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Installation
There are several ways to install MAGeCK.
Method 1: through conda/bioconda channel
To install MAGeCK through bioconda channel, first download and install the Python 3 variant of the Miniconda Python distribution. Then, in the command line, type
conda install -c bioconda -c conda-forge mageck
That's it!
An optional step (but recommended) is, you can create an isolated software environment for mageck by executing
conda create -c bioconda -c conda-forge -n mageckenv mageck
in a terminal. The environment can be activated via
source activate mageckenv
To update mageck, run
conda update mageck
from within the environment.
This environment can be deactivated via
source deactivate
You can install MAGeCK-VISPR (which includes MAGeCK) using conda, a commonly used package management softare. The instructions to install MAGeCK-VISPR can be found on MAGeCK-VISPR manual.
Method 2: through Docker Image
You can also run MAGeCK via Docker image which is automatically built upon each commit in our bitbucket source code.
To run through Docker image, install Docker on your own system, and follow the instructions in tutorials on running Docker images.
Method 3: through source code
You can also download the software and install it by yourself. See the detailed instructions below.
Download
The latest version of MAGeCK (0.5.9) can be downloaded here:
Or click the link here (in cases the button points to a wrong file).
For earlier versions (< 0.5.4), the zip file is encrypted, but you can get the password easily by one of the following options:
- Join our MAGeCK Google group and the password is shown on the top of the forum; or
- Send an email to mageck.help@gmail.com with the subject "password", and you will get an automatic reply with password within 1 minute.
You need to go to the Terminal to unzip and install the software. See the instructions for Installation below.
System requirement
MAGeCK can be run on either Mac or Linux system. Since MAGeCK is written in Python and C, Python (version 3) and a C compiler is needed.
Other dependencies include numpy and scipy.
Due to the end of Python 2 life cycle,mageck 0.5.9 or higher versions are not designated to run on Python 2.
Optional dependencies
Since version 0.5.9.3, MAGeCK updates the visualization module by generating a R markdown file (.Rmd) for count and test subcommand. This allows users to easily create a html-based report webpage using RStudio. No additional dependencies are needed for running MAGeCK. However, to generate the report webpage, a computer with Rstudio and rmarkdown are needed.
To use the --pdf-report option, which is mainly used for visualization before 0.5.9.3, two optional softwares include R and pdflatex. MAGeCK relies on both softwares to generating PDF reports if the --pdf-report option is used. If it is not possible to install them, you can also generate PDF reports by copying some MAGeCK output files to another computers with R and pdflatex are properly installed. See Q and A for more information.
If you use the --pdf-report option, xtable is required, and gplots as well as ggplot2 is optional. Use install.packages("xtable") and install.packages(c("gplots","ggplot2")) in R to install them.
You won't get any error messages if you don't have gplots, but you will get a more beautiful clustering figure in the pdf report of the count command.
You can run MAGeCK without --pdf-report option, and copy some files to another machine with these R packages to generate pdf report. See Q and A for more details.
What if I run into issues of latex
You can still get some figures generated from MAGeCK, by adding the "--keep-tmp" option to keep intermediate files.
Installation
Since version 0.3, MAGeCK uses standard Python installation procedures (distutils) for compiling and installation of the software.
The installation procedure is extremely easy. First, download the source code, unzip it by using the following command (or just double-clicking it), and go into the directory in the command line:
tar xvzf mageck-0.5.4.tar.gz
cd mageck-0.5.4
After that, invoke python setup.py:
python setup.py install
And it is done! If you want MAGeCK to be installed on your own directory , use the following command instead:
python setup.py install --user
This is the easiest way to install mageck. An alternative approach is (you may have one additional step to set up the environment variables; see below)
python setup.py install --prefix=$HOME
where $HOME is the root directory you want to install (usually the user home).
Manual installation
The manual installation is deprecated since version 0.3. Please refer to the installation instructions above.
After downloading the source code, follow the instructions below for manual installation.
Setting up the environment variables
In most systems you don't need to set up the environment variables. Just type "mageck" in the command line to see if the mageck program works.
If you get a "command not found" error, that indicates the environment variables are not properly set up. There are several additional steps to finish the installation. First you need to add the path of the mageck program to your PATH variable.
There are several different situations.
1. If you use the --prefix=$HOME option during installation
Set up the PATH variable by typing:
export PATH=$PATH:$HOME/bin
2. If you use the --user option during installation (and other situations)
You first need to determine where MAGeCK is installed. See this Q and A for additional steps to determine the correct bin directory.
If your bin directory is located in /Users/john/.local/bin, then type the following:
export PATH=$PATH:/Users/john/.local/bin
Setting up PYTHONPATH variable
You may also need to add the path of the MAGeCK module to the PYTHONPATH variable. Again, follow the steps above to determine the correct Python installation path (see the Q&A). This variable should be set as, for example,
export PYTHONPATH=/Users/john/.local/lib/python2.7/site-packages:$PYTHONPATH
Save your PATH or PYTHONPATH variable
To save the path configuration (so you don't have to type it every time), place the above command in your ~/.bashrc (for Linux) or ~/.bash_profile (for Mac).
Experimental version
The experimental version of MAGeCK is available at bitbucket. Note that the source codes on BitBucket are experimental and are not fully tested, and it may not be stable or function well. It is strongly recommended to use the MAGeCK software downloaded from sourceforge or from bioconda.
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