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How to install Relion on a Mac

UPDATE 26/06/17: The Dunn School of Pathology have relion running on a cluster setup, which will give much faster results than a local install of Relion; please contact Joseph Caesar in the Dunn School for more information.

If you wish to use the less computationally intensive elements of Relion on your local machine, then please carry on with the steps below

The open-source software "Relion" is tricky to install due to its many dependencies - here are our boiled-down steps to get it working on Mac OS X

Some of the steps produce a lot of teminal output, and it's easy to forget which stage you have got to. Printing this page and ticking off the steps as you go is highly recommended.

Please note we have experienced problems installing Relion on Mac OS Sierra, due to the clang compiler being apparently unsupported. Earlier versions of Mac OS seem OK.


Contact julian.jordan@bioch.ox.ac.uk for more details

Further Information

1  Are the Xcode command line tools installed?

Test by typing clang --version at the terminal. A response something like this indicates all is well:
 
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
 
If not, install the command line tools at the terminal with: xcode-select --install


2  Is cmake installed?

Test by typing cmake at the terminal and you should see a "Usage" dialog, not an error.

If you need to install cmake, download cmake-3.8.1-Darwin-x86_64.dmg from https://cmake.org/download/ , copy the cmake application to /Applications and then run:

sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install

to make it work from the command line whenever you type cmake


3  You will need gfortran

Download from https://gcc.gnu.org/wiki/GFortranBinaries#MacOS , choosing the version appropriate for your Mac OS version.

Install the package


4  You will also need Open MPI

Download openmpi-2.1.1.tar.gz from https://www.open-mpi.org/software/ompi/v2.1/ and expand the archive. cd to the folder created by expanding the archive and run:
 
./configure --prefix=/usr/local
make all
sudo make install
(Entering your admin password at this last step)
 
Test your openMPI is working by typing: 
 
ompi_info
 
You should see some lines of information rather than an error 

Distilled from this more comprehensive guide

5  Install the most recent version of XQuartz

Download and install XQuartz from: https://www.xquartz.org

If you have an existing install then you may be able to skip this step but if the "cmake .." fails in the next stage with an X11 error then do this step


6  Now complete the steps for your relion install

Type the following at the terminal:
cd ~
git clone https://github.com/3dem/relion.git
git pull
cd relion
mkdir build
cd build
cmake ..
make -j 3
make install


7  Launch Relion

You should now be able to start the relion gui by typing relion at the terminal


8  You may also need CTFFIND

If you need Relion to talk to CTFFIND, please see our guide at:

http://www.bioch.ox.ac.uk/ctffind



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Page Last Updated: 26/06/2017 by Julian Jordan
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