Ian,

Although the fastx tools have been migrated to the tool shed, this migration has not yet been released to the stable branch, but is planned to be included in the upcoming release. In the meantime, I would suggest maintaining the binary installation of the fastx dependencies using one of the options described on this page:

http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

After the release, you can then run the automated process to install the migrated tools from the tool shed as described here:

http://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution

  --Dave B.

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

Dave,

Here is my information on the revision.

$ hg heads | more
changeset:   10421:a477486bf18e
branch:      stable
tag:         tip
user:        Nate Coraor <nate@bx.psu.edu>
date:        Thu Sep 26 11:02:58 2013 -0400
summary:     Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased.

changeset:   10411:c42567f43aa7
user:        greg
date:        Mon Aug 19 13:19:56 2013 -0400
summary:     Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy.

On Oct 14, 2013, at 9:11 AM, Dave Bouvier <dave@bx.psu.edu> wrote:

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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