Re: [galaxy-dev] Error in loading tools.

[Nikhil Joshi]

On Fri, Aug 3, 2012 at 11:07 PM, Nikhil Joshi  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  
> 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  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  tag is
>> ).
>>
>> 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  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
>>> /cloud/admin/) to the latest version.
>>>
>>> -Dannon
>>>
>>> On Jul 31, 2012, at 12:11 PM, Mohammad Heydarian 
>>> 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
>>> >
>>> >
>>> >
>>> > ___
>>> > 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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>
>
>
> --
> 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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Re: [galaxy-dev] Error in loading tools.

[Mohammad Heydarian]

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 ** 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
** tag
is **).

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  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
> /cloud/admin/) to the latest version.
>
> -Dannon
>
> On Jul 31, 2012, at 12:11 PM, Mohammad Heydarian 
> 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
> >
> >
> >
> > ___
> > 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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Re: [galaxy-dev] Error in loading tools.

[Dannon Baker]

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 
/cloud/admin/) to the latest version.

-Dannon

On Jul 31, 2012, at 12:11 PM, Mohammad Heydarian  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
> 
> 
> 
> ___
> 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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