2013/11/27 John Chilton <chilton(a)msi.umn.edu>
On Tue, Nov 26, 2013 at 5:40 AM, Mikel Egaña Aranguren
> I have developed a tool generator that performs a SPARQL query (defined
> 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
> tool_conf.xml in the "traditional" way) but I would like my tool
> 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
I don't think there is.
> I have come across this thread
> 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
) and would be happy to review a
community contributed pull request to add this :).
OK thanks I will stay tuned.
Also, there was a good Galaxy talk that is I assume follow up work
from this old thread: http://vimeo.com/channels/581875/74399518
would be very interesting to get their perspective on this.
I'm trying to use their WS Extensions tool in my Galaxy server but it
fails, precisely, in the dynamic tool generator step, so I can't even
reproduce the behaviour in order to hack something for my own tool. I guess
I'm using a Galaxy version that is too modern
> - If it has been implemented, what should be the output of my tool
> Mikel Egaña Aranguren, Ph.D.
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Mikel Egaña Aranguren, Ph.D.