1. You can upload and create a built-in/locally cached genome from your own genome of interest. First, upload the genome to your history.
2. You’ll need to log in as an administrator. Login: email@example.com, Password: galaxy.
3. Click on the Admin link and then click on Manage local data.
4. Click on Create DBKey and Reference Genome. Choose New for creating a new key and fill in the text boxes with appropriate values. Choose History as the source for the genome (you can also download genomes directly from UCSC and other places), choose your fasta file as the file, and choose As Is for the last dropdown. Click Execute.
5. Click on Manage local data, again. Go to one of the index creators under Run Data Manager Tools, e.g. BWA Index. Choose your newly uploaded genome as the source, fill in the text boxes appropriately, and click Execute.
6. Neither of these jobs will appear in your history. In order to see their progress, click on BWA Index under View Data Manager Jobs. This will show you the jobs that are running from the Data Managers and under the State column, it will tell you the status of that job. Depending upon the size of your genome, it may take a while to finish. You will have to refresh the page to update the status. Once the status is Ok, then the job is done.
7. Now, when you go to BWA, you will see your newly indexed genome as one of the options for a built-in genome. You can also check out all the built-in genomes available by going to the Admin menu, clicking on Manage local data, and then under View Tool Data Table Entries, click on the link for the table in question.