Hi Paul,

You should be able to get things working using the same sql command in the 
email below.  This process will be a new UI feature in the next Galaxy release.

Greg Von Kuster

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 <g...@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 <g...@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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