Installation¶
With pip¶
ngs_toolkit
is available for Python 3 only. Is is tested in Python 3.6 and 3.7.
To install, simply do:
pip install ngs-toolkit
you might need to add a --user
flag if not root or running in a virtual environment.
This will install all the Python dependencies needed too. See here a list of all Python dependencies used.
To install the latest development version:
pip install git+https://github.com/afrendeiro/toolkit.git#egg=ngs-toolkit
Using a conda environment¶
Get the latest Python 3 installation of miniconda from the conda website and follow the instructions for installation and activation of the environment.
Setup the bioconda channel:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
Install non-Python dependencies:
conda install -y bedtools==2.27.1
conda install -y ucsc-twobittofa
conda install -y bioconductor-deseq2
conda install -y bioconductor-cqn
And then install the ngs-toolkit
library with pip (available only through PyPi).
pip install ngs-toolkit
Non-Python requirements¶
ngs_toolkit
makes use of some non-Python dependencies.
bedtools: version should be at least 2.27.1
The following are highly recommended only for some data or analysis types:
R and some bioconductor libraries (optional): - DESeq2 (optional): used for differential testing of genes/regulatory elements and variance stabilization transformation of data. - cqn (optional): used for GC-content aware normalization of NGS data.
Kent tools (optional): - the
twoBitToFa
binary from UCSC’s Kent bioinformatics toolkit is used to convert between the 2bit and FASTA formats.
For region-based enrichment analysis, you may also want to have the following software installed (entirely optional):
You can see how to install all requirements in an Ubuntu-based system in the provided Dockerfile.
Docker¶
A Docker image containing ngs_toolkit
and its dependencies is also available: https://hub.docker.com/r/afrendeiro/ngs-toolkit
To pull the image and run a module for example in this way:
docker pull afrendeiro/ngs-toolkit
docker run ngs-toolkit python3 -m ngs_toolkit.recipes.ngs_analysis --help
You can also run an interactive session of ngs_toolkit
based on the docker image on Gitpod.
The Dockerfile that produced the image is available in the github repository: https://github.com/afrendeiro/toolkit/blob/master/Dockerfile