Software Requirements

The Zonkey pipeline requires PALEOMIX version 1.2.7 or later. In addition to the requirements listed for the PALEOMIX pipeline itself in the Installation section, the Zonkey pipeline requires that other pieces of software be installed:

The following R packages are required in order to carry out the plotting:

The R packages may be installed using the following commands:

$ R
> install.packages(c('RColorBrewer', 'ape', 'ggrepel', 'ggplot2', 'reshape2'))

Installing under OSX

Installing the Zonkey pipeline under OSX poses several difficulties, mainly due to SmartPCA. In the follow, it is assumed that the Brew package manager has been installed, as this greatly simplifies the installation of other, required pieces of software.

Firstly, install software and libraries required to compile SmartPCA:

$ brew install gcc
$ brew install homebrew/dupes/lapack
$ brew install homebrew/science/openblas

In each case, note down the values indicated for LDFLAGS, CFLAGS, CPPFLAGS, etc.

Next, download and unpack the EIGENSOFT software. The following has been tested on EIGENSOFT version 6.1.1 (‘EIG6.1.1.tar.gz’).

To build SmartPCA it may further be nessesary to remove the use of the ‘real-time’ library:

$ sed -e's# -lrt##' Makefile > Makefile.no_rt

Once you have done this, you can build SmartPCA using the locally copied libraries:

$ env CC="/usr/local/opt/gcc/bin/gcc-6" LDFLAGS="-L/usr/local/opt/openblas/lib/" CFLAGS="-flax-vector-conversions -I/usr/local/opt/lapack/include/" make -f Makefile.no_rt

The above worked on my installation, but you may need to correct the variables using the values provided by Brew, which you noted down after running the ‘install’ command. You may also need to change the location of GGC set in the CC variable.

Testing the pipeline

An example project is included with the BAM pipeline, and it is recommended to run this project in order to verify that the pipeline and required applications have been correctly installed. See the Zonkey Pipeline example project section for a description of how to run this example project.