Thank you both for the replies!
So, is there a plan to add this functionality in Galaxy's codebase? It would seem that the changes are minimal.
Cheers, Kostas
On 22 November 2010 17:03, Bossers, Alex Alex.Bossers@wur.nl wrote:
The previous post does support the add, update and remove of new tools :) Alex
-----Oorspronkelijk bericht----- Van: Nate Coraor [mailto:nate@bx.psu.edu] Verzonden: maandag 22 november 2010 16:25 Aan: Bossers, Alex CC: Kostas Karasavvas; Galaxy Dev Onderwerp: Re: [galaxy-dev] dynamic loading of tools?
It's also possible to reload a tool's configuration via the Admin interface. However, it's not possible to add and remove tools. This is something we'd like to support, but have not yet done. There's an issue for it which you can track here:
http://bitbucket.org/galaxy/galaxy-central/issue/279/restart-required-after-...
--nate
Bossers, Alex wrote:
Kostas Some time ago a similar idea was posted to the dev list. We have taken
that to modify our source code as well that adds a tool to the list which allows a dynamic refresh of the tools/server without a reboot of it....
Maybe it can give you a lead to start. Not sure if the attachment is filtered.... But I try to add the original
post we used successfully.
Alex
Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Kostas Karasavvas Verzonden: maandag 22 november 2010 11:41 Aan: Galaxy Dev Onderwerp: [galaxy-dev] dynamic loading of tools?
Hi all!
It is my understanding that galaxy does not support dynamic loading of
tools, i.e. for every new tool you add you need to manually change the conf file and restart the server.
I am working on integrating functionality of another system into galaxy.
To do this I am actually generating Galaxy tools automatically with certain scripts. The tools generated depend on certain parameters so there can be an arbitrary number of tools generated. Installing them manually and restarting the server is not ideal in this situation since it would depend on an administrator doing the work (rather than the user).
The ideal scenario would be for me to create a tool that can dynamically
create and add new tools. However, the latter (adding new tools dynamically) does not seem to be possible right now.
I can think of other reasons that people would like that as well (e.g.
for administration purposes). I am not sure if that was already discussed in the past but I was wondering if that is that something that you consider implementing in the near future.
Thank you in advance, Kostas
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Hello,
We here at the Universoty of Georgia have developed a suite of tools to
enable accessing Web services through Galaxy's interface, one time and also in workflows. We do this by reading the descriptions of the Web services (from WSDLs and WADLs) and adding tools dynamically to Galaxy that are able to take correct inputs from the user and invoke these services.
Though most of this functionality was added by adding tools, we had to
make minimal change in Galaxy's source code to support the capability of refreshing Galaxy toolbox without restarting the server.
This is hardly 5 lines of code that was added to Galaxy's code base. These tools will be available shortly on the community page. I was wondering if it will be possible to add the
support for dynamic tool addition to the main instance of Galaxy. Please find the details below:
Changes to Galaxy to add refresh toolbox ability:
- change the execute method of the class tool in
lib/galaxy/tools/__init__.py to
def execute( self, trans, incoming={}, set_output_hid=True ): """ Execute the tool using parameter values in `incoming`. This just dispatches to the `ToolAction` instance specified by `self.tool_action`. In general this will create a `Job` that when run will build the tool's outputs, e.g. `DefaultToolAction`. """
############# #add code to verify if user has administrative privileges #added by sumedha ganjoo, sganjoo@uga.edu: line 1104 to 1109 -to refresh toolbox
if self.id == 'REFRESH_ID': self.app.refreshToolBox() ############# return self.tool_action.execute( self, trans,incoming=incoming, set_output_hid=set_output_hid )
- add refreshToolBox method (find below) to UniverseApplication class
in lib/galaxy/app.py
########### # added by sumedha ganjoo,sganjoo@uga.edu, line 86-90 def refreshToolBox( self): self.toolbox = tools.ToolBox( self.config.tool_config,self.config.tool_path, self )
###########
- Add Refresh tool. Attached.
Thanks, Sumedha
<tool id="REFRESH_ID" name="Refresh" Version="1.0.0"> <description> :Refresh Galaxy</description> <command interpreter="python"> refreshTool.py $input $output
</command> <inputs> <param name="input" type="select" display="radio" size="250"
label="Execute this tool by clicking on Execute button">
<option value="refresh">Refresh Galaxy</option> </param>
</inputs> <outputs> <data format="tabular" name="output" /> </outputs> <tests> </tests> <help>
**Click on "Galaxy" on the top left corner of this window to refresh the page.**
</help> </tool>
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