Getting started

Running PEGS requires:

  • The PEGS Python package, and

  • The bedtools program from BEDTools2

Installing PEGS from PyPI using virtualenv and pip

The recommended way to get started with PEGS is to create a Python virtual environment, and then install the software using the pip utility.

For example: to create and activate a virtual environment called venv.pegs using the virtualenv utility:

virtualenv venv.pegs
source venv.pegs/bin/activate

The PEGS package can then be installed using pip, for example:

pip install pegs

which will make the pegs and mk_pegs_intervals utilities available.

Note

If using PEGS from a virtual environment, make sure to activate the environment each time before using it:

source venv.pegs/bin/activate

To deactive the virtual environment afterwards, do deactivate.

Note

PEGS is compatible with both Python2 and Python3; please check known problems section if you encounter any errors when installing or running the software.

Note

If installing PEGS on Mac OS X it is possible that you will get an error at runtime relating to Python not being installed as a framework; in this case please try reinstalling PEGS using the workaround in known problems section.

Installing PEGS using Conda

Another approach for installing PEGS to use Conda (most easily obtained via the Miniconda Python distribution).

Once you have Conda installed you can create a new Conda environment with PEGS installed using the following command:

conda create -c bioconda -c conda-forge -n pegs pegs

Alternatively you can install PEGS into an existing Conda environment using:

conda install -c bioconda -c conda-forge pegs

Warning

We recommend installing PEGS into a new Conda environment to avoid issues with incompatible packages, which has been observed for example when trying to install directly into the base Conda distribtion.

Installing BEDTOOLS

PEGS uses the bedtools program from the BEDTools2 package to generate the overlaps for the enrichment calculations.

If bedtools is not available when PEGS is run then PEGS will attempt to download and install it in the user’s home area, under:

${HOME}/.pegs/bin/

Subsequently runs of PEGS will use this version of bedtools if no other versions can be found.

Alternatively bedtools can to be installed separately and then made available on the user’s PATH at runtime.

For example for a Linux system:

wget https://github.com/arq5x/bedtools2/releases/download/v2.29.2/bedtools.static.binary
mv bedtools.static.binary bedtools
chmod a+x bedtools

See https://bedtools.readthedocs.io/en/latest/content/installation.html for more information on how to install BEDTools2.