examples/rosettafold_all_atom.md
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+## Rosettafold-All-Atom Example
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+Below we provide a sample bash script, a fasta file renamed from one of the RFAA examples and a config yaml file.
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+You must run RFAA outside of the installation directory.
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+In order to so this you must provide your own config yaml file(s) and set the location of this yaml file. We show an example using the --config-dir option frmo hydra.
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+These environment variables must be set:
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+
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+ROSETTAFOLDAA_X
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+
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+ROSETTAFOLD_DB_PATH
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+
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+RFAA_DIR
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+
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+DGLBACKEND
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+In addition the script below uses a proect directory that needs to be set or changed:
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+```MY_PROJ_DIR=<project directory> ```
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+The example script expects two files in the current directory:
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+sbgrid_example.yaml
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+
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+and
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+sbgrid_example.fasta
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+We purposely renamed these example files to be sure we're using our own files and not the examples files that come with RFAA.
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```
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#!/usr/bin/env bash
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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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+## help@sbgrid.org
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## May 13, 2024
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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 -t 2:00:00
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#SBATCH -p gpu_quad
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#SBATCH --gres=gpu:1
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+MY_PROJ_DIR=<project directory>
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+cd ${MY_PROJ_DIR}
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-# Change to project directory - cannot be run from RFAA source directory
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-cd /temp_work/ch199734/114504_rosettafoldaa
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-
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-# Load cuda
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module load cuda/11.2
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# Start SBGrid environment
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# Set critical env variables
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export DGLBACKEND=pytorch
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-export ROSETTAFOLD_DB_PATH=/programs/local/biogrids/rosettafold
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-export MY_RFAA_DIR=/programs/x86_64-linux/rosettafoldaa/${ROSETTAFOLDAA_X}/RoseTTAFold-All-Atom
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+export ROSETTAFOLD_DB_PATH=/n/shared_db/RoseTTAFold
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+export RFAA_DIR=/programs/x86_64-linux/rosettafoldaa/${ROSETTAFOLDAA_X}/RoseTTAFold-All-Atom
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# Call the correct python bundled with RFAA
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python.rfaa --version
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# Run inference, override hydra parameters from YAML file
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python.rfaa -m rf2aa.run_inference \
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- --config-name sbgrid_example -cd ./ \
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- checkpoint_path=${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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+ --config-name sbgrid_example --config-dir ./ \
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+ checkpoint_path=${RFAA_DIR}/RFAA_paper_weights.pt \
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+ database_params.command=${RFAA_DIR}/make_msa.sh \
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+ database_params.hhdb=${ROSETTAFOLD_DB_PATH}/pdb100_2021Mar03/pdb100_2021Mar03
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```