lh3 / bwa-docker

Minimal docker image for bwa. Not developed any more.

In this repo, bwa is a statically linked binary (i.e. linked with gcc -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.