Thanks John. I guess I'm looking at options "enable_tool_shed_install"
and "tool_shed_install_config_file" that were added in rev 6398 and
dropped in rev 6747 when the tool migration scripts were added. I
don't know why they were dropped, but they would be immensely useful
This is related to the CLIA pipeline, and a separate effort to
simplify galaxy VM provisioning with puppet. From my perspective,
copying in changes to that one file is significantly easier than
grooming a mounted disk image. My end goal is dozens of independent
galaxy instances running different tool chests.
I might just merge the old code back in and submit a pull request, or
I also see that a few scripted calls to
scripts/api/install_tool_shed_repositories.py should also take care of
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
On Tue, May 20, 2014 at 5:01 PM, John Chilton <jmchil...@gmail.com> wrote:
> Hey Evan,
> Out of curiosity, are you trying to update MSI's CLIA pipeline to
> utilize tool shed installed tools? (It sounds kind of like yes.)
> I don't think that file you mentioned exists in either place - is it a
> typo or maybe a configuration file with overridden location in
> Reading between the lines, it sounds like you want Galaxy cloud images
> with completely fresh Galaxy instances but with preinstalled tools?
> There are many variants of the following approach that I think could
> work - but one approach is:
> Create a persistent directory (...or at least a directory that can be
> recreated when you launch a new VM) like:
> It should have the following contents:
> shed_tools/ (empty directory)
> shed_tool_conf.xml (contents like <toolbox
> dependencies/ (empty directory)
> Now create a throw away Galaxy instance and update its
> universe_wsgi.ini with the following properties:
> tool_dependency_dir = /mnt/gx_tools/dependencies
> install_database_connection =
> tool_config_file = tool_conf.xml,/mnt/gx_tools/shed_tool_conf.xml
> Bootstrap and install tools. Throw away or wipe out Galaxy data and
> take a snapshot.
> Now just ensure new Galaxy VM instances starts with the above 3
> properties set the same way.
> Hope this helps.
> On Tue, May 20, 2014 at 3:40 PM, Evan Bollig <boll0...@umn.edu> wrote:
>> I want to setup a tool_shed_install.xml to roll out tools at first
>> boot for Galaxy.
>> 1) Is it possible to get Galaxy to generate this based on the tools
>> currently installed from the tool shed?
>> 2) Is it required to list every tool provided by each repository, or
>> can I simply add the repository to the file and Galaxy will assume all
>> tools are included?
>> 3) The tool_shed_install.xml.sample file exists only in the
>> galaxy-central#default branch. This should probably be included in the
>> galaxy-dist#stable too.
>> -Evan Bollig
>> Research Associate | Application Developer | User Support Consultant
>> Minnesota Supercomputing Institute
>> 599 Walter Library
>> 612 624 1447
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