examples/rosettafold_all_atom.md
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+#!/usr/bin/env bash
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+
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+## SBGrid RosettaFold-All-Atom example
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+##
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+## James Vincent - help@sbgrid.org
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+## May 13, 2024
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+
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+
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+# SLURM
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+#SBATCH --mem=64G
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+#SBATCH -t 0:30:00
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+#SBATCH -p gpu_quad
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+#SBATCH --gres=gpu:1
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+
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+
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+# cd /temp_work/ch199734/114504_rosettafoldaa # BCH E3
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+cd /home/jjv16/tickets/114504_rosettafoldaa # O2
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+
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+module load cuda/11.2
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+
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+# Start SBGrid environment
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+source /programs/sbgrid.shrc
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+
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+# Set version of RFAA
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+export ROSETTAFOLDAA_X=bf21483
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+
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+# Set critical env variables
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+export DGLBACKEND=pytorch
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+#export ROSETTAFOLD_DB_PATH=/programs/local/biogrids/rosettafold/ # BCH E3
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+export ROSETTAFOLD_DB_PATH=/n/scratch/users/j//jjv16/rosettafold # O2
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+export MY_RFAA_DIR=/programs/x86_64-linux/rosettafoldaa/${ROSETTAFOLDAA_X}/RoseTTAFold-All-Atom
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+
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+# Call the correct python bundled with RFAA
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+python.rfaa --version
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+
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+# Run inference, override hydra parameters from YAML file
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+python.rfaa -m rf2aa.run_inference \
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+ --config-name sbgrid_example -cd ./ \
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+ checkpoint_path=${MY_RFAA_DIR}/RFAA_paper_weights.pt \
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+ database_params.command=${MY_RFAA_DIR}/make_msa.sh \
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+ database_params.hhdb=${ROSETTAFOLD_DB_PATH}/pdb100_2021Mar03/pdb100_2021Mar03
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+