On Fri, Aug 3, 2012 at 11:07 PM, Nikhil Joshi <najo...@ucdavis.edu> wrote:
> Hey Mo,
>
> So I'm figuring out the same issues, and I think I have been able to
> figure it out.... but for sure you need to uncomment the
> tool_config_file and tool_path lines in your universe_wsgi.ini file,
> probably should create a new directory one above your install
> directory called "shed_tools", and then restart galaxy.  I also ran
> into the problem where I needed to create a TMPDIR shell variable that
> pointed to the correct tmp directory.  I know you guys don't like the
> command line, so if this sounds like gibberish to you, I'm hoping the
> galaxy team can provide a simpler solution.
>
> - Nik.
>
> P.S. I'm working on creating a DESeq repository that can be
> automatically installed from the toolbox.  I will let you know when I
> am successful.  It was nice to meet you at the conference! :)
>
> On Wed, Aug 1, 2012 at 9:07 AM, Mohammad Heydarian <mheydar...@gmail.com> 
> wrote:
>> Thanks for this.
>>
>> I updated my local version of Galaxy Cloudman and tried loading a tool and
>> got a new error:
>>
>> The tool_config_file setting in universe_wsgi.ini must include at least one
>> shed tool configuration file name with a <toolbox> tag that includes a
>> tool_path attribute value which is a directory relative to the Galaxy
>> installation directory in order to automatically install tools from a Galaxy
>> tool shed (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is
>> <toolbox tool_path="../shed_tools">).
>>
>> See the Automatic installation of Galaxy tool shed repository tools into a
>> local Galaxy instance section of the Galaxy tool shed wiki for all of the
>> details.
>>
>>
>> Any help interpreting this would be greatly appreciated!
>>
>>
>>
>> Cheers,
>>
>> Mo Heydarian
>>
>>
>>
>>
>> On Tue, Jul 31, 2012 at 4:11 PM, Dannon Baker <dannonba...@me.com> wrote:
>>>
>>> The problem here is that the public toolshed interface has been updated
>>> more recently than the galaxy install on that cloud instance.   You should
>>> be good to go if you update galaxy (possible through the admin interface at
>>> <your_ec2_instance>/cloud/admin/) to the latest version.
>>>
>>> -Dannon
>>>
>>> On Jul 31, 2012, at 12:11 PM, Mohammad Heydarian <mheydar...@gmail.com>
>>> wrote:
>>>
>>> > Hi Galaxy Community!
>>> > Hope all is well.
>>> >
>>> > I've been trying to install some tools in my Galaxy Cloudman instance
>>> > (using image:  ami-da58aab3 ) from the main toolshed. When I try to 
>>> > "install
>>> > to local Galaxy" I get the error:
>>> >
>>> > Not Found
>>> >
>>> > The resource could not be found.
>>> > No action for /admin_toolshed/prepare_for_install
>>> >
>>> >
>>> >
>>> > I have tried to load tools on a couple of different Cloudman instances
>>> > and tried to load a variety of tools and end up with the same error. Any
>>> > help would be fantastic.
>>> >
>>> > Cheers,
>>> > Mo Heydarian
>>> >
>>> >
>>> >
>>> > ___________________________________________________________
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>>>
>>
>>
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>
>
>
> --
> Nikhil Joshi
> Bioinformatics Analyst/Programmer
> UC Davis Bioinformatics Core
> http://bioinformatics.ucdavis.edu/
> najoshi -at- ucdavis -dot- edu
> 530.752.2698 (w)



-- 
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
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