Installing MACS (Markovian Coalescent Simulator) on OS X 10.7 Lion

Posted: October 15th, 2011 | Author: | Filed under: Uncategorized | No Comments »

After a few years break from my dissertation research on coalescent modeling of HIV sequences, I’ve decided to dive in again. I am interested in generating some sequences from coalescent models with various characterestics. Though ms and msHOT from the Hudson lab are what I’ve used previously, I decided to see what else is out there.

The paper describing their methodology can be found here. The files are available here. In the extracted directory simply run “make all”.

I ran into two compilation errors:

g++ -Wall -g -I /Users/garychen/software/boost_1_36_0 -c algorithm.cpp
algorithm.cpp: In member function ‘void GraphBuilder::build()’:
algorithm.cpp:1272: error: ‘uint’ was not declared in this scope
algorithm.cpp:1272: error: expected `;’ before ‘iSegLength’
algorithm.cpp:1273: error: ‘iSegLength’ was not declared in this scope
make: *** [algorithm.o] Error 1

I changed uint to int on line 1272 and combined the cout onlines 1273 and 1274 into one line, which fixed the complaints. Then the build complained:

g++ -o macs simulator.o algorithm.o datastructures.o -static
ld: library not found for -lcrt0.o

Simply comment out “LINKFLAGS = -static” and everything should happily compile.

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