Ian,

To help track down this issue, could you provide the revision of Galaxy you're running?


   --Dave B.

On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:
Hello all,

I'm still dealing with an error regarding Fastx toolkit. I all of the
fastx commands in my /usr/local and I have installed fastx via the
toolshed. I'm am still receiving the following error. Any help would be
great.

Cheers
Ian

An error occurred with this dataset://bin/sh: fasta_formatter: command
not found cat: stdout: Broken pipe/
/
/
/
/
On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
<bioinformatics....@gmail.com <mailto:bioinformatics....@gmail.com>> wrote:

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.gruen...@pharmazie.uni-freiburg.de
<mailto:bjoern.gruen...@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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