Thanks for the corrections Will, and I'm glad this worked for you.

Greg Von Kuster

On Jun 18, 2014, at 12:22 PM, Will Holtz <> wrote:

> Hi Greg,
> I used the toolshed bootstrapping script and was able to get capsules from 
> testtoolshed to import. Here are a couple of notes that you may find 
> interesting.
> 1) In a few places you reference the directory 
> ~/lib/tool_shed/scripts/api/bootstrap_from_toolshed/ and these should be 
> changed to ~/lib/tool_shed/scripts/bootstrap_from_toolshed/
> 2) I was worried that 'use_remote_user=True' was going to negatively impact 
> the bootstrap process, as accounts are being created that don't exist in 
> LDAP. However, there didn't appear to be any such negative interaction. In 
> user_info.xml I used my email address that maps to my LDAP login 
> (, a long gibberish password, and wholtz for my username.
> Thank you for your help Greg.
> -Will
> On Tue, Jun 17, 2014 at 7:51 PM, Greg Von Kuster <> wrote:
> Hello Will,
> On Jun 17, 2014, at 6:06 PM, Will Holtz <> wrote:
>> It looks like Dave fixed this issue in 4c58aa19a3d7. Thank you!
>> However I am still having import issues. I am now getting the message:
>> "Archive of repository package_bowtie_0_12_7 owned by devteam
>> Import failed: repository owner devteam does not have an account in this 
>> Tool Shed."
>> This is on a local toolshed running 9b78595ec11 where I am performing the 
>> input from an admin account. I'm guessing the issue is that I have 
>> 'use_remote_user=True' for LDAP authentication and that means that a devteam 
>> account cannot be automatically created to allow this capsule to be added 
>> without modification.
> Sorry you're still running into problems.  No regular development or testing 
> is done using the use_remote_user setting due to resource limitations.
>> Perhaps on import of a capsule (by an administrator) they could be given the 
>> option of preserving the existing owners or re-assigning ownership to an 
>> existing user (defaulting to self)?
> This would be non-trivial, and probably would introduce fragility into the 
> process.  However, I believe there is a solution (see my next comment) 
> although I haven't tested it with the use_remote_user setting.
>> Of course, what I really want is inter-toolshed dependancies. Maybe I'm 
>> missing something, but I'm finding it quite painful just to get a tool 
>> development environment setup that makes use of any existing repositories.
> There was some work done in this area in the June 2, 2014 release.  Here is 
> some information for more easily setting up a local development Tool Shed 
> that use new features introduced in the release.  Hopefully this will help.
> Greg Von Kuster
> Bootstrapping a New Development Tool Shed
> The June 2, 2014 release introduces the ability to easily bootstrap a new 
> development Tool Shed to prepare it for importing a repository capsule whose 
> contained repositories can be used as the foundation for developing new 
> Galaxy tools and other utilities.  This development Tool Shed can be treated 
> as a component in a multi-step process that simplifies and streamlines Galaxy 
> tool development and validation in the local Tool Shed and moving the 
> validated repositories into the test or main public Galaxy Tool Sheds.  Tool 
> Shed framework enhancements included in the June 2, 2014 release support this 
> overall process, which will be explained fully in a future article.  Here 
> we’ll restrict our discussion to highlights of the enhancements.
> Several files are included in a new directory named 
> ~/lib/tool_shed/scripts/api/bootstrap_from_toolshed.  The file named 
> user_info.xml.sample should be copied to a file  with the same name, but 
> eliminating the .sample extension (i.e., user_info.xml).  The information in 
> this file is used to automatically create a new “admin” user account in your 
> local development Tool Shed.  This should be the account you use in the test 
> and main public Galaxy Tool Sheds if you plan to export your work from your 
> development Tool Shed and import it into one or both of the public Tool Sheds.
> If you plan to use this new bootstrapping process, make sure your local 
> development Tool Shed environment is pristine:
> The hgweb.config file must be empty or missing (it will automatically get 
> created if it doesn’t exist) and the configured location for repositories 
> must be an empty directory.
> The configured database must be new and not yet migrated.
> Make sure the 
> ~/lib/tool_shed/scripts/api/bootstrap_from_toolshed/user_info.xml file 
> contains the desired account information.
> The ~/ script, used for starting up a Tool Shed, has been 
> enhanced to enable this bootstrapping process by using a new 
> -bootstrap_from_tool_shed flag.  Here’s an example.
> %sh -bootstrap_from_tool_shed
> The above example will initialize a local development Tool Shed (here we’ll 
> assume its URL is http://localhost:9009) by bootstrapping from the main 
> public Galaxy Tool Shed.  The bootstrapping process will perform the 
> following actions in the order listed.
> Ensure the Tool Shed environment is pristine (e.g., empty hgweb.config file 
> and new database that has not been migrated).
> Copy all .sample files configured in
> Run the database migration process.
> Execute the script 
> ~/lib/tool_shed/scripts/bootstrap_tool_shed/ 
> ~/tool_shed_wsgi.ini to create a new user and an associated API key using the 
> information defined in 
> ~/lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.
> Automatically modify the ~/tool_shed_wsgi.ini file to configure the above 
> user as an admin_user for the Tool Shed.
> Start the Tool Shed web server.
> Execute the script ~/lib/tool_shed/scripts/api/ -a <api_key> 
> -f -t http://localhost:9009.
> Execute the script ~/lib/tool_shed/scripts/api/ -a 
> <api_key> -f http://toolshed.g2.bx.psu./edu -t http://localhost:9009.
> Executing the script using this new flag as shown in the 
> example above will create a new local development Tool Shed with an admin 
> user automatically created and configured and the Tool Shed populated with 
> all of the users and categories from the main public Galaxy Tool Shed.  This 
> simplifies the process of exporting a repository capsule from the main public 
> Tool Shed and importing it into the local development Tool Shed for further 
> development.
>> thank you for your help,
>> -Will
>> On Wed, Jun 11, 2014 at 12:40 PM, Will Holtz <> wrote:
>> I am now able to export capsules from the main/test toolsheds -- thanks 
>> Dave! When attempting to import these capsules into my local toolshed 
>> (latest_2014.06.02 for changeset fb68af9a775a) I receive the following error:
>> URL:
>> File 
>> '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/', 
>> line 149 in __call__
>>   app_iter = self.application(environ, sr_checker)
>> File 
>> '/home/galaxy/galaxy-dist/eggs/Paste-',
>>  line 106 in __call__
>>   environ,
>> File 
>> '/home/galaxy/galaxy-dist/eggs/Paste-', 
>> line 543 in intercept_output
>>   app_iter = application(environ, replacement_start_response)
>> File 
>> '/home/galaxy/galaxy-dist/eggs/Paste-', 
>> line 84 in __call__
>>   return self.application(environ, start_response)
>> File 
>> '/home/galaxy/galaxy-dist/lib/galaxy/webapps/tool_shed/framework/middleware/',
>>  line 74 in __call__
>>   return environ, start_response )
>> File 
>> '/home/galaxy/galaxy-dist/eggs/Paste-',
>>  line 633 in __call__
>>   return self.application(environ, start_response)
>> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/', line 132 
>> in __call__
>>   return self.handle_request( environ, start_response )
>> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/', line 190 
>> in handle_request
>>   body = method( trans, **kwargs )
>> File 
>> '/home/galaxy/galaxy-dist/lib/galaxy/webapps/tool_shed/controllers/',
>>  line 1992 in import_capsule
>>   import_util.check_status_and_reset_downloadable( trans, 
>> import_results_tups )
>> File '/home/galaxy/galaxy-dist/lib/tool_shed/util/', line 34 
>> in check_status_and_reset_downloadable
>>   tip_changeset_revision = repository.tip( )
>> AttributeError: 'NoneType' object has no attribute 'tip'
>> I have seen the same behavior for capsules based on the following 
>> repositories from the test toolshed: package_biopython_1_62, 
>> package_vienna_rna_2_1, and package_bowtie_0_12_7. I am logged in as an 
>> admin user for the import process.
>> thanks,
>> -Will
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