Question: Custom tool in local bio Linux Galaxy does not work.
1
Grishin • 10 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.
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modified 3.8 years ago
by
Martin Čech ♦♦ 4.9k
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written
3.8 years ago by
Grishin • 10
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.