SF_biocontainer

SF_biocontainer is a github repo with the Dockerfile used to build containers for CCRSF pipelines.

Publicly available images

Many of the popular tools have been containerized by the community, including Biocontainer community and different institutes. These resources can be found either on Docker hub or Quay

CCRSF maintained images

There are two scenarios that we need to build our own images:

  1. If the tool we want to use is not containerized before, we can build the container ourselves and deposite the image on Docker hub.

  2. For a particular task, multiple packages are required, so a customized environment is needed. For example, for analysis of single cell RNA-seq data, multiple R packages are required (Seurat, SingleR, etc). We can build an image with all the required packages: https://github.com/CCRSF-IFX/SF_biocontainer/blob/main/dockerhub_repos/sc-smk-wl/vr1.0.0/Dockerfile

Here is a diagram to show the current workflow used for containerization:

CCRSFIFX maintained images can be found here