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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