singularity-conda-multiple-envs's Introduction

Singularity image from Conda multi-environment script

Singularity containerization of a Conda-based multi-environment bash script.

Requirements

Conda (install) for manual execution and
Docker for local Singularity image build.

Manual execution

# environments creation
./create_conda_envs.sh

# run.sh in different environments
conda activate first-env
./run.sh

conda activate second-env
./run.sh

conda activate third-env
./run.sh

Local Singularity image build

Run quay.io/singularity Docker image and access its bash with

docker run \
  --interactive --tty --rm --privileged \
  --volume $(pwd)/create_conda_envs.sh:/go/create_conda_envs.sh \
  --volume $(pwd)/environment-01.yml:/go/environment-01.yml \
  --volume $(pwd)/environment-02.yml:/go/environment-02.yml \
  --volume $(pwd)/environment-03.yml:/go/environment-03.yml \
  --volume $(pwd)/run.sh:/go/run.sh \
  --volume $(pwd)/runscript.sh:/go/runscript.sh \
  --volume $(pwd)/singularity-image.def:/go/singularity-image.def \
  --volume $(pwd)/out:/go/out \
  --entrypoint /bin/bash \
  quay.io/singularity/singularity:v3.7.2

then, from within the container's bash run

export IMAGE_FILENAME=/go/out/image.sif

# build
singularity build $IMAGE_FILENAME singularity-image.def

# inspect
ls -lah $IMAGE_FILENAME
singularity inspect $IMAGE_FILENAME
singularity inspect --deffile $IMAGE_FILENAME

# run
singularity run $IMAGE_FILENAME

Singularity image signing

Login into Sylabs.io and generate a Singularity Cloud token. Download the token file and save it to ~/.singularity/sylabs-token.

To generate a new key to sign a Singularity image in a GitHub Action, run

singularity keys newpair

and publish the public key on the Singularity Cloud.

Then update the repository secrets as follows

SINGULARITY_CLOUD_TOKEN: run < ~/.singularity/sylabs-token | pbcopy (on macOS) and paste the content of your clipboard as value of the secret,
SINGULARITY_PGP_PASSPHRASE: newly generated key's passphrase and
SINGULARITY_PGP_SECRET_BASE64: run < ~/.singularity/sypgp/pgp-secret | base64 | pbcopy (on macOS) and paste the content of your clipboard as value of the secret.

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