Dave,

Thanks for the information. I've added the bin folder to the fastx_toolkit as 
described in the document. I also copied the executables from /usr/local/bin 
for fastx_toolkit to the devteam/backage_fastx_toolkit/0_0_13/ec66ae4c269b/bin 
as described. I've restarted Galaxy but I'm still getting an error.  My PATH 
has both /usr/local/bin and the devfolder in therm. I'm not sure why this won't 
work. 

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

I have my PATH set as well as the env.sh and my ./bash_profile. Again this all 
works fine from the command line. I don't know where else Galaxy is trying to 
find the fastx commands. This is very frustrating.

Cheers
Ian

On Oct 14, 2013, at 12:05 PM, Dave Bouvier <d...@bx.psu.edu> wrote:

> 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 <n...@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 <d...@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....@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
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> ___________________________________________________________
>>>>>>> Please keep all replies on the list by using "reply all"
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>>>>>>> 
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>>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> ___________________________________________________________
>>>>>> Please keep all replies on the list by using "reply all"
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>>>>>> 
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>>>>>> http://galaxyproject.org/search/mailinglists/
>>>>> 
>>>> 
>>>> 
>>>> 
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>   http://lists.bx.psu.edu/
>>>> 
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>>>> 
>> 
>> 

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