diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..05f860af6e978d0de35b96e28adc83321ed2dfae --- /dev/null +++ b/README.md @@ -0,0 +1,29 @@ +## installing a jupyter minimal environment in singularityCE/apptainer and docker + +Merging https://gitlab.pasteur.fr/tru/singularity-miniconda3-jupyter and https://gitlab.pasteur.fr/tru-docker-miniconda3-jupyter +with 2 parallel CI builds. + +Attn: `:main` is the docker image, `:latest` is the OCI container + +## singularity (singularityCE or apptainer installed) +``` +singularity build miniconda3-jupyter.sif oras://registry-gitlab.pasteur.fr/tru/singularity-docker-miniconda3-jupyter:latest +singularity exec miniconda3-jupyter.sif jupyter-lab --no-browser +``` + +## on Maestro.pasteur.fr +``` +module add apptainer +apptainer build miniconda3-jupyter.sif oras://registry-gitlab.pasteur.fr/tru/singularity-docker-miniconda3-jupyter:latest +apptainer exec -B /pasteur miniconda3-jupyter.sif jupyter-lab --no-browser +``` + +## from cache only +``` +singularity exec oras://registry-gitlab.pasteur.fr/tru/singularity-docker-miniconda3-jupyter:latest jupyter-lab --no-browser +``` + +## docker image +``` +docker run -ti docker://registry-gitlab.pasteur.fr/tru/singularity-docker-miniconda3-jupyter:main +``` diff --git a/docker.yml b/docker.yml deleted file mode 100644 index da084f5bad00a001fc5e36ae00ff4ac1e62cffac..0000000000000000000000000000000000000000 --- a/docker.yml +++ /dev/null @@ -1,14 +0,0 @@ -image: registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:latest - -services: - - registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:dind -stages: - - build - -build: - stage: build - script: - - docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr - - export MY_TIME=`date +"%F-%H%M"` - - docker build --pull -t "$CI_REGISTRY_IMAGE:$CI_BUILD_REF_NAME" -t "$CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA" -t "$CI_REGISTRY_IMAGE:latest" -t "$CI_REGISTRY_IMAGE:$MY_TIME" . -f Dockerfile - - docker push "$CI_REGISTRY_IMAGE" diff --git a/sing.yml b/sing.yml deleted file mode 100644 index f1880768e9251629cf78a82d4cae8769afb67244..0000000000000000000000000000000000000000 --- a/sing.yml +++ /dev/null @@ -1,13 +0,0 @@ -singularity: - stage: build - image: - name: quay.io/singularity/singularity:v3.11.0 - entrypoint: [""] - script: - - type singularity && singularity version - - singularity build singularity.sif Singularity - - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" singularity.sif oras://"$CI_REGISTRY_IMAGE":latest - - ls -lh singularity.sif - artifacts: - paths: - - singularity.sif