This roll bundles relion, eman2 and frealign

For more information about the various packages included in the cryoem roll please visit their official web pages:

• relion is is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)
• frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles
• eman2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes

To build/install this roll you must have root access to a Rocks development machine (e.g., a frontend or development appliance).

If your Rocks development machine does not have Internet access you must download the appropriate cryoem source file(s) using a machine that does have Internet access and copy them into the src/<package> directories on your Rocks development machine.

The sdsc-roll must be installed on the build machine, since the build process depends on make include files provided by that roll.

The roll sources assume that modulefiles provided by SDSC compiler, cmake, and mpi rolls are available, but it will build without them as long as the environment variables they provide are otherwise defined.

The build process requires the FFTW and MKL libraries and assumes that the modulefiles provided by the corresponding SDSC rolls are available. It will build without the modulefiles as long as the environment variables they provide are otherwise defined.

To build the cryoem-roll, execute this on a Rocks development machine (e.g., a frontend or development appliance):

% make 2>&1 | tee build.log

A successful build will create the file cryoem-*.disk1.iso. If you built the roll on a Rocks frontend, proceed to the installation step. If you built the roll on a Rocks development appliance, you need to copy the roll to your Rocks frontend before continuing with installation.

This roll source supports building with different compilers and for different MPI flavors. The ROLLCOMPILER and ROLLMPI make variables can be used to specify the names of the compiler and MPI modulefiles to use for building the software, e.g.,

make ROLLCOMPILER=intel ROLLMPI=mvapich2_ib 2>&1 | tee build.log

The build process recognizes "gnu", "intel" or "pgi" as the value for the ROLLCOMPILER variable; any MPI modulefile name may be used as the value of the ROLLMPI variable. The default values are "gnu", "rocks-openmpi".

Note that eman2 is always built with the gnu compiler.

To install, execute these instructions on a Rocks frontend:

% rocks add roll *.iso
% rocks enable roll cryoem
% cd /export/rocks/install
% rocks create distro

Subsequent installs of compute and login nodes will then include the contents of the cryoem-roll. To avoid cluttering the cluster frontend with unused software, the cryoem-roll is configured to install only on compute and login nodes. To force installation on your frontend, run this command after adding the cryoem-roll to your distro

% rocks run roll cryoem host=NAME | bash

where NAME is the DNS name of a compute or login node in your cluster.

In addition to the software itself, the roll installs cryoem environment module files in:

/opt/modulefiles/applications/cryoem

The cryoem-roll includes a test script which can be run to verify proper installation of the roll documentation, binaries and module files. To run the test scripts execute the following command(s):

% /root/rolltests/cryoem.t