Install MACS2/any Python software into your user space You can pass '-no-deps' option to pip and let it skip all dependencies. For example, you already have a workable Numpy, and when 'pip install -U MACS2', pip downloads newest Numpy but unable to compile and install them. Sometimes, you don't want pip to fix dependencies.To upgrade, type $ pip install -U MACS2 It will check currently installed MACS2, compare the version with the one on PyPI repository, download and install new version while necessary.Under command line, type $ pip install MACS2 PyPI will install Numpy automatically if they are absent.You may want to check the solution of 'virtual environment' to install software to your own user space, check the section ' The virtual environment' for detail.

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 don't have Numpy, install Numpy first either through source code (recommended) or rpm/dpkg (including numpy and numpy-dev).

Download source code package from MACS2 page on PyPI then type $ python setup.py install.

If you want to install MACS2 to your user space, check the section ' Manually install Python software to your home directory' for detail.

Normally, you need to have root permission to install software.

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. Although if you are lucky, you can let pip to fix the dependancies.) Note, you need numpy header files to compile MACS2 and some Linux distribution has numpy-dev package separately.

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 ImgDrive 2.1.2