command tag and fix the white spaces in your command (between the path and samtools). Hopefully that will work.

Cheers,

Bjoern
ADD COMMENT • link written 4.6 years ago by Bjoern Gruening ♦ 5.1k

Thanks Bjoern,

ADD REPLY • link written 4.5 years ago by shirish.ambhore • 0
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