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dolphinnext/atacseq: Local Configuration

Install NextFlow

Nextflow runs on most POSIX systems (Linux, Mac OSX etc). It can be installed by running the following commands:

# Make sure that Java v8+ is installed:
java -version

# Install Nextflow
curl -fsSL get.nextflow.io | bash

# Add Nextflow binary to your PATH:
mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin

See nextflow.io for further instructions on how to install and configure Nextflow.

Install the pipeline

Automatic

This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub if dolphinnext/atacseq is specified as the pipeline name.

Docker

First, install docker on your system: Docker Installation Instructions

Then, running the pipeline with the option -profile docker tells Nextflow to enable Docker for this run. An image containing all of the software requirements will be automatically fetched and used from dockerhub (https://hub.docker.com/r/dolphinnext/atacseq).

nextflow run dolphinnext/atacseq -profile docker --DOWNDIR /path/to/save/genome-data --reads '*_R{1,2}.fastq.gz' --genome_build mouse_mm10_refseq

Singularity

If you're not able to use Docker then Singularity is a great alternative. The process is very similar: running the pipeline with the option -profile singularity tells Nextflow to enable singularity for this run. An docker image will be automatically converted into singularity image and used in the pipeline.

nextflow run dolphinnext/atacseq -profile singularity --DOWNDIR /path/to/save/genome-data --reads '*_R{1,2}.fastq.gz' --genome_build mouse_mm10_refseq