In this repo,
bwa is a statically linked binary (i.e. linked with
-static). To build a docker image, run the following in this directory:
docker build -t mybwa .
To create the BWA index for MT.fa:
docker run -v `pwd`:/tmp -w /tmp mybwa index MT.fa
To run BWA-MEM:
docker run -v `pwd`:/tmp -w /tmp mybwa mem MT.fa test.fq > test.sam
You can use pipe, too:
cat test.fq | docker run -iv `pwd`:/tmp -w /tmp mybwa mem MT.fa /dev/stdin > test.sam
This github repo has also been linked to lh3lh3/bwa at the Docker Hub.
You can use the following to get the docker image and run it:
docker pull lh3lh3/bwa docker run -v `pwd`:/tmp -w /tmp lh3lh3/bwa index MT.fa
This image has no dependencies on any other images and is thus very small.