$REPOSITORY_INSTALL_DIRhttp://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zipmake$INSTALL_DIR/bin$INSTALL_DIR/bin$INSTALL_DIR/binchmod +x $INSTALL_DIR/bin/bowtie2$INSTALL_DIR/bin
Compiling bowtie2 requires zlib and libpthread to be present on your system.
http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zipmake$INSTALL_DIR/bin$INSTALL_DIR/bin$INSTALL_DIR/bin$INSTALL_DIR/bin