On Tue, Nov 26, 2013 at 5:40 AM, Mikel Egaña Aranguren mikel.egana.aranguren@gmail.com wrote:
Hi;
I have developed a tool generator that performs a SPARQL query (defined by the user) and creates new Galaxy tools depending on result.
I have the basic system (i.e. it generates the tool XML files and edits the tool_conf.xml in the "traditional" way) but I would like my tool generator to be a regular Galaxy tool that is able to "inject" the new tools in the Galaxy menu without having to restart Galaxy. Is there an easy way of doing so?
I don't think there is.
I have come across this thread (http://osdir.com/ml/galaxy-development-source-control/2010-07/msg00094.html) but it is not clear for me:
- If this change has been implemented in Galaxy.
Nope. This thread predates my interactions with Galaxy - but the proposed solution doesn't look like it was ever integrated into galaxy-central. In 2013, rather than creating a special tool to handle this I think a better solution would be a new API method in lib/galaxy/webapps/galaxy/api/tools.py to do the toolbox refresh - I could be wrong though.
One problem with the proposed solution or my API based alternative is that it assumes there is only one Galaxy process - it is broken if there are multiple Galaxy processes (web and handler threads). Unfortunately others parts of Galaxy make this same assumption - tool reload functionality (.. and potentially tool shed installs as well?). So I am happy to add more code to Galaxy that is similarly broken until multiple Galaxy processes have some way to communicate - if they work for a single Galaxy setup and they are useful to people deploying in that configuration.
I have created a Trello card for this request (https://trello.com/c/m8nuCkFA) and would be happy to review a community contributed pull request to add this :).
Also, there was a good Galaxy talk that is I assume follow up work from this old thread: http://vimeo.com/channels/581875/74399518. It would be very interesting to get their perspective on this.
-John
- If it has been implemented, what should be the output of my tool
generator.
Thanks
Regards
-- Mikel Egaña Aranguren, Ph.D.
http://mikeleganaaranguren.com
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