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Warning

This is as a Lab Notebook which describes how to solve a specific problem at a specific time. Please keep this in mind as you read and use the content. Please pay close attention to the date, version information and other details.

Installing r8s on HPCC

r8s (pronounced 'rates') is software for modeling rates of evolution across phyologenetic trees without relying on the assumption of constant molecular clock. However, while the original paper is highly cited and while it remains one of the few programs for clockless evolutionary modeling, as of the writing of the document, r8s is no longer being actively developed and no longer available from the original link in the paper. This creates some challenges with installing r8s on modern Linux architectures.

Obtaining a copy of r8s

Version 1.81 can be obtained from SourceForge. As of the writing of this document, this appears to be the most recent version publicly available.

Note that this version has removed certain features reliant on NRC (Numerical Recipes in C) due to licensing issues.

Compiling r8s in Linux

For compiling r8s, we will be relying on a blog post from PhyloBotanist, which is also an excellent source why and how to use r8s.

First, we will need make (which should always be available on HPCC) as well as gcc and gfortran (which can be obtained by loading one of the GCC modules).

Second, we will need to unpack the 'r8s1.81.tar.gz' file we obtained for SourceForge and enter the source directory.

Third, we need make the following changes to the make file:

  1. Replace the line "memory.o: /usr/include/errno.h /usr/include/sys/errno.h" with "memory.o: /usr/include/errno.h"
  2. If using GCC >= 10, which should be the case on HPCC:
    1. add '-fcommon' to CFLAGS options (line 11)
    2. add the line 'FFLAGS = -fallow-argument-mismatch' after CFLAGS

For an explanation as to why these options are needs for GCC >= 10, please see the following post from StackOverflow and a related discussion on gfortran

Finally, run 'make' within the src folder and hit enter when prompted to install after waiting a minute or so for configuration to run

It should then take a few minutes to build all the programs associated with r8s