Galaxy toolshed installation of the tool
- Git clone Galaxy by following instructions here.
- cd </path/to/galaxy>
- Configure Galaxy (config/galaxy.yml) with settings below:
- admin_users: <your_email_id>
- conda_prefix: </valid/path/>
- conda_auto_install: true
- conda_auto_init: true
- Run Galaxy:
sh run.sh - Register and login with your admin email id used in config/galaxy.yml as below:
- Go to the Admin tab on the top panel
- Select Install new tools and select Galaxy Tool Shed
- Search for star-fusion and install it
- Similarly install ctat_genome_resource_libs_data_manager
- Next download to ctat_genome_resource_libs_data_manager on your server/machine, click on Local Data (under Admin Tab). Under Data Manager Tools select ctat_genome_resource_libs_data_manager and fill the form as below (this may take a while):
- If install and download was a success then upload a right and left fastq files using the Get Data tool. Some test data is available here.
- Run the STAR-Fusion tool, leave all settings to default and select required genome.
- In the right side history panel you will notice among other outputs, a web report. Click on eye button to view the report.