That should be sufficient. Thanks,

Nils

On 5/27/10 1:13 PM, "Daniel Blankenberg" dan@bx.psu.edu wrote:

Hi Nils,

At this point we're going to go with the approach that jars should be placed in the directory specified by '${GALAXY_DATA_INDEX_DIR}/shared/jars/', ordinarily this is 'GALAXY_ROOT/tool-data/shared/jars/', but the tool-data directory can be configured as the value of the 'tool_data_path' variable in universe_wsgi.ini.

This allows jars to be accessible in tool configurations by specifying e.g. '${GALAXY_DATA_INDEX_DIR}/shared/jars/FOO.jar', where FOO.jar is the desired jar. Let us know if this is inadequate.

(added in changeset: 3844:8fe924966a6a)

Thanks for using Galaxy,

Dan

On May 12, 2010, at 6:03 PM, Nils Homer wrote:

...

A jar bin would be great. That would make it easy to add in new JARs.

On 5/12/10 1:22 PM, "Daniel Blankenberg" dan@bx.psu.edu wrote:

...

Hi Nils,

We do not currently have a best way to directly execute JARs in Galaxy. It does not appear that setting $classpath or $path, etc, will allow the direct execution of jars without providing the path or when not found in the current working directory.

One simple possibility is for Galaxy to allow a configurable directory where required JARs can dropped / linked to; this variable would then be available for use in tool configurations. Do you have any suggestions/ideas/thoughts?

Thanks for using Galaxy,

Dan

On May 6, 2010, at 3:59 AM, Nils Homer wrote:

...

What is the best way to include wrap a JAR file in galaxy? Also, what is the best way to submit tools and their associated wrappers?

Thank-you for your help in advance,

Nils Homer

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