RoseTTAFold

/fs00/software/rosettafold/1.1.0
注意：
apptainer默认会bind用户的
home目录，如果用户本来就有
RoseTTAFold或者
folding的conda环境则可能会发生冲突。用户可通过添加
--no-home选项避免此问题。
#BSUB -J RoseTTAFold
#BSUB -q gpu
#BSUB -n 8
#BSUB -gpu num=1
###### Configurie Numpy threads  ######
export OMP_NUM_THREADS="$LSB_DJOB_NUMPROC"
export MKL_NUM_THREADS="$LSB_DJOB_NUMPROC"
###### Definition ######
ROSETTAFOLD_DATADIR=/fsb/data/rosettafold      # path to RoseTTAFold data (host)
ROSETTAFOLD_IMAGE=RoseTTAFold-1.1.0.sif         # path to RoseTTAFold image (host)
ROSETTAFOLD_APPDIR=/app/RoseTTAFold             # path to RoseTTAFold working directory (container)
###### Database ######
UNIREF30_DB=$ROSETTAFOLD_DATADIR/UniRef30_2020_06
BFD_DB=$ROSETTAFOLD_DATADIR/bfd
PDB100_DB=$ROSETTAFOLD_DATADIR/pdb100_2021Mar03
###### Example ######
RUN_ROSETTAFOLD="apptainer run --bind $UNIREF30_DB:$ROSETTAFOLD_APPDIR/UniRef30_2020_06 \
                --bind $BFD_DB:$ROSETTAFOLD_APPDIR/bfd \
                --bind $PDB100_DB:$ROSETTAFOLD_APPDIR/pdb100_2021Mar03 \
                --nv $ROSETTAFOLD_IMAGE"
# For monomer structure prediction (e2e)
${RUN_ROSETTAFOLD} $ROSETTAFOLD_APPDIR/run_e2e_ver.sh $ROSETTAFOLD_APPDIR/example/input.fa output/
# For monomer structure prediction (pyrosetta)
${RUN_ROSETTAFOLD} $ROSETTAFOLD_APPDIR/run_pyrosetta_ver.sh $ROSETTAFOLD_APPDIR/example/input.fa output/
# For complex modeling
${RUN_ROSETTAFOLD} python $ROSETTAFOLD_APPDIR/network/predict_complex.py \
                -i $ROSETTAFOLD_APPDIR/example/complex_modeling/paired.a3m \
                -o output/ -Ls 218 310
# For PPI screening using faster 2-track version (example input and output are at example/complex_2track)
${RUN_ROSETTAFOLD} python $ROSETTAFOLD_APPDIR/network_2track/predict_msa.py \
                -msa $ROSETTAFOLD_APPDIR/example/complex_2track/input.a3m \
                -npz output/complex.npz -L1 218