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Quang tru HUYNH
singularity-docker-miniconda3-jupyter
Commits
0376c90a
Commit
0376c90a
authored
2 years ago
by
Quang tru HUYNH
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readme + remove legacy yml
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2 years ago
Stage: build
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README.md
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README.md
docker.yml
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docker.yml
sing.yml
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sing.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
```
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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 "$CI_REGISTRY_IMAGE"
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sing.yml
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singularity
:
stage
:
build
image
:
name
:
quay.io/singularity/singularity:v3.11.0
entrypoint
:
[
"
"
]
script
:
-
type singularity && singularity version
-
singularity build singularity.sif Singularity
-
singularity push --docker-username "${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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