Installation

This pipeline will require nextflow. The rest fo the dependencies can be installed via miniconda, Docker, or Singularity

nextflow -version

nextflow run isugifNF/polishCLR -r main --help

For ag100pest projects, we have been installing dependencies in a miniconda environment. Dependencies may also be installed via docker or singularity.

Since nextflow caches pulled pipelines in a ~/.nextflow folder somewhere on your system, to update the pipeline we recommend:

nextflow drop isugifNF/polishCLR
nextflow pull isugifNF/polishCLR -r main
  

Miniconda

Install dependencies in a miniconda environment.

wget https://raw.githubusercontent.com/isugifNF/polishCLR/main/other_dependencies.yml

[[ -d env ]] || mkdir env
conda env create -f other_dependencies.yml -p ${PWD}/env/polishCLR_env

conda activate env/polishCLR_env

nextflow run isugifNF/polishCLR -r main \
  --check_software
  

Docker

Start up docker and pull the csiva2022/polishclr:latest image.

docker pull csiva2022/polishclr:latest

# Option 1
docker run -it csiva2022/polishclr:latest \
  nextflow run isugifNF/polishCLR -r main \
  --check_software

# Option 2
nextflow run isugifNF/polishCLR -r main \
  --check_software \
  -profile docker

# Option 3
nextflow run isugifNF/polishCLR -r main \
  --check_software \
  --with-docker csiva2022/polishclr:latest
  

Run the polishCLR pipeline with an added -with-docker csiva2022/polishclr:latest parameter. See nextflow docker run documentation for more information.

Singularity

Install dependencies as a singularity image.

singularity pull polishclr.sif docker://csiva2022/polishclr:latest

# Option 1:
singularity exec polishclr.sif \
  nextflow run isugifNF/polishCLR -r main \
  --check_software

# Option 2:
nextflow run isugifNF/polishCLR -r main \
  --check_software \
  -profile singularity

# Option 3:
nextflow run isugifNF/polishCLR -r main \
  --check_software \
  -with-singularity polishclr.sif
  

Run the polishCLR pipeline with an added -with-singularity polishclr.sif parameter. See nextflow singularity run documentation for more information.