Galaxy toolshed installation of the tool - STAR-Fusion/STAR-Fusion GitHub Wiki

  1. Git clone Galaxy by following instructions here.
  2. cd </path/to/galaxy>
  3. Configure Galaxy (config/galaxy.yml) with settings below:
    1. admin_users: <your_email_id>
    2. conda_prefix: </valid/path/>
    3. conda_auto_install: true
    4. conda_auto_init: true
  4. Run Galaxy: sh run.sh
  5. Register and login with your admin email id used in config/galaxy.yml as below: register
  6. Go to the Admin tab on the top panel
  7. Select Install new tools and select Galaxy Tool Shed new_tools
  8. Search for star-fusion and install it install_sf
  9. Similarly install ctat_genome_resource_libs_data_manager search_dm
  10. 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): local_data ctat_dm_form
  11. 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.
  12. Run the STAR-Fusion tool, leave all settings to default and select required genome. star_fus
  13. In the right side history panel you will notice among other outputs, a web report. Click on eye button to view the report.