get-reference-genomes

Gets reference genomes from UCSC and prepares them for use by IGV.js.

Here's a list and demonstration of the currently available reference genomes.

Setup

Install pip dependencies, and make sure twoBitToFa and bedToBigBed are on your PATH:

pip install -r requirements.txt
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa && chmod a+x twoBitToFa
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed && chmod a+x bedToBigBed

Usage

./tools/genome-to-local.sh GENOME1 [ GENOME2 ... ]
# or, if you have AWS credentials in place:
./tools/genome-to-s3.sh GENOME1 [ GENOME2 ... ]

Development

Run tests/test.sh to confirm that the scripts perform the expected transformations.