docker2singularity

This script exports a Docker image as a Singularity .sif file. This can be useful for porting Dockerized code to run on shared user systems like clusters, which sometimes run Singularity rather than Docker.

Prerequisites

• Install Docker (tested on Mac OS 10.14.6 with Docker 20.10.6)

Usage

1. Build or pull the Docker image you wish to export to a Singularity .sif file

   docker pull ubuntu:latest

2. Run docker2singularity.sh to export the image as a .sif file

   cd docker2singularity
   ./docker2singularity.sh ubuntu

   This should write a file called ubuntu.sif in the current working directory, e.g., docker2singularity/ubuntu.sif

   Optionally, you can specify where to save the output .sif file:

   ./docker2singularity.sh ubuntu $HOME/ubuntu_singularity.sif

   Expected Output

   If it worked, you'll see output similiar to the following:

   Exporting docker image ubuntu --> /Users/matt/ubuntu_singularity.sif 
   
   Image Format: squashfs
   Docker Image: ubuntu
   Container Name: ubuntu_singularity.sif
   
   Inspected Size: 73 MB
   
   (1/10) Creating a build sandbox...
   (2/10) Exporting filesystem...
   (3/10) Creating labels...
   (4/10) Adding run script...
   (5/10) Setting ENV variables...
   (6/10) Adding mount points...
   (7/10) Fixing permissions...
   (8/10) Stopping and removing the container...
   (9/10) Building squashfs container...
   INFO:    Starting build...
   INFO:    Creating SIF file...
   INFO:    Build complete: /tmp/ubuntu_singularity.sif
   (10/10) Moving the image to the output folder...
        27,717,632 100%   80.25MB/s    0:00:00 (xfr#1, to-chk=0/1)
   Final Size: 27MB
    Exported Docker image ubuntu --> /Users/matt/ubuntu_singularity.sif 
   

   Help

   Run ./docker2singularity -h to print the help screen, including usage.

Caveats

In order to export a Docker image to .sif file, one of the following must be true:

1. The Docker image is available locally (i.e., it has already been built using docker build or pulled using docker pull)

2. A file named Dockerfile exists in the current working directory.

If a Dockerfile is found, you are given the option to build the docker image and then export it to .sif.

If neither of these conditions is met, an error message is printed and the program exits without doing anything.