There are three ways to install and run NanoCaller, via Docker, Singularity or Conda.
NanoCaller has been developed and tested to work with Linux OS; we do not recommend using Windows or Mac OS. However, if you use Windows or Mac OS and have Docker installed on your machine, you can run NanoCaller inside a Docker container. NanoCaller does not require a GPU or any other special hardware to run.
Please check the NanoCaller Docker Hub repository for the most up to date version of NanoCaller docker image.
If you do not have Anaconda, you will need to install it first. Here, we show how to install Miniconda, a minimal installation of Anaconda, which is much smaller and has a faster installation:
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
Go through all the prompts (installation in $HOME is recommended). The installation should take about 10 minutes, including the installation of Miniconda.
You can install NanoCaller in conda using Bioconda recipe:
conda install -c bioconda nanocaller
It is recommened that you install NanoCaller in a new conda environment to avoid any package conflict and use mamba for fast installation, in the following way:
conda create -n nanocaller_env -c conda-forge mamba
conda activate nanocaller_env
mamba install -c bioconda nanocaller
You can obtain the latest NanoCaller version from github that has not yet been pushed to bioconda via manual installation.
git clone https://github.com/WGLab/NanoCaller.git
conda env create -f NanoCaller/environment.yml
chmod +x NanoCaller/NanoCaller
conda activate nanocaller_env
Then you can run NanoCaller using PATH_TO_NANOCALLER_REPO/NanoCaller --help.
For instructions regarding Docker installation, please visit Docker website. There are three ways to obtain a Docker image for NanoCaller.
You can pull NanoCaller docker images from Docker Hub by specifiying a version number.
VERSION="3.4.1"
docker pull genomicslab/nanocaller:${VERSION}
docker run genomicslab/nanocaller:${VERSION} NanoCaller --help
If you want to build an image for the latest commit of NanoCaller Github repository, use the following commands:
git clone https://github.com/WGLab/NanoCaller.git
docker build -t nanocaller NanoCaller
docker run nanocaller NanoCaller --help
For instructions regarding Singularity installation, please visit [Singularity website] (https://sylabs.io/guides/3.7/user-guide/quick_start.html).
VERSION="3.4.1"
singularity pull docker://genomicslab/nanocaller:${VERSION}
singularity run --pwd /app nanocaller_${VERSION}.sif NanoCaller --help