soft_requirements.md

Software Requirements

To run the pipeline, several software packages are required. How you satisfy these requirements is essentially up to you and depends on your system.
If possible, we highly recommend using either Docker or Singularity.

Please see the installation documentation for how to run using the below as a one-off. These instructions are about configuring a config file for repeated use.

Docker

Docker is a great way to run h3abionet/chipimputation, 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 - nextflow will automatically fetch the nfcore/imp image that we have created and is hosted at dockerhub at run time.

To add docker support to your own config file, add the following:

profiles {
    docker {
        docker.enabled = true
        process.container = "nfcore/imp"
}

Note that the dockerhub organisation name annoyingly can't have a hyphen, so is nfcore and not nf-core.

You can now run the pipeline using the command:

 nextflow run h3abionet/chipimputation -profile docker

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.

To specify singularity usage in your pipeline config file, add the following:

singularity.enabled = true
process.container = "shub://h3abionet/chipimputation"

If you intend to run the pipeline offline, nextflow will not be able to automatically download the singularity image for you. Instead, you'll have to do this yourself manually first, transfer the image file and then point to that.

First, pull the image file where you have an internet connection:

singularity pull --name nf-core-imp.simg shub://h3abionet/chipimputation

Then transfer this file and point the config file to the image:

profiles {
    singularity {
        singularity.enabled = true
        process.container = "/path/to/nf-core-imp.simg"
}

The pipeline can then be run using the command

 nextflow run h3abionet/chipimputation -profile singularity

Conda

If you're not able to use Docker or Singularity, you can instead use conda to manage the software requirements. To use conda in your own config file, add the following:

process.conda = "$baseDir/environment.yml"