NB! : Low maintenance. Replaced by HISAT2
wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
tar -xvzf tophat-2.1.1.Linux_x86_64.tar.gz
mv tophat-2.1.1.Linux_x86_64/ /usr/local/bin/tophat/
export PATH=/usr/local/bin/tophat:$PATH