Dockerfiles for miscellaneous tools.
Docker can't run directly on Mac but a solution exists using VirtualBox: boot2docker. https://docs.docker.com/installation/mac/
Summary:
- Download boot2docker from https://github.com/boot2docker/osx-installer/releases
- Click to open the archive. This will start the installation process.
- When finished, just click on Boot2Docker in folder Applications to start it.
- A terminal will open, where you can type your docker commands.
Installation tested: Boot2Docker version 1.1.2
See this page for a step-by-step "how to" to enable folder sharing with your images https://github.com/boot2docker/boot2docker#folder-sharing
Just copy all suggested commands in a boot2docker terminal, as described.
Build image
docker build -t samtools:0.1.19 .
Run samtools through the image
(assuming that you followed the "How to" described above, and that you copied a file named my_test_file.bam
in your shared partition (/Volumes/data on host).
docker run -it --volumes-from my-data samtools:0.1.19 samtools index /data/my_test_file.bam