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Commit 0376c90a authored by Quang tru HUYNH's avatar Quang tru HUYNH
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readme + remove legacy yml

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## 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
```
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 "$CI_REGISTRY_IMAGE"
singularity:
stage: build
image:
name: quay.io/singularity/singularity:v3.11.0
entrypoint: [""]
script:
- type singularity && singularity version
- singularity build singularity.sif Singularity
- singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" singularity.sif oras://"$CI_REGISTRY_IMAGE":latest
- ls -lh singularity.sif
artifacts:
paths:
- singularity.sif
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