Ticket #5578: run_af.sh

File run_af.sh, 464 bytes (added by Tom Goddard, 4 years ago)

Script to run singularity image to do an AlphaFold prediction

Line 
1#!/bin/bash
2
3SEQUENCE_FILE="$1"
4
5# Sequence and PDB databases
6export ALPHAFOLD_DATABASES=/wynton/group/databases/alphafold_CASP14
7
8# Specify which GPU to use. Important for Wynton cluster queue submissions.
9GPU_ID=${SGE_GPU:-0}
10
11# Load the version of CUDA we want.
12module load cuda/11.0
13
14singularity exec --nv -B "$ALPHAFOLD_DATABASES" -B "$PWD" /wynton/home/ferrin/goddard/alphafold_singularity/alphafold.sif /opt/alphafold/run.sh -f "$SEQUENCE_FILE" -a $GPU_ID