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

Dependencies

Bellman's GAP was tested on the following dependencies.

compile time:

• C++ compiler (GCC g++ for example)
• C compiler (GCC for example)
• Flex >= 2.5.34
• GNU bison >= 2.4.1
• GNU make >= 3.81
• Mercurial >= 0.9.5
• boost >= 1.36 (1.34 without the Accumulators Framework)
  • 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)
  • pool
  • program options
  • cstdint
  • the accumulator framework (with -DSTATS)

SOURCES

Always get the latest sources from github: git clone https://github.com/jlab/gapc.git

INSTALLATION

from source

To install Bellman's GAP 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>

conda

You can find conda packages for linux-64 and osx-64 in the bioconda channel: https://anaconda.org/bioconda/bellmans-gapc for easy installation into your conda environment:

conda install -c bioconda bellmans-gapc

Ubuntu

Bellman's GAP is available as a pre-compiled Debian package via Ubuntus launchpad system, a Ubuntu Personal Package Archive (PPA). Packages for Ubuntu versions 16.04 (Xenial) and newer can be obtained from janssenlab/software. On your command line, execute the three following commands

sudo add-apt-repository ppa:janssenlab/software
sudo apt-get update
sudo apt-get install bellmansgapc

For older Ubuntu releases, have a look at bibi-help/bibitools (Ubuntu versions 10.04, 11.10, 12.04, 12.10, 13.04, 13.10, 14.04, 14.10, 15.04)

sudo add-apt-repository ppa:bibi-help/bibitools
sudo apt-get update
sudo apt-get install bellmansgapc

MacPorts

Under Mac OS X you may want to use MacPorts to install the compiler. There is a (most likely outdated) ports description on the BiBiServ MacPorts repository. You can install GAP-C via:

$ sudo port install http://bibiserv.techfak.uni-bielefeld.de/resources/macports/ports/lang/gapc.tgz