Build and run BRAKER2 pipeline in a container

Docker container to run BRAKER2, a pipeline for gene prediction.

Currently, this container runs the master versions of BRAKER (>= v2.15) and Augustus (>= v3.3.3).

1. Get the Dockerfile:

git clone https://github.com/dcourtine/BRAKER2-docker.git
cd BRAKER2-docker

2. Get your own copy of GeneMark, GeneMark-ES/ET/EP ver X.XX_lic for Linux 64 from: http://exon.gatech.edu/GeneMark/license_download.cgi.

   • Do not forget to download the license key!
   • Move the files gm_key_64.gz and gm_et_linux_64.tar.gz in this repo.

3. Build the Docker

docker build -t braker2 .

4. Run the container. Move to the directory where you have your data (genome, rnaseq_align.bam, prot.fa, ...)
   • interactive

   docker run --rm -v $(pwd):/data braker2:latest
   #Once in the container:
   braker.pl --genome=<path/to/genome.fa> <other_parameters>

   • run directly braker (not tested)

   docker run --rm -v $(pwd):/data braker2:latest braker.pl --genome=<path/to/genome.fa> <other_parameters>