____       _ _                       _        _____          _____  
 |  _ \     | | |                     ( )      / ____|   /\   |  __ \ 
 | |_) | ___| | |_ __ ___   __ _ _ __ |/ ___  | |  __   /  \  | |__) |
 |  _ < / _ \ | | '_ ` _ \ / _` | '_ \  / __| | | |_ | / /\ \ |  ___/ 
 | |_) |  __/ | | | | | | | (_| | | | | \__ \ | |__| |/ ____ \| |     
 |____/ \___|_|_|_| |_| |_|\__,_|_| |_| |___/  \_____/_/    \_\_|     

Usage

Modified Bellman's GAP compiler for incorporation of RNA 3D Motifs into RNA secondary structure prediction. The compiler retains full functionality but output is formatted to comma separated format.

Dependencies

Bellman's GAP was tested on the following dependencies.

compile time:

• C++ compiler (GCC g++ for example, tested on g++ 13.2.0)
• C compiler (GCC for example, tested on gcc 13.2.0)
• Flex >= 2.5.34 (tested on flex 2.6.4)
• GNU bison >= 2.4.1 (tested on 3.8.2)
• GNU make >= 3.81 (tested on 4.3)
• GSL (tested on 2.7.1)
• boost >= 1.36 (1.34 without the Accumulators Framework, installation with Boost 1.83 works)
  • unittest framework (libboost-test-dev)
  • pool
  • program options (libboost-program-options-dev)
  • cstdint
  • the accumulator framework (with -DSTATS)
• ksh93 - or - bash >= 2.03.0(1) (only needed for test scripts)

runtime:

• boost >= 1.36 (1.34 without the Accumulators Framework, works with Boost 1.83)
  • pool
  • program options
  • cstdint
  • the accumulator framework (with -DSTATS)

SOURCES

Always get the latest sources from github: git clone https://github.com/RNABioInfo/gapcM.git

INSTALLATION

from source

To install the Bellman's GAP compiler from source call:

1. ./configure --prefix=<install-path>
2. make
3. make install

If --prefix is not set the path defaults to /usr/local

More options for ./configure are:

CXX=<g++ path>
CC=<gcc path>
SED=<sed path>
FLEX=<flex path>
BISON=<bison path>
--with-boost=<path to booth installation>
--with-boost-program-options=<path to boost library program options> and --with-boost-unit-test-framework=<path to boost library unit test>

CMake

Installing the Bellman's GAP compiler with CMake is slightly more convenient as it will automatically install FLEX, BISON, GSL and Boost for you. This will install the Bellman's GAP compiler and it's dependencies locally and does not require sudo privileges. To install the Bellman's from source (but more convenient!) with CMake:

1. Create a build directory in /gapcM/, e.g. mkdir build
2. Move into the build directory with cd build
3. Call cmake ..
4. Call cmake --build .