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 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. - If it has been implemented, what should be the output of my tool generator. Thanks Regards -- Mikel Egaña Aranguren, Ph.D. http://mikeleganaaranguren.com
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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2013/11/27 John Chilton <chilton@msi.umn.edu>
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
On Tue, Nov 26, 2013 at 5:40 AM, Mikel Egaña Aranguren <mikel.egana.aranguren@gmail.com> wrote: 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 :).
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. It 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 Regards
-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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Mikel Egaña Aranguren, Ph.D. http://mikeleganaaranguren.com
participants (2)
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John Chilton -
Mikel Egaña Aranguren