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

PALEOMIX command-line aliases invokes wrong tools:

When upgrading an old PALEOMIX installation (prior to v1.2.x) using pip, the existence of old files may result in all command-line aliases (‘bam_pipeline’, ‘phylo_pipeline’, ‘bam_rmdup_collapsed’, etc.) invoking the same command (typically ‘phylo_pipeline’):

$ bam_pipeline makefile.yaml
Phylogeny Pipeline v1.2.1

[...]

This can be solved by removing these aliases, and then re-installing PALEOMIX using ‘pip’, shown here for a system-wide install:

$ sudo rm -v /usr/local/bin/bam_pipeline /usr/local/bin/conv_gtf_to_bed /usr/local/bin/phylo_pipeline /usr/local/bin/bam_rmdup_collapsed /usr/local/bin/trim_pipeline
$ sudo python setup.py install

Alternatively, this may be resolved by downloading and manually installing PALEOMIX:

$ wget https://github.com/MikkelSchubert/paleomix/archive/v1.2.4.tar.gz
$ tar xvzf v1.2.4.tar.gz
$ paleomix-1.2.4/
# Either for the current user:
$ python setup.py install --user
# Or, for all users:
$ sudo python setup.py install