Throubleshooting the installation

Pysam / Cython installation fails with "Python.h: No such file or directory" or "pyconfig.h: No such file or directory":

Installation of Pysam and Cython requires that Python development files are installed. On Debian based distributions, for example, this may be accomplished by running the following command:

$ sudo apt-get install python-dev

Pysam installation fails with "zlib.h: No such file or directory":

Installation of Pysam requires that "libz" development files are installed. On Debian based distributions, for example, this may be accomplished by running the following command:

$ sudo apt-get install libz-dev

Command not found when attempting to run 'paleomix':

By default, the PALEOMIX executables ('paleomix', etc.) are installed in ~/.local/bin. You must ensure that this path is included in your PATH:

$ export PATH=$PATH:~/.local/bin

To automatically apply this setting on sub-sequent logins (assuming that you are using Bash), run the following command:

$ echo "export PATH=\$PATH:~/.local/bin" >> ~/.bash_profile