Installing TopHat version 1.2.0ΒΆ

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.