Question: (Closed) How to solve this error: cut: write error: Broken pipe
1
GPS • 20 wrote:
I am a new Ubuntu user I installed the Galaxy Project and integrate tool softsearch and then execute the tool by using two commands:
samtools index Small_test.bam
perl ./SoftSearch.pl -b Small_test.bam -f chr1.small.faafter execution of softsearch tool it will show the error
cut: write error: Broken pipe
so please tell me how i solve this error ?
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modified 4.6 years ago
by
Martin Čech ♦♦ 4.9k
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written
4.6 years ago by
GPS • 20
Are you running softsearch via commandline or within Galaxy? Can you point us to the used Galaxy wrapper?
yes i integrate a softsearch as a tool in galaxy and write this command
in command tag of XML file inside the galaxy.
You need to separate both commands, with ';'. Please also provide the complete XML file, if possible.
hii
i was separate both the command by ' ; ' .but still i getting same problem.
This is 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
</command>
<outputs>
<data format="tabular" name="out_file1" />
</outputs>
<help>
</help>
</tool>
please tell me am i doing correct or wrong.