Install Mageck on the server

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OmicSoft implementation is benchmarked with MAGeCK v.0.5.8

Contents

Installation

ArrayServer administrators will need to install MAGeCK and its dependencies on the same machine as ArrayServer. Please contact your administrator and request they perform the following steps:

Install required packages for MAGeCK

MAGeCK suggests users to install numpy which will calculate the negative binomial p value. In cases where numpy is not found, MAGeCK will use the normal p value instead.

Install MAGeCK

The MAGeCK sourceforge wiki page is https://sourceforge.net/p/mageck/wiki/Home/

pre-required package scipy

pip install scipy

It is important to make sure scipy was installed corresponding to the default Python, as in my CentOS server, the default Python is Python2.7; If Python3.6 is also installed, sometimes after updating some packages, dependencies the default pip might be switched to pip3, so users might need to pay attention to the default python.

Sudo pip install scipy.png


Download the source code at https://sourceforge.net/projects/mageck/files/latest/download, unzip it, and install in a directory mapped within ArrayServer

tar xvzf mageck-0.5.7.tar.gz
cd mageck-0.5.7
python setup.py install


After the installation, type mageck in the terminal:

Mageck installed 0311.png

Test Code

The MAGeCK comes with a "demo" folder, which contains sample data and script. Please run it to make sure MAGeCK is correctly installed.

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