Installing TopHat version 1.2.0
===============================

    - wget http://tophat.cbcb.umd.edu/downloads/tophat-1.2.0.tar.gz

::

    INSTALL_DIR=/share/apps

    cp samtools-X.X.X/libbam.a to $INSTALL_DIR/lib
    mkdir $INSTALL_DIR/include/bam
    cp samtools-X.X.X/*.h $INSTALL_DIR/include/bam

    ./configure --prefix=$INSTALL_DIR --with-bam=$INSTALL_DIR

    {...}

    configure: creating ./config.status
    config.status: creating Makefile
    config.status: creating src/Makefile
    config.status: creating config.h
    config.status: executing depfiles commands

    -- tophat 1.2.0 Configuration Results --
    C compiler:          gcc -Wall -m64 -O3  -DNDEBUG
    C++ compiler:        g++ -Wall -m64 -O3  -DNDEBUG -I/share/apps//include
    GCC version:         gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-46)
    Host System type:    x86_64-unknown-linux-gnu
    Install prefix:      /share/apps/
    Install eprefix:     ${prefix}

See also `Cufflinks installation instructions <http://cufflinks.cbcb.umd.edu/tutorial.html>`_.