Installation
If it is not already the case, Download the DeCoSTAR standalone archive and unpack it using
> tar -zxvf DeCoSTAR_standalone.tar.gz
> cd DeCoSTAR_standalone
If you are lucky, the bin/ folder already an executable that run on your computer. try it by typing:
> ./bin/DeCoSTAR
If it does not work you will need to compile the C++ code.
Its compilation requires that Bio++ is installed
(see the installation intructions) and that
you know in which directory it is installed.
You will also need to have the boost library installed on your computer.
Then edit the makefile file and go to the lines
BPP_INCLUDE=$(HOME)/local/bpp/dev/include
BPP_LIB=$(HOME)/local/bpp/dev/lib
BOOST_INCLUDE=/usr/include
BOOST_LIB=/usr/lib
Change BPP_INCLUDE and BPP_LIB values from $(HOME)/local to the directory in which Bio++ is installed on your system (it can be /usr/local or somewhere in your home directory for example).
Then, do the same thing for BOOST_INCLUDE and BOOST_LIB to specify where the boost library is installed.
Then type
> make
Usage
Numerous examples are included as tests in the archive provided; they are in the tests/ folder.
To launch all tests, simply tape
> sh scripts/allDeCoTests.sh > test.log
This should execute DeCoSTAR using various options and output the results in tests/testResults/. The expected results are in tests/expected/
(expect small differences in the adjacency histories. specifically concerning the boltzmann sampling examples).
This script along with the various tests/*.param.txt files and associated data will show you the different ways in which DeCoSTAR can be used.
A more detailed document describing the various options along with input and ouput formats can be find in the docs/ folder.
Page hosted by the PRABI and LBBE, Last modification July 2016
Contact: Eric dot Tannier at inria dot fr