Installation

Assuming you're running a modern version of Linux, firstly install Nextflow:

$ curl -s https://get.nextflow.io | bash 

The minimal supported version of Nextflow is 21.04.3. If you have already installed an older version of Nextflow, you can update the version like this:

$ nextflow self-update 

Make sure to add nextflow to PATH so you can run nextflow in your terminal from anywhere. Then simply run:

$ git clone --branch v0.1.7 https://github.com/nebfield/snpQT.git

Where --branch v0.1.7 reflects the current latest release of snpQT. You can find different releases of snpQT on our releases page. You should see a helpful message in your terminal if everything went well. In case you wish to pull the latest changes to the snpQT repository check our Advanced Installation guide.

Finally, you must download some reference data (10.5281/zenodo.4916468) for snpQT to work. Download the reference files to the local path:

$ cd snpQT
$ mkdir db
$ wget 'https://zenodo.org/record/4916469/files/core.tar.gz?download=1' -O db/core.tar.gz
$ cd db && tar -xvf core.tar.gz 

And, if you wish to perform imputation you can download the reference files (in the same directory) using the following commands:

$ wget 'https://zenodo.org/record/4916469/files/impute.tar.gz?download=1' -O impute.tar.gz
$ tar -xvf impute.tar.gz --strip-components=1 

snpQT is now installed. However, to run snpQT you will need to pick (and possibly set up) a profile and make a parameter file.

Profiles tell snpQT how to run bioinformatics software and where to run it.

The parameter file tells snpQT what types of things you would like to do with your input data. It's important that you make this file and understand what each parameter does. For convenience, we provide an example parameter file with sensible defaults.