Similar entries for other tool shed tools that are installed into a Galaxy instance using the Galaxy Admin interface (not the tool migration stage process) are available in the shed_tool_con.xml file (or whatever shed-related files you have defined in your Galaxy config). You can also find tool ids for all of the tools loaded into your Galaxy tool panel by inspecting the single file name integrated_tool_conf.xml. Using this file, you won't have to inspect more than the single file. These files are all described in the tool shed wiki at the following page. http://wiki.galaxyproject.org/GalaxyToolPanel Greg Von Kuster On Nov 16, 2012, at 2:52 AM, Andreas Kuntzagk wrote:
Thanks, that helps in this case. But I might also need the ids for other toolshed tools to adjust the job runner settings.
Andreas
On 15.11.2012 15:23, Greg Von Kuster wrote:
Hi Andreas,
Assuming you have executed the migration process for the tools so they are now installed into your Galaxy instance from the tool shed, you can check the entries in the migrated_tools_conf.xml file and get the ids. Entries will look something like the following where you can get the id from the <id> tag.
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/picard/e0232cbac965/picard/rgPicardMarkDups.xml" guid="toolshed.g2. bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>picard</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>e0232cbac965</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0</id> <version>1.56.0</version> </tool>
Greg Von Kuster
On Nov 15, 2012, at 9:10 AM, Andreas Kuntzagk wrote:
Hi,
I upgraded to the latest version and again some tools moved to tool_shed. I now need to set job runners for these tools. Is there an easy way to get the tool_ids other then hovering the mouse over the tool name and write down the id?
regards, Andreas
-- Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany
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-- Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany