GalaxyAddTool: Difference between revisions
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#* /lustre/project/''your_project'' (email mhanby@uab.edu to get the directory created) | #* /lustre/project/''your_project'' (email mhanby@uab.edu to get the directory created) | ||
#* /share/apps/galaxy/galaxy-tools (only if this will ONLY be used in Galaxy) | #* /share/apps/galaxy/galaxy-tools (only if this will ONLY be used in Galaxy) | ||
# Create a personal galaxy for developement & testing | |||
#* See Shantanu's [https://projects.uabgrid.uab.edu/galaxy/wiki/GalaxyDevelopment Create a personal galaxy] page. | |||
# Add the executable path to the galaxy environment | # Add the executable path to the galaxy environment | ||
#* $galaxyroot/modulefiles/galaxy*: edit the module definition file to add your tool location to the path | |||
# Load the updated module and make sure the command works from the commandline! | |||
#* module load galaxy | |||
#* test, test, test... | |||
== Special Case: REST or SPARQL endpoints== | |||
There are already tools for integrating these through a wizard. | |||
See the [http://toolshed.g2.bx.psu.edu/repository?webapp=community Galaxy Toolshed] and | |||
navigate to ''Tools Shed -> Data Source'' | |||
== creating a command-wrapper by hand== | |||
Revision as of 20:50, 2 November 2011
How-to for adding a new tool into UAB's Galaxy instance. This details adding a tool that has it's own executable(s), rather than a pure python script.
pre-requisits
- Install the tools on the cluster
- /share/apps/your_tool (email mhanby@uab.edu to get the directory created)
- /lustre/project/your_project (email mhanby@uab.edu to get the directory created)
- /share/apps/galaxy/galaxy-tools (only if this will ONLY be used in Galaxy)
- Create a personal galaxy for developement & testing
- See Shantanu's Create a personal galaxy page.
- Add the executable path to the galaxy environment
- $galaxyroot/modulefiles/galaxy*: edit the module definition file to add your tool location to the path
- Load the updated module and make sure the command works from the commandline!
- module load galaxy
- test, test, test...
Special Case: REST or SPARQL endpoints
There are already tools for integrating these through a wizard. See the Galaxy Toolshed and navigate to Tools Shed -> Data Source