RFD-seq

Pipeline for calculating replication fork directionality from methods such as OK-seq or GLOE-seq

1. Load slurm and miniconda

Note. The commands to do this will be different on your machine. These commands are specific to an HPC using slurm with these modules installed.

ml slurm
ml miniconda

3A. FIRST TIME ONLY: Setup conda environment with snakemake

# -f is the location of the environment .yml file. 
## The relative path assumes that you are in the root directory of this repository.
# -p is the path where you want to install this environment
conda env create -f workflow/envs/SnakemakeEnv.yml -p /s/sansam-lab/SnakemakeEnv 

3B. Activate conda environment with snakemake

conda activate /s/sansam-lab/SnakemakeEnv

git clone https://github.com/sansamcl/SnakemakeRepositoryTemplate.git

7A. Use conda environments

If conda is to be used for rule-specific environments, you may find it useful to create the environments first. Running 'snakemake' with the '--conda-create-envs-only' option will create the environments without running the pipeline. The '--conda-prefix' option is used to set a directory in which the ‘conda’ and ‘conda-archive’ directories are created. This directory may be changed to a stable or shared location.

sbatch --mem 32G \
--wrap="\
snakemake \
--cores all \
--use-conda \
--conda-prefix ../condEnvs/ \
--conda-create-envs-only \
--conda-frontend conda"

Once the environments are setup, you may execute pipeline with conda environments using the following command:

sbatch --constraint=westmere \
--wrap="\
snakemake \
-R \
-j 999 \
--use-conda \
--conda-prefix ../condEnvs/ \
--conda-frontend conda \
--latency-wait 100 \
--cluster-config config/cluster_config.yml \
--cluster '\
sbatch \
-A {cluster.account} \
-p {cluster.partition} \
--cpus-per-task {cluster.cpus-per-task}  \
--mem {cluster.mem} \
--output {cluster.output}'"

7B. Use environment modules.

Rather than using conda environments, you may prefer to use modules installed on your computing cluster. These modules are defined for each rule in 'workflow/Snakefile'. This must be customized for your environment, and you must modify the Snakefile yourself.

To execute the pipeline with environment modules, enter the following:

sbatch --constraint=westmere \
--wrap="\
snakemake \
-R \
-j 999 \
--use-envmodules \
--latency-wait 100 \
--cluster-config config/cluster_config.yml \
--cluster '\
sbatch \
-A {cluster.account} \
-p {cluster.partition} \
--cpus-per-task {cluster.cpus-per-task}  \
--mem {cluster.mem} \
--output {cluster.output}'"