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eQTL-Catalogue/qtlmap: Local Configuration

If running the pipeline in a local environment, we highly recommend using either Docker or Singularity.

Docker

Docker is a great way to run eQTL-Catalogue/qtlmap, as it manages all software installations and allows the pipeline to be run in an identical software environment across a range of systems.

Nextflow has excellent integration with Docker, and beyond installing the two tools, not much else is required. The eQTL-Catalogue/qtlmap profile comes with a configuration profile for docker, making it very easy to use.

First, install docker on your system: Docker Installation Instructions

Then, simply run the analysis pipeline:

nextflow run eQTL-Catalogue/qtlmap -profile docker --studyFile ...

Nextflow will recognise eQTL-Catalogue/qtlmap and download the pipeline from GitHub. The -profile docker configuration lists the eQTL-Catalogue/qtlmap image that we have created and is hosted at quay.io, and this is downloaded.

Singularity image

Many HPC environments are not able to run Docker due to security issues. Singularity is a tool designed to run on such HPC systems which is very similar to Docker. Even better, it can use create images directly from dockerhub or any other image repository.

git clone https://github.com/eQTL-Catalogue/qtlmap.git
cd qtlmap
nextflow run main.nf -profile singularity,test