- conda-pack
- either Docker, Podman or Singularity
- source conda environment needs to be on a linux x64 machine.
- Clone this repository (retrieve
Dockerfile/Singularity)
git clone git@github.com:grst/containerize-conda.git
cd containerize-conda/conda-pack
- Pack the environment
conda-pack -n <MY_ENV> -o packed_environment.tar.gz
- Build the container
# With singularity
singularity build --fakeroot <OUTPUT_CONTAINER.sif> Singularity
# With Docker
docker build . -t <TAG>
# With Podman/Buildah
podman build . -t <TAG>
Conda environment can't be just "moved" to another location, as some paths are
hardcoded into the environment. conda-pack takes care of replacing these paths
back to placeholders and creates a .tar.gz archive that contains the
environment. This environment can be unpacked to another machine (or, in our
case, a container). Running conda-unpack in the environment replaces the
placeholders back to the actual paths matching the new location.
find . -xtype lfinds broken symbolic links which leads to a failed container creation...