Normally, you need to have root permission to install software with pip, unless you have installed a different Python distribution by your own. Follow this instruction to get pip if it's not available in your system.If you have older version of GCC or saw an error complaining 'invalid option argument ‘-Ofast’', please manually download MACS2 source code and modify the 'setup.py' script to replace '-Ofast' with '-O3'. As a sidenote, current setup script for MACS2 needs GCC>=4.6 so that the optimization flag '-Ofast' can be accepted.

As for Mac OSX users, it means you have to install Xcode then select 'install command line tools' within Xcode program. Check the next section.) Note, you need numpy header files to compile MACS2 and some Linux distribution has numpy-dev package separately. Although if you are lucky, you can let pip to fix the dependancies. Numpy (I recommend you install your own through rpm for Redhat variants or dpkg for Debian variant linux, or install from source code.This bug has been fixed in Python 2.7.5 which was released on. Fix it according to this report in MACS user group. Python 2.7 ( Note that Python 2.7.4 has a bug which causes error while reading compressed BAM file'.Typical Installation Instructions PlatformĪ *nix system including Linux, Mac OSX and other *nix variants Manually install Python software to your home directory.Install MACS2/any Python software into your user space.

For mac instal It Takes Two