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
universe_wsgi.ini?

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:

/mnt/gx_tools

It should have the following contents:

shed_tools/ (empty directory)
shed_tool_conf.xml (contents like <toolbox
tool_path="/mnt/gx_tools/shed_tools"></toolbox>).
dependencies/ (empty directory)

Now create a throw away Galaxy instance and update its
universe_wsgi.ini with the following properties:

[app:main]
tool_dependency_dir = /mnt/gx_tools/dependencies
install_database_connection =
sqlite:////mnt/gx_tools/install_database.sqlite?isolation_level=IMMEDIATE
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.

-John


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.
>
> Cheers,
>
> -Evan Bollig
> Research Associate | Application Developer | User Support Consultant
> Minnesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> e...@msi.umn.edu
> boll0...@umn.edu
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