Installation

Installation

Git pull code

git pull [email protected]:remap-cisreg/remap-pipeline.git

Conda install

You don't need to install specific Conda environments. Snakemake will create them from recipes in 2.scripts/conda_envirronment during its first run. Conda environments will be in the .snakemake/conda folder in the working directory.

Docker images install

Docker images are found in the Repository list on DockerHub

Pull all necessary images

docker pull benoitballester/remap_bowtie2:latest
docker pull benoitballester/remap_aria2:latest
docker pull benoitballester/remap_phantompeakqualtools:latest
docker pull benoitballester/remap_trimgalore:latest
docker pull benoitballester/remap_bedtools:latest
docker pull benoitballester/remap_samtools:latest
docker pull benoitballester/remap_ucsc_apps:latest

Singularity images install

If you use singularity, you will need to convert them into singularity images. Please refer to Sylabs.io