💻Installation

SUMMER can be installed through Docker or Singularity. We currently provide handy commend to run pipelines in Docker (rather than in singularity).

Method 1 - Docker pull summer (Recommended)

# docker pull the preinstalled and precompiled software
docker pull chuhongyuan/summer:latest 
# download SUMMER workflow from github
download SUMMER at https://github.com/carolhuaxia/summer
chmod +x PATH_TO_SUMMER/summer
# get help
python PATH_TO_SUMMER/summer -h

Method 2 - Singularity

#On cluster:
#module avial #check avialable singularity version
#module load singularity/avial.version
singularity pull summer.sif docker://chuhongyuan/summer:latest
singularity exec summer.sif bash

Then usage on singularity is shown at:

🐼Singularity User Guide