Create a Singularity container from DockerHub¶

There are multiple ways how to create a Singularity container.

This page shows how to create a Singularity container from a Docker script on DockerHub.

Procedure¶

The hardest part of this procedure may be to have Linux with Singularity installed on a computer where you have super-user rights.

In this example, we create a Singularity container for https://github.com/lindenb/jvarkit with a DockerHub script at https://hub.docker.com/r/lindenb/jvarkit.

1. Create the Singularity container¶

Here we build a Singularity container from a Docker file:

sudo singularity build my_container.sif docker:[owner/file]

The magic is in docker:[owner/file], which for us becomes docker:lindenb/jvarkit:

sudo singularity build my_container.sif docker:lindenb/jvarkit

In some case, the Singularity container is now created.

How does that look like?

$ sudo singularity build my_container.sif docker:lindenb/jvarkit
INFO:    Starting build...
INFO:    Fetching OCI image...
28.2MiB / 28.2MiB [================================================================================================================================================] 100 % 2.5 MiB/s 0s
1.0GiB / 1.0GiB [==================================================================================================================================================] 100 % 2.5 MiB/s 0s
INFO:    Extracting OCI image...
INFO:    Inserting Singularity configuration...
INFO:    Creating SIF file...
INFO:    Build complete: my_container.sif

1.1 Troubleshooting¶

In our case, however, we get the MANIFEST_UNKNOWN error:

[sudo] password for sven: 
INFO:    Starting build...
INFO:    Fetching OCI image...
FATAL:   While performing build: conveyor failed to get: GET https://index.docker.io/v2/lindenb/jvarkit/manifests/latest: MANIFEST_UNKNOWN: manifest unknown; unknown tag=latest

This means that DockerHub cannot conclude with Docker script we want to use exactly. To solve this, we need to find a tag that allows us to find an exact script. On DockerHub, we can find the tags for our Docker script ar https://hub.docker.com/r/lindenb/jvarkit/tags.

How does that page look like?

Here is how https://hub.docker.com/r/lindenb/jvarkit/tags looks like:

jvarkit tags

We can see there that 1b2aedf24 is the tag for the latest version.

sudo singularity build my_container.sif docker:lindenb/jvarkit:1b2aedf24

How does that look like?

$ sudo singularity build my_container.sif docker:lindenb/jvarkit
INFO:    Starting build...
INFO:    Fetching OCI image...
28.2MiB / 28.2MiB [================================================================================================================================================] 100 % 2.5 MiB/s 0s
1.0GiB / 1.0GiB [==================================================================================================================================================] 100 % 2.5 MiB/s 0s
INFO:    Extracting OCI image...
INFO:    Inserting Singularity configuration...
INFO:    Creating SIF file...
INFO:    Build complete: my_container.sif

Works!

2. Use the Singularity container¶

./my_container.sif [your command-line arguments]

For example, in this case:

./my_container.sif --help

However, this container is setup differently. From the documentation, one find that this container is used as such:

./jvarkit.sif java -jar /opt/jvarkit/dist/jvarkit.jar --help