kjsanger / containers

Singularity and Docker material

NPG Docker images

The images

base/ubuntu/16.04

A base image with curl and gosu installed, intended for multi-stage builds where curl is later dropped.

base/ubuntu/18.04

A base image with curl and gosu installed, intended for multi-stage builds where curl is later dropped.

base/ubuntu/20.04

A base image with curl and gosu installed, intended for multi-stage builds where curl is later dropped.

irods/ubuntu/16.04

This is a Docker image of a vanilla iRODS 4.2.7 server that works out of the box. To be used for running tests only.

irods/ubuntu/18.04

This is a Docker image of a vanilla iRODS >=4.2.11 server that works out of the box. To be used for running tests only.

The server version may be chosen by passing the Docker build argument --build-arg IRODS_VERSION=<version> (default is 4.3.0).

Build instructions

A makefile is supplied that will by default build all images and add metadata to them based on git describe.

cd ./docker
make

NPG Singularity wrappers

Each container that provides command line programs is self-documenting and is able to install its own proxy wrappers outside of the container, to allow these programs to be run transparently.

The images include the singularity-wrapper tool which allows programs to be listed and their wrappers installed. The install target should be set to a volume mounted into the container and the -p (install prefix) option of the tool set accordingly. The -h option will show online help.

e.g. Show online help:

$ docker run wsinpg/ub-18.04-irods-clients-4.2.11:latest \
    singularity-wrapper -h

e.g. List the programs provided by a container:

$ docker run wsinpg/ub-18.04-irods-clients-4.2.11:latest \
    singularity-wrapper list
{
    "package": "irods-clients",
    "executable": [
        "baton-chmod",
        ...
        "samtools"
    ]
}

e.g. Install wrappers to $PREFIX/bin:

$ docker run -v $PREFIX:/mnt/tmp \
    wsinpg/ub-18.04-irods-clients-4.2.11:latest \
      singularity-wrapper -p /mnt/tmp install

$ ls $PREFIX/bin
-rwxr-xr-x 1 kdj staff 406 Apr 12 15:47 baton-chmod
...
-rwxr-xr-x 1 kdj staff 409 Apr 12 15:47 samtools

Author

Keith James [email protected]