This is a place to put Dockerfiles for bioimage analysis tools, which can be used in bioimage analysis workflows. It is structured in the style of BioContainers/containers.
These containers are currently used in Nextflow Modules, but could also be used in Galaxy and other workflow tools.
We want containers that:
- Are reproducible - if you rebuild the same Dockerfile a year later, you should get basically the same container.
- Are optimized - We use standard techniques to speed up builds and we use multistage builds to reduce the size of the final image.
- Include metadata - every image includes OCI metadata
Containers in this repository are published as packages in the GitHub Container Registry using these steps:
-
Obtain a GitHub personal authentication token and save it into your terminal environment as
$GITHUB_PACKAGE_TOKEN. -
Log into the registry
echo $GITHUB_PACKAGE_TOKEN | docker login ghcr.io --username $USER --password-stdin- Build your image
./build.sh stitching-spark/1.10.0The build script adds important metadata to the image, and then asks you if you want to push it to GCR.
- Reference your image
The image will be available in GHCR, but needs to be made public manually. After that, it can be referenced like this:
ghcr.io/bioimagetools/toolname:1.0.0