compiling Codon Optimizer on ubuntu 18.04

There is a cool old piece of software for codon optimization, inventively named "Codon Optimizer"

http://www.cs.ubc.ca/labs/beta/Projects/codon-optimizer/

It's not really very useful from a practical standpoint because its codon optimization strategy is to try to replace every codon with the highest CAI codon for the same amino acid. Which turns out to not be a very good strategy in practice. The software also can only optimize for E. coli, and has the translation tables and codon frequency tables hard-coded in.

Nevertheless, it's one of the few Open Source programs for codon optimization, so it might be useful to use as a starting point for a more fully-featured program, by adding more tables or some alternative algorithms for picking codons to use.

Unfortunately, it won't compile on Ubuntu 18.04.

To get it to compile, I had to do the following:



install automake:
sudo apt install automake

install boost:
sudo apt install libboost-all-dev

In the file "configure.ac" change the line:
AM_INIT_AUTOMAKE([1.11 foreign -Wall -Werror dist-zip])
to
AM_INIT_AUTOMAKE([1.11 foreign -Wall -Werror dist-zip subdir-objects])

execute:
$ make

make will fail with an error about the boost library.

now, in the file "configure" comment out the line:

boost_major_version=`echo "$boost_cv_lib_version" | sed 's/_//;s/_.*//'`
and add the line:

boost_major_version=165
in its place.

execute:
make

It should compile now.