File	Date	Author	Commit
cmake	2015-03-24	Andras Aszodi	[82b008] Added Zlib detection to FindBamTools.cmake for ...
config	2011-10-29	Agyaras	[8ff4d8] Initial commit: putting Multovl under GIT
doc	2015-03-24	Andras Aszodi	[2b6c07] Updated config/build.c.in so that the bitness o...
src	2015-03-28	agyaras	[1b0aa2] Fixed BAM support detection bug in config/third...
.gitattributes	2014-11-22	aszodi	[1a6b98] Changes needed to compile with Visual Studio 20...
.gitignore	2015-01-03	AA	[c2ad19] Second part of the large commit: all files that...
CMakeLists.txt	2015-03-28	AA	[afc9ab] Fixed top-level CMakeLists.txt Boost_CHRONO_FOU...
LICENSE	2012-05-22	Andras Aszodi	[9fe3ac] Moved the license to LICENSE in the top-level d...
NERDS_ONLY.txt	2014-12-09	aszodi	[dd0513] Modified FindBamTools.cmake so that it finds Zl...
README.txt	2012-05-22	Andras Aszodi	[e80eee] Modified Doxygen documentation generation and t...

Read Me

MULTIPLE OVERLAP OF GENOMIC REGIONS
===================================

by Andras Aszodi
Version 1.2

See doc/html/guide.html for installation instructions
and a detailed documentation.

This program is is licensed under the terms of the BSD Open Source license.
See the file LICENSE for details.

Installation for the Impatient
------------------------------

You will need cmake 2.8 or above, a C++98-compliant compiler, 
and the Boost libraries (1.44 or above) to build Multovl.
If you want BAM file support, define BAMTOOLS_ROOT.
If you want to build 'pgmultovl' that reads/writes tracks from/to
a PostgreSQL database using libpqxx, then define PQXX_ROOT.

By default all these external libraries will be linked statically.
To link all of them dynamically instead, specify
-DMULTOVL_USE_DYNAMIC_LIBS:BOOL=ON

The basic steps:

mkdir build 
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DBOOST_ROOT=/path/to/boost \
	-DBAMTOOLS_ROOT=/path/to/bamtools \                <=== optional
	-DPQXX_ROOT=/path/to/pqxx \                        <=== optional
    -DCMAKE_INSTALL_PREFIX=/path/to/installdir ..

make [all]

Or you can spell out what make all does:

make apps
make doc    (this generates Doxygen documentation if you have Doxygen installed)

And then finally:

make install (this you may need to run as root, depending on installdir permissions)

The tools should now be installed in ${CMAKE_INSTALL_PREFIX}/multovl-1.2/bin.

Additional Cmake settings are listed in the top-level CMakeLists.txt, or you may run
cmake -i for interactive options, or ccmake.