Warning

Iceberg was decommissioned on 30th November 2020. Users of Iceberg need to switch to using ShARC and/or Bessemer instead.

relion¶

RELION is a software package that performs an empirical Bayesian approach to (cryo-EM) structure de-termination by single-particle analysis. Note that RELION is distributed under a GPL license.

Making RELION available¶

The following module command makes the latest version of gemini available to your session

module load apps/gcc/4.4.7/relion

Alternatively, you can make a specific version available

module load apps/gcc/4.4.7/relion/1.4

Installation notes¶

These are primarily for system administrators.

Install instructions: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Download_%26_install

RELION was installed using the gcc 4.4.7 compiler and Openmpi 1.8.8
install_relion.sh
Note - the environment variable RELION_QSUB_TEMPLATE points to an SGE qsub template, which needs customizing to work with our environment

Modulefile¶

The module file is on the system at /usr/local/modulefiles/apps/gcc/4.4.7/relion/1.4

The contents of the module file is

#%Module1.0#####################################################################
##
## relion module file
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

proc ModulesHelp { } {
    global bedtools-version

    puts stderr "   Setups `relion-$relionversion' environment variables"
}

set     relionversion 1.4

module load apps/gcc/4.4.7/ctffind/3.140609
module load apps/binapps/resmap/1.1.4
module load mpi/gcc/openmpi/1.8.8

prepend-path PATH /usr/local/packages6/apps/gcc/4.4.7/relion/1.4/bin
prepend-path LD_LIBRARY_PATH /usr/local/packages6/apps/gcc/4.4.7/relion/1.4/lib
setenv RELION_QSUB_TEMPLATE /usr/local/packages6/apps/gcc/4.4.7/relion/1.4/bin/relion_qsub.csh
setenv RELION_CTFFIND_EXECUTABLE ctffind3_mp.exe
setenv RELION_RESMAP_EXECUTABLE /usr/local/packages6/apps/binapps/resmap/1.1.4