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Galaxy toolshed installation

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asmariyaz23 edited this page Nov 27, 2018 · 5 revisions
  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:
    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 ctat_mutations and install it install
  9. Similarly install ctat_genome_annotations_data_manager data_mgr
  10. Next download to ctat_mutations data resource on your server/machine, click on Local Data (under Admin Tab). Under Data Manager Tools select CTAT annotations Data Manager and fill the form as below (this may take a while): local_data data_mgr_form
  11. If install and download was a success then upload a BED file using the Get Data tool. Some test data is available here.
  12. Run the ctat-mutations tool, leave all settings to default and select required genome. form
  13. In the right side history panel you will notice a number of outputs including cancer variants and BAM file generated.
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