Installing dependencies

On Linux, EMBOSS and HMMER can be installed through the package manager but we want to get the latest HMMER to ensure that hmmer2go works with all models from Pfam. For example, on Ubuntu the following command would install the dependencies.

wget http://selab.janelia.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
tar xzf hmmer-3.1b2-linux-intel-x86_64.tar.gz
sudo cp hmmer-3.1b2-linux-intel-x86_64/binaries/* /usr/bin
sudo apt-get install -y emboss

# clean up (optional)
rm -rf hmmer-3.1b2-linux-intel-x86_64

On a Mac or other system, it will be necessary to download the correct binaries for your platform. The binaries from EMBOSS can be obtained from the EMBOSS download page. The HMMER binaries can be obtained from the HMMER software page. The HMMER webpage will detect your platform and suggest a package to download, so be careful to choose the right package for where you plan to run the programs.