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NPG Samtools Docker images

The images

This is a Docker image of samtools

Build instructions

A makefile is supplied that will by build the image and add metadata based on git describe.

cd ./docker
make

Release instructions

When tagging a new version please use annotated tags in the command line interface.

git clone --branch master git@github.com:wtsi-npg/samtools_container.git samtools_container && cd $_
git tag -a 'x.y.z' -m 'release x.y.z'
git push origin x.y.z

Releases are created and published automatically by a GitHub Action on tag creation. Using the web interface to create a release will cause that automation to fail.

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 ghcr.io/wtsi-npg/samtools:latest \
    singularity-wrapper -h

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

$ docker run ghcr.io/wtsi-npg/samtools:latest \
    singularity-wrapper list
bcftools
...
tabix

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

$ docker run -v $PREFIX:/mnt/tmp \
    ghcr.io/wtsi-npg/samtools:latest \
      singularity-wrapper -p /mnt/tmp install

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

Author

Keith James kdj@sanger.ac.uk Jennifer Liddle js10@sanger.ac.uk