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_shedtoolshed.g2.bx.psu.edu/tool_shed
repository_namepicard/repository_name
repository_ownerdevteam/repository_owner
installed_changeset_revisione0232cbac965/installed_changeset_revision
idtoolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0/id
version1.56.0/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
http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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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
http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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and other Galaxy lists, please use the interface at:
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