BRAKER container

Docker container which should provide an easy and portable method to run BRAKER. Inspired by https://github.com/Dfam-consortium/TETools

Using the container

Requirements

• A 64-bit Linux operating system.
• docker installed with permission to run containers.
• GeneMark-ES. The license terms of GeneMark-ES does not allow me to redistribute it inside the container directly, but you can obtain it free of charge from http://exon.gatech.edu/GeneMark/license_download.cgi. The container has been tested with GeneMark-ES 4.* ("Last modified: January, 2020").

Building the container

You'll need:

• curl
• docker, with permissions to build containers

# Download dependencies
$ ./getsrc.sh

# Build a docker container
$ docker build -t org/name:tag .

Replace org/name:tag with a custom tag of your own (e.g. braker_docker:latest).

Running the container

The complete folder of Genemark-ES must be bind-mounted into the container at /opt/gmes_linux_64. You will also need to set the UID/GID, directories to mount, and so on according to your specific situation.

E.g. to run BRAKER in working directory /mnt/scratch/braker_results on soft-masked genome genome.fa with RNA-seq alignments RNAseq.bam:

mkdir -p workdir_braker_docker && \
docker run -it --mount type=bind,source=/mnt/scratch/braker_results,target=/work --mount type=bind,source=/path/to/gmes_linux_64,target=/opt/gmes_linux_64,ro --mount type=bind,source=~/.gm_key,target=~/.gm_key,ro --user "$(id -u):$(id -g)" --workdir "/work" --env "HOME=/work" braker_docker:latest braker.pl --genome=genome.fa --bam=RNAseq.bam --softmasking --workingdir=workdir_braker_docker &> braker_output.log

Replace /path/to/gmes_linux_64 with the path to gmes_linux_64 on your system accordingly. All output files will be found in /mnt/scratch/braker_results, which was mounted to the container.

Testing the container

The following commands will test BRAKER with RNA-seq data example command:

mkdir -p test_braker_docker && \
cd test_braker_docker && mkdir work_test \
wget http://bioinf.uni-greifswald.de/bioinf/braker/RNAseq.bam && \
docker run -it --mount type=bind,source="$PWD",target=/work --mount type=bind,source=/path/to/gmes_linux_64,target=/opt/gmes_linux_64,ro --mount type=bind,source=~/.gm_key,target=~/.gm_key,ro --user "$(id -u):$(id -g)" --workdir "/work" --env "HOME=/work" braker_docker:latest /usr/bin/time -v braker.pl --genome=/opt/src/BRAKER-2.1.5/examples/genome.fa --bam=RNAseq.bam --softmasking --workingdir=work_test &> test1.log

Replace /path/to/gmes_linux_64 with the path to gmes_linux_64 on your system and other directories accordingly.