Installing SGA(String Graph Assembler) on Ubuntu 10.04 Server(64bit)

SGA dependencies:
    -google sparse hash library (http://code.google.com/p/google-sparsehash/)
        $ wget http://sparsehash.googlecode.com/files/sparsehash_2.0-1_amd64.deb
        $ sudo dpkg -i sparsehash_2.0-1_amd64.deb
        
    -the bamtools library (https://github.com/pezmaster31/bamtools)
        $ git clone git://github.com/pezmaster31/bamtools.git
        $ sudo apt-get install cmake (Skip if cmake exists)
        $ cmake --version (version >= 2.6.4)
        In the top-level directory of BamTools, type the following commands:
            $ mkdir build
            $ cd build
            $ cmake ..
        Then go back up to the BamTools root directory.
            $ cd ..
        Assuming the build process finished correctly, you should be able to find the toolkit executable here:
            ./bin/
        The BamTools API and Utils libraries will be found here:
            ./lib/
        The BamTools API headers will be found here:
            ./include/*
            
    -zlib (http://www.zlib.net/)
        $ sudo apt-get install zlib1g zlib1g-dev
        
    -(optional but suggested) the hoard memory allocator (http://www.hoard.org/)
        $ wget http://www.cs.umass.edu/~emery/hoard/hoard-3.8/source/hoard-38.tar.gz
        $ tar xf hoard-38.tar.gz
        $ cd hoard-38/src
        $ make linux-gcc-x86-64
        
        Append to /etc/profile
        LD_PRELOAD="/path/libhoard.so" (Change /path/to to real path)
    
Additionally, the pipeline python scripts use the following modules. These are not required to build SGA but must be available if you want to use the relevant python helper scripts:
    -pysam (http://code.google.com/p/pysam/)
        SAMtools depends on the zlib library <http://www.zlib.net>
        $ sudo aptitude install samtool
        $ sudo aptitude install python-pyrex
        $ wget http://pysam.googlecode.com/files/pysam-0.6.tar.gz
        $ tar xf pysam-0.6.tar.gz
        $ cd pysam-0.6
        $ python setup.py build
        $ sudo python setup.py install
        
    -ruffus (http://www.ruffus.org.uk/)    
        $ sudo easy_install -U ruffus
        
        Ruffus relies on the dot programme from Graphviz (“Graph visualisation”)
        $ sudo easy_install -U ruffus

Installing SGA
    $ ./configure --prefix=/share/sga/ --with-bamtools=/home/kimth/SGA_related_library/bamtools --with-hoard=/home/kimth/SGA_related_library/hoard-38/src/ && make && make install
    
Testing SGA
    Append sga path to /etc/profile
    $ sga --help