Question: Custom tool in local bio Linux Galaxy does not work.
1
gravatar for Grishin
3.2 years ago by
Grishin10
Russian Federation
Grishin10 wrote:

For example, i want to have an opportunity to convert sam to bam via samtools in my local galaxy. I have such definition file:

<tool id="samtools" name="samtools">
  <descripton>run samtools</descripton>
  <command>samtools view -bS $input > $output</command>
  <inputs>
    <param format="sam" name="input" type="data" label="Select .sam file"/>
  </inputs>
  <outputs>
    <data format="bam" name="output" />
  </outputs>
  <help>
This tool convert .sam file into .bam file
  </help>
</tool>

Also i have a simple .sam file test.sam. I upload this file into galaxy, then i try to use samtools and get an error(screenshot at the bottom of the page). What am i doing wrong?
I apologize in advance in case of stupidity of the question.

dev tool galaxy samtools • 1.0k views
ADD COMMENTlink modified 3.2 years ago by Martin Čech ♦♦ 4.5k • written 3.2 years ago by Grishin10
1

Your tool seems to be working correctly, the dataset status is set to error because samtools printed something to the stderr and you did not teach the tool to handle it. See Dannon's answer on how to solve it.

ADD REPLYlink written 3.2 years ago by Martin Čech ♦♦ 4.5k
2
gravatar for Dannon Baker
3.2 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

The problem here is that your wrapper isn't capturing extra information printed to stderr, which galaxy then perceives as an error. The correct way to handle this is to add logic to your tool wrapper for detecting success. See information here; https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Dannon Baker3.7k

Thank you, now everything is OK!

ADD REPLYlink written 3.2 years ago by Grishin10
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