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Installation

Since some of the callers are only available for Linux, this guide will only focus on Linux installation. We will create a folder for all the callers and then a subfolder for each caller.

• mkdir Tools && cd Tools

• mkdir macs2

• mkdir homer

• mkdir PeakRanger

macs2

pip3 install --target='/path-to-Tools/macs2' --ignore-installed macs2==2.2.6

There are two versions of pip, the PyPA recommended tool for installing Python packages, pip for python2 and pip3 for python3, macs2 needs python >= 3.6 so we will use pip3. Currently the latest version is 2.2.7.1, so if we don't specify the version it will download the latest one. We should add --ignore-installed so that it would not uninstall any other version if already installed in our system .

Numpy 1.19.1 is required and will be installed.

Q

git clone https://github.com/charite/Q.git

This will create a Q subfolder

cd Q

and run the following command

./configure --prefix=/path-to-Tools/Q/

make; make install

homer

For homer we move to homer subfolder (cd homer) and download from their website

wget "http://homer.ucsd.edu/homer/configureHomer.pl"

perl configureHomer.pl -install homer -version v4.11.1

This will check for all the required utilities of homer and alert us if any program is missing.

PeakRanger

Move to the PeakRanger subfolder, cd PeakRanger

wget "https://sourceforge.net/projects/ranger/files/PeakRanger-1.18-Linux-x86_64.zip"

and then

unzip PeakRanger-1.18-Linux-x86_64.zip

spp

spp is an R package and can be installed inside R, using:

githubinstall("spp", ref = "88bbd37")

we used this spp commit due to a problem we had with the main one during the simulations

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Using the Peak Callers

We have two options now that we have the folder with all the peak callers installed, either add them to path or specify the exact location for each caller when we call the wrapper function.

• Add to Path

If we want to add the peak callers to our path in order to use them, independently of the wrapper package we can vim ~/.bashrc file and add at the end e.g for homer:

PATH=$PATH:~/path-to-Tools/homer/bin

• Give them as command line arguments

For example if we haven't add Q to our path we can give the path to the executable as an argument:

--Q_path ~/path-to-Tools/Q/bin/Q

This way we can keep these peak callers locally installed. The --tool_path option does not apply for spp since it is a R package.