If working at a Galaxy server that you do not administrate, use the genome as a Custom reference genome.
- Preparing and using a Custom Reference Genome or Build
- Use the "Send to" menu at NCBI to export the fasta data locally to your computer, then upload it to Galaxy.
- The NCBI "Send to" options should be set like this: https://imgur.com/a/5S61x
- Uploading to Galaxy is explained here: Loading Data
- All support FAQs https://galaxyproject.org/support/
If working at your own Galaxy, the manual instructions 18Kbeyond give should work, but using Data Managers instead is recommended unless you are very familiar with line-command admin tasks within Galaxy.
- Data Managers are installed from the Tool Shed like other tools (from the Admin panel)
- Fetch the genome creating a dbkey
- Index for Samtools, Picard, and TwoBit (2bit)
- Index for downstream tools
- The DMs are named similar to the data they index, see Category Data Managers at http://usegalaxy.org/toolshed to review
Thanks, Jen, Galaxy team
First, index samples and save them in a path. say home/galaxy/galaxy_data/genomes/
Then, make changes like below in tool-data/bwa_mem_index.loc according to tool-data/bwa_mem_index.loc.sample
hg19bwa hg19 hg19 Canonical /home/galaxy/galaxy_data/genomes/hg19/bwa/hg19.fa
mm10bwa mm10 mm10 Canonical /home/galaxy/galaxy_data/genomes/mm10/bwa/mm10.fa