Relion (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a software package that employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination. It is developed in the group of Sjors Scheres at the MRC Laboratory of Molecular Biology.

Versions

4.0

5.0

Pour charger le module

module load mcs_mod/softwares/relion/version

Exemple de script de job de relion-4.0

#!/bin/bash

#SBATCH --account=<group>
#SBATCH --partition=gpu

## GPU Request
#SBATCH --gres=gpu:2

## Resource Request
#SBATCH --nodes=2
#SBATCH --ntasks=16
#SBATCH --cpus-per-task=8
#SBATCH --ntasks-per-node=1
#SBATCH --time=0-10:00:00

# Set the file for output (stdout)
#SBATCH --output=Class3D-%j.out

# Set the file for error log (stderr)
#SBATCH --error=Class3D-%j.err

# Load the modules
module purge
module load mcs_mod/compenv/intel/2019.4
module load mcs_mod/softwares/relion/4.0

env | grep -i slurm 

echo ""
echo "  JOB started: $(date) "
echo ""

cd $SLURM_SUBMIT_DIR

# Creating temporary directory 
# do not run your JOB in the HOME or $SLURM_SUBMIT_DIR 
WORKDIR="$SCRATCHDIR/job.$SLURM_JOB_ID.$USER"
mkdir -p $WORKDIR

echo ""
echo "  WORKDIR: $WORKDIR"
echo ""

cp $SLURM_SUBMIT_DIR/* $WORKDIR

cd $WORKDIR

#Paste Command here
srun relion_refine_mpi --i Particles/shiny_2sets.star --ref emd_2660.map:mrc --firstiter_cc --ini_high 60 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 4 --particle_diameter 360 --K 6 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --random_seed 0 --o class3d --gpu --j 6 --dont_combine_weights_via_disc

cp $WORKDIR/* $SLURM_SUBMIT_DIR

cd $SLURM_SUBMIT_DIR

# removing the $WORKDIR 
rm $WORKDIR/*
rmdir $WORKDIR

echo ""
echo "  JOB finished: $(date) "
echo ""