Initial commit

.gitlab-ci.yml

+image: registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:latest
+
+services:
+    - registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:dind
+stages:
+    - build
+
+docker:
+  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 "$CI_REGISTRY_IMAGE"
+
+singularity:
+  stage: build
+  image:
+    name: quay.io/singularity/singularity:v3.11.0
+    entrypoint: [""]
+  script:
+    - singularity build singularity.sif Singularity
+    - ls -lh singularity.sif
+    - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" singularity.sif oras://"$CI_REGISTRY_IMAGE":latest
+  artifacts:
+    paths:
+    - singularity.sif

Dockerfile

+From continuumio/miniconda3
+# update conda and the OS
+RUN	conda update conda && \
+	conda upgrade --all -y && \
+	apt-get update && \
+	DEBIAN_FRONTEND=noninteractive apt-get -y upgrade && \
+	DEBIAN_FRONTEND=noninteractive apt-get -y autoremove && \
+	DEBIAN_FRONTEND=noninteractive apt-get -y clean autoclean
+
+RUN	conda install ipykernel jupyterlab
+# download the yml file
+#RUN curl  https://gitlab.pasteur.fr/tru/conda-container-howto/-/raw/main/pythonnet.yml > pythonnet.yml
+#RUN conda env create --file pythonnet.yml

Singularity

+BootStrap: docker
+From: continuumio/miniconda3
+
+%post
+# update conda and the OS
+conda update conda && \
+conda upgrade --all -y && \
+apt-get update && \
+DEBIAN_FRONTEND=noninteractive apt-get -y upgrade && \
+DEBIAN_FRONTEND=noninteractive apt-get -y autoremove && \
+DEBIAN_FRONTEND=noninteractive apt-get -y clean autoclean
+
+conda install ipykernel jupyterlab
+# download the yml file
+# curl  https://gitlab.pasteur.fr/tru/conda-container-howto/-/raw/main/pythonnet.yml > pythonnet.yml
+# conda env create --file pythonnet.yml

docker.yml

+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"

sing.yml

+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