On Jun 17, 2014, at 6:06 PM, Will Holtz <who...@lygos.com> 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
> 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 ~/run_tool_shed.sh 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 run_tool_shed.sh -bootstrap_from_tool_shed http://toolshed.g2.bx.psu.edu
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_tool_shed.sh.
Run the database migration process.
Execute the script
~/tool_shed_wsgi.ini to create a new user and an associated API key using the
information defined in
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/create_users.py -a <api_key> -f
http://toolshed.g2.bx.psu.edu -t http://localhost:9009.
Execute the script ~/lib/tool_shed/scripts/api/create_categories.py -a
<api_key> -f http://toolshed.g2.bx.psu./edu -t http://localhost:9009.
Executing the run_tool_shed.sh 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
> thank you for your help,
> On Wed, Jun 11, 2014 at 12:40 PM, Will Holtz <who...@lygos.com> 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: https://galaxy.lygos.com:99/repository/import_capsule
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__
> app_iter = self.application(environ, sr_checker)
> line 106 in __call__
> environ, self.app)
> line 543 in intercept_output
> app_iter = application(environ, replacement_start_response)
> line 84 in __call__
> return self.application(environ, start_response)
> line 74 in __call__
> return self.app( environ, start_response )
> line 633 in __call__
> return self.application(environ, start_response)
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in
> return self.handle_request( environ, start_response )
> File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in
> body = method( trans, **kwargs )
> 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/import_util.py', line 34 in
> tip_changeset_revision = repository.tip( trans.app )
> 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.
> 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:
> To search Galaxy mailing lists use the unified search at:
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:
To search Galaxy mailing lists use the unified search at: