Relion

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.

Pour plus d'information sur la version 4.0 et sur la version 5.0

Exécution de Relion

Module	Version
relion	4.0 5.0

Pour voir les versions disponibles lorsque vous êtes connecté à eXplor, exécutez la commande :

module spider relion

Pour utiliser relion, tapez :

module load relion/<version>

en spécifiant l'une des versions disponibles.

Exemple de Script GPU de Job relion

#!/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=1
#SBATCH --ntasks-per-node=8
#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 compenv/intel/2019.4
module load 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 ""