Getting started¶
Running PEGS
requires:
The
PEGS
Python package, andThe
bedtools
program fromBEDTools2
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.