Tophat (1.4.1 from binary)

A spliced read mapper for RNA-Seq.

wget http://tophat.cbcb.umd.edu/downloads/tophat-1.4.1.Linux_x86_64.tar.gz
tar xvzf tophat-1.4.1.Linux_x86_64.tar.gz

mv tophat-1.4.1.Linux_x86_64 /usr/local/bin/
ln -s /usr/local/bin/tophat-1.4.1.Linux_x86_64/tophat /usr/local/bin/

wget http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz
tar zxvf test_data.tar.gz
cd test_data/
tophat -r 20 test_ref reads_1.fq reads_2.fq