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Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

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