Note if you have already installed numpy system-wide, you can use 'virtualenv.py -system-site-packages /home/foobar/MyVE' to let your virtual Python environment have access to system-wide numpy library so that you don't need to install them again. Now you can create your own virtual environment located anywhere you want, for example '/home/foobar/MyVE':
You will find a script inside to make a virtual python environment isolated from the one for whole system: On the project PyPI page, you can download the source code as a tar ball. The website for 'virtualenv' can be found at.
To save your time, you can put the two export commands at the bottom of your '.bashrc' file if you are using BASH.Īs a general recommendation to all people processing their own data on Linux/Unix and wondering how to control bioinformatics tools by themselves, the 'virtualenv' tool will help to establish a virtual environment that users can install/remove/upgrade software. One thing you have to remember is that PYTHONPATH and PATH need to be set, by using export commands as previously shown, every time you enter the terminal/shell. Then, install both Numpy and MACS2 by going to their source code directories: $ export PYTHONPATH=$HOME/lib/python2.7/site-packages/:$PYTHONPATH $ export PATH=$HOME/bin/:$PATH To do so with Python setup script, first, you need to setup PYTHONPATH and PATH, type:
Normally, Linux/Unix users tend to install software to their home directory where they can fully control, such as '/home/foobar'. Manually install Python software to your home directory
Please use this instruction as a general guidance to install any Linux/Unix software to your own user space for full control. To install MACS2 globally is not always a good option, especially while you don't have permission to write to '/usr/' or /usr/local/', or you find the required Python library, Numpy, is not available in the system. 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.
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.