singularity-samtools

Singularity for samtools

Prerequisites

• Singularity 2.2 must be installed on your system. Here is the instruction.

Build

1. Download Singularity file from this git repository.

2. Create an empty container image of 200MB:

   $ sudo singularity create -s 200 samtools.img

3. Bootstrap the image using the Singularity image definition file you downloaded from the previous step:

   $ sudo singularity bootstrap samtools.img Singularity

Run

$ singularity run samtools.img --help

Other Notes

• This uses Alpine Linux as base image.
• Note that the image definition file being used here contains a bunch of commands that downloads and compiles the source code of samtools, which is the main reason why the container image requires about 200MB. It would be nice if Singularity provides a way to shrink the image down to the only necessary size. Another workaround would be Dockerfile.