Bjöern,

Here is the error message. 

An error occurred with this dataset:/bin/sh: fastq_to_fasta: command not found gzip: stdout: Broken pipe

On Oct 10, 2013, at 7:06 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:

Hi Ian,

what mean broken pipe error, can you post the error message here?

Thanks,
Bjoern

Hello,

I've got a local install of galaxy with fastx tools installed. I'm getting a broken pipe error but I'm not sure why. I install fastx using the compiler outside galaxy and it was working fine inside galaxy previously. Fastx works fine via the command line. I've checked the xml files and I don't see how galaxy cannot find the commands. I am running this off and external volume, but I don't think that matters.

Cheers
Ian





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