2. Installation

Istallation of Ninetails

Currently, Ninetails is not available on CRAN/Bioconductor, so you need to install it using devtools.

If you do not have devtools installed already, you can do this with the following command in R/RStudio:

install.packages("devtools")

Note

For Windows users:

Before installation of devtools on Windows, you should install Rtools, so the packages would be correctly compiled: https://cran.r-project.org/bin/windows/Rtools/

Once you have devtools installed, you can install Ninetails using the command below in R/RStudio:

devtools::install_github('LRB-IIMCB/ninetails')
library(ninetails)

Manual installation of additional components

In case of fully manual installation, Additional requirements has to be fulfilled.

Installation of additional components with conda (easy)

The latest conda (miniconda) installers can be obtained here

The recipe for a virtual environment in conda (r-ninetails.yml) can be found in the preprint accompanying repository

To create virtual environment, clone the repo or download r-ninetails.yml file, navigate to its directory and run the following command in your terminal:

conda env create -f r-ninetails.yml

This would create r-ninetails environment. Remember to activate it in R/RStudio before launching Ninetails:

reticulate::use_condaenv("r-ninetails")

Using docker

We provide a docker image with all dependencies necessary to run the Ninetails. It can be retrieved with the following command:

docker pull ghcr.io/nemitheasura/ninetails-docker:latest

Note

This image does not contain Guppy, Nanopolish, minimap2, samtools and other software which is not directly linked with the Ninetails pipeline.

This command launches docker with RStudio: (username: rstudio, password:123)

docker run -it -p 8787:8787 -e PASSWORD=123 --rm r-ninetails

The access to RStudio is provided through the web browser: http://localhost:8787/ (username: rstudio, password:123).