INSTALL.md

INSTALL Guide For PEALS

Time-stamp: <2023-03-21 16:35:26 Keren Zhou>

Please check the following instructions to complete your installation.

Prerequisites

PEALS is developed under python3 environment and has been tested in python 3.8 and Linux with kernel-version #1 SMP Mon Dec 4 23:52:40 UTC 2017.

Please be sure that the following software or R packages have been properly installed and are available in PATH variable or can be directly loaded by R.

Software:

• bedTools (>=2.30.0)
• samtools (>=1.14)
• featureCounts (>=2.0.2)

R packages:

• getopt (>=1.20.3)
• DESeq2 (>=1.32.0)
• ggplot2 (>=3.4.1)
• ashr (>=2.2.54)
• apeglm (>=1.14.0)
• glmGamPoi (>=1.4.0)

3 ways to install PEALS

Install through PyPI

The easiest way to install PEALS is through PyPI system. Get pip if it's not available in your system.

pip3 install peals --user

Install from source using pip

git clone https://github.com/kerenzhou062/PEALS.git
cd PEALS
pip3 install . --user

Install from source using setup.py

git clone https://github.com/kerenzhou062/PEALS.git
cd PEALS
python3 setup.py install --user

PYTHONPATH

Usually, you don't need to care about the PYTHONPATH enrivonment unless you install PEALS to a specific path.

To set up your PYTHONPATH environment variable, you'll need to add the value PREFIX/lib/pythonX.Y/site-packages to your existing PYTHONPATH. In this value, X.Y stands for the major–minor version of Python you are using (such as 3.8; you can find this with sys.version[:3] from a Python command line). PREFIX is the install prefix where you installed PEALS.

If you did not specify a prefix on the command line, PEALS will be installed using Python's sys.prefix value.

On Linux, using bash, I include the new value in my PYTHONPATH by adding this line to my ~/.bashrc:

$ export PYTHONPATH=/home/kzhou/lib/python3.8/site-packages:$PYTHONPATH