File	Date	Author	Commit
doc	2012-07-10	Toshiro K. Ohsumi	[beaac0] Initial git commit for public version of MolBio...
src	2012-07-10	Toshiro K. Ohsumi	[beaac0] Initial git commit for public version of MolBio...
COPYING	2012-07-10	Toshiro K. Ohsumi	[beaac0] Initial git commit for public version of MolBio...
Doxyfile	2012-07-10	Toshiro K. Ohsumi	[beaac0] Initial git commit for public version of MolBio...
MakeAllApps.pl	2012-07-10	Toshiro K. Ohsumi	[beaac0] Initial git commit for public version of MolBio...
README.txt	2012-07-10	Toshiro K. Ohsumi	[beaac0] Initial git commit for public version of MolBio...

Read Me

##############################################################################
## MolBioLib: A C++11 framework for rapidly developing bioinformatics tasks ##
## Copyright (C)  2012  Massachusetts General Hospital                      ##
##                                                                          ##
## This program is free software: you can redistribute it and/or modify     ##
## it under the terms of the GNU General Public License as published by     ##
## the Free Software Foundation, version 3 of the License.                  ## 
##                                                                          ##
## This program is distributed AS IS.                                       ##
##############################################################################


The GNU license text may be found in the COPYING file.

To build the documentation, build and/or install Doxygen, 
obtained from the site

http://www.doxygen.org

and then run doxygen in this, the top-level, directory.  To view the 
documentation, use a web browser to open the file

doc/doxygen/index.html

relative to this directory.  The usage, compilation, etc. information may be
found in the table of contents page.


For those who wish to skip the documentation, one can either use clang++ which
should be based on at least LLVM 3.0[svn] or g++ which should be at least 
version 4.7.0.  After installation of clang++ or g++ (if needed), please edit:

1. src/include/PrimitiveTypes.hpp.  Please note the last entries in the file,
   MOLBIOLIB_IO_PRECISION, HAVE_WC_AWK, and RM_COMMAND.  Depending on your
   operating system and output preferences, these may need to be changed.
   Unusually, in MAC OS X, one should comment out HAVE_WC_AWK due to the lack
   of the -L parameter in wc.

2. MakeAllApps.pl, specifically the locations where the $CPP, $CPPOPTS, 
   $CPPLIBS, $CC, and $CPPDEBUG variables are set.  Some suggestions are given. 

Then run MakeAllApps.pl by doing
./MakeAllApps.pl

Note that if one is going to compile the external packages, g++ is required, 
even if one has clang++.  To skip compiling the external packages, pass 
--NO_EXTERN to the MakeAllApps.pl script as a parameter.