On Tue, Nov 26, 2013 at 5:40 AM, Mikel Egaña Aranguren
<mikel.egana.arangu...@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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