2013/11/27 John Chilton <chil...@msi.umn.edu> > 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 :). > 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
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