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.umd@gmail.com <mailto:bioinformatics.umd@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.gruening@pharmazie.uni-freiburg.de <mailto: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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