A-Z Index of IT Support

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 at the time of writing, for MacOS Sierra and later, some trickery needs to be done which boils down to "backdating" the command line tools to give a version of the compiler which works with the Relion source code. Please follow the appropriate instructions for your OS.

...And finally: The compiling process seems to go smoothly with the exact version numbers of the various components specified below, simply using the "latest" version hasn't always worked out. If you get a positive result with newer versions, we'd love to hear from you, in order to revise this guide.


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

Further Information
1  Are the Xcode command line tools installed?

Sierra and Later:
 
If you've already installed XCode and/or the XCode command line tools, you'll need to delete them for now (You can reinstall once Relion has been compiled). Delete XCode from /Applications and the command line tools folder /Library/Developer as appropriate.
Download this file:
Unzip and install DevSDK_OSX1010.pkg and then CLTools_Executables.pkg
 
Test by typing clang --version at the terminal. A response with these version numbers indicates all is well:
 
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
 
Earlier versions of MacOS:
 
Test by typing clang --version at the terminal. A response with these version numbers 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.

Please note that the version number seems to be important - compiling has failed with versions of cmake more recent than 3.8.1.

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

Test your gfortran install by following steps 1, 3 and 4 from:

https://www.thegeekstuff.com/2009/11/fortran-hello-world-example-how-to-write-and-execute-fortran-program-on-linux-os/

gfortran Gotcha: 

Some software (package managers, Python etc.) may permanently install special extras into your $PATH variable by putting some lines of code into the file ~/.profile

These "specials" have been known to break the gfortran compiler

You may want to edit your ~/.profile file and temporarily comment out these lines with a "#". Save the file and restart terminal.

The default $PATH (type echo $PATH into the terminal) should look like this:

/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin

You can reverse your edits to ~/.profile once Relion has compiled.


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)
 
Please note that the version number seems to be important - compiling has failed with versions of openmpi more recent than 2.1.1
 
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
cd relion
mkdir build
cd build
cmake ..
make -j 4
sudo make install


7  Launch Relion

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

Sierra and Later: If your compiling has worked, you'll most likely want to reverse the "backdating" of the command line tools from step (1). Do this by deleting the folder /Library/Developer 

Once this folder is deleted, type a command requiring the tools (e.g. clang --version) and your Mac will prompt you to install the comand line tools which go with your OS version.


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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