On Sep 13, 2012, at 6:15 PM, Paul Tanger wrote:
> Thanks for your help with this. So I updated to the latest version,
> but didn't read the instructions about creating a tools directory and
> so I have repositories stuck in limbo, like described here:
> -------------------------------------------------------------------------------------------------------------
> Re: [galaxy-dev] Can't get automatic toolshed installation to work....
> Greg Von Kuster
> Fri, 03 Aug 2012 17:58:58 -0700
>
> To get the repositories out of the limbo state, you'll have to get into your
> database and run the following sql command. Doing this will allow you to
> install those repositories that were in limbo. After they are installed, you
> can uninstall them if you want to. The case on the Strings is necessary.
>
> update tool_shed_repository set status = 'New' where status = 'Cloning';
>
> It was great to talk with you at the conference as well!
>
> Greg
>
http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg06437.html
> -------------------------------------------------------------------------------------------------------------
>
> I'm just using the sqlite that came with the galaxy-dist, so I don't
> know how to enter that sql command?
>
> On Thu, Sep 13, 2012 at 3:58 PM, Greg Von Kuster <
greg@bx.psu.edu> wrote:
>> Hi Paul,
>>
>> You have to be running the latest Galaxy dist release from
>>
https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance.
>> Your repository tip should be e6444e7a1685.
>>
>> Greg Von Kuster
>>
>> On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
>>
>> Hmm, ok this tool shed is all new to me. I followed the instructions
>> until when I click on the "preview and install", I get this error:
>>
>> Not Found
>>
>> The resource could not be found.
>> No action for /admin_toolshed/prepare_for_install
>>
>> On Thu, Sep 13, 2012 at 2:51 PM, Greg Von Kuster <
greg@bx.psu.edu> wrote:
>>
>> Hi Paul,
>>
>>
>> It seems that you probably did not use the Emboss tools in your local Galaxy
>> instance before (maybe you have a new instance). If this is the case, you
>> can install the emboss_datatypes repository and the emboss_5 repository from
>> the main Galaxy tool shed using the Admin UI features on your local galaxy
>> instance. See the following sections of the tool shed wiki for details.
>>
>>
>>
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
>>
>>
>>
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_data_types_into_a_local_Galaxy_instance
>>
>>
>> Greg Von Kuster
>>
>>
>>
>> On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
>>
>>
>> Hi,
>>
>>
>> I'm trying to enable all the emboss tools on a local galaxy install.
>>
>> I found this tidbit (below) which I thought might help, but when I
>>
>> look at the tool_conf.xml, I don't see a list of emboss tools to
>>
>> uncomment.
>>
>> What should I try next?
>>
>>
>>
>> Kelly Vincent kpvincent at
bx.psu.edu
>>
>> Fri Jan 14 11:26:37 EST 2011
>>
>> Previous message: [galaxy-dev] Restricted user builds
>>
>> Next message: [galaxy-dev] API connection error
>>
>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>>
>> Rob,
>>
>>
>> When you start the Galaxy server, it looks in tool_conf.xml for which
>>
>> tools to load. Note that functional tests use tool_conf.xml.sample,
>>
>> and we leave the EMBOSS tools commented out in that file, so your
>>
>> tool_conf.xml file will still have them commented out if you haven't
>>
>> changed that. Uncomment the relevant lines and the EMBOSS tools should
>>
>> show up. After making changes to tool_conf.xml, you'll have to restart
>>
>> the server.
>>
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>>
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>>
>>
>>
>>
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