avalind / optitype

Singularity port of OptiType for precision HLA typing from next-generation sequencing data

Singularity Optitype

This will produce a Singularity image (suitable for running in a cluster environment) using https://github.com/FRED-2/OptiType. We do this by way of a bootstrap file for the Docker image.

1. Install Singularity

Instructions can be found on the singularity site.

2. Bootstrap the image

sudo singularity create --size 4000 optitype.img
sudo singularity bootstrap optitype.img Singularity

3. Run commands

How to access the OptiType runtime executable?

  ./optitype.img -h

Mount a data directory

  singularity run -b /path/to/data:/data/ optitype.img

To specify inputs and outputs, and run with data (not tested)

  singularity run -b /path/to/data:/data/ -i input1 [input2] (-r|-d) -o /data/ optitype.img