X-omics Docker containers collection

A collection of Docker containers that are used in X-omics workflows

Dockerhub

Containers in this repository can be pulled from Dockerhub

Build Docker images locally

Docker images can be built locally using the Dockerfiles in this repository, for example:

git clone https://github.com/Xomics/Docker_containers.git
cd Docker_containers/miniconda-snf
docker build -t image/name:$VERSION .

Build Singularity containers locally

Create Docker image, convert to Singularity

Define a Dockerfile (example: Container_files\r-base-phenotypes\Dockerfile), build Docker image, push to registry, save to archive, and convert to Singularity image.

Build Docker image locally and push to the Gitlab registry:

docker login registry.cmbi.umcn.nl
docker build -t registry.cmbi.umcn.nl/${repository_name}/r-base-phenotypes:$VERSION .
docker push registry.cmbi.umcn.nl/${repository_name}/r-base-phenotypes:$VERSION

Run in a DRE VM (or locally):

docker pull registry.cmbi.umcn.nl/${repository_name}/r-base-phenotypes:$VERSION
docker images # to get IMAGE_ID
docker save $IMAGE_ID -o r-base-phenotypes.tar
sudo singularity build r-base-phenotypes.sif docker-archive://r-base-phenotypes.tar