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Unpack the Cufflinks source tarball:
tar zxvf cufflinks-0.7.0.tar.gz
Change to the Cufflinks directory:
cd cufflinks-0.7.0
Configure Cufflinks. If Boost is installed somewhere other than /usr/local, you will need to tell the installer where to find it using the --with-boost option. Specify where to install Cufflinks using the --prefix option.
./configure --prefix=/path/to/cufflinks/install --with-boost=/path/to/boost
If you see any errors during configuration, verify that you are using Boost version 1.38 or higher, and that the directory you specified via --with-boost contains the boost header files and libraries. See the Boost Getting started page for more details. If you copied the SAM tools binaries to someplace other than /usr/local/, you may need to supply the --with-bam configuration option.
Finally, make and install Cufflinks.
make
make install
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