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Update impress setup instructions #20

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89 changes: 47 additions & 42 deletions src/setup/readme.md
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Original file line number Diff line number Diff line change
Expand Up @@ -77,56 +77,61 @@ eval "$(conda shell.posix hook)"
conda activate $WORK_DIR/ve.impress
```

### AlphaFold2
### AlphaFold2 (apptainer-overlay.sh)

```shell
export AF_INPUTS=$BASE_DIR/alphafold/inputs
export AF_OUTPUTS=$BASE_DIR/alphafold/outputs
export AF_ETC=$BASE_DIR/alphafold/etc

export XLA_PYTHON_CLIENT_PREALLOCATE="false"
export XLA_PYTHON_CLIENT_MEM_FRACTION=".75"
export XLA_PYTHON_CLIENT_ALLOCATOR="platform"

mkdir -p $BASE_DIR/alphafold/inputs $BASE_DIR/alphafold/outputs
cat > $BASE_DIR/alphafold/inputs/test.fasta <<EOF
>3SFJ_1|Chains A, C|Tax1-binding protein 3|Homo sapiens (9606)
VTAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQ
>3SFJ_2|Chains B, D|decameric peptide iCAL36|
ANSRWPTSII
EOF
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@mtitov mtitov May 27, 2025 •
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this shouldn't be removed, this is a test example


singularity run -B $AF_INPUTS:/inputs -B $AF_OUTPUTS:/outputs -B $AF_ETC:/etc \
-B $AF_DB:/data --pwd /app/alphafold --nv $AF_CONTAINER \
--data_dir=/data \
--uniref90_database_path=/data/uniref90/uniref90.fasta \
--mgnify_database_path=/data/mgnify/mgy_clusters_2022_05.fa \
--template_mmcif_dir=/data/pdb_mmcif/mmcif_files/ \
--obsolete_pdbs_path=/data/pdb_mmcif/obsolete.dat \
--fasta_paths=/inputs/test.fasta \
--output_dir=/outputs \
--model_preset=multimer \
--db_preset=reduced_dbs \
--small_bfd_database_path=/data/small_bfd/bfd-first_non_consensus_sequences.fasta \
--pdb_seqres_database_path=/data/pdb_seqres/pdb_seqres.txt \
--uniprot_database_path=/data/uniprot/uniprot.fasta \
--max_template_date=2020-12-01 \
--use_gpu_relax=True

singularity run -B $AF_INPUTS:/inputs -B $AF_OUTPUTS:/outputs -B $AF_ETC:/etc \
-B $AF_DB:/data --pwd /app/alphafold --nv $AF_CONTAINER \
--data_dir=/data \
--uniref90_database_path=/data/uniref90/uniref90.fasta \
--mgnify_database_path=/data/mgnify/mgy_clusters_2022_05.fa \
--template_mmcif_dir=/data/pdb_mmcif/mmcif_files/ \
--obsolete_pdbs_path=/data/pdb_mmcif/obsolete.dat \
--fasta_paths=/inputs/test.fasta \
--output_dir=/outputs \
--model_preset=multimer \
--db_preset=full_dbs \
--bfd_database_path=/data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
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@mtitov mtitov May 27, 2025

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there are two configurations for tests (depends on what's available), thus would be good to preserve both of them

--pdb_seqres_database_path=/data/pdb_seqres/pdb_seqres.txt \
--uniprot_database_path=/data/uniprot/uniprot.fasta \
--uniref30_database_path=/data/uniref30/UniRef30_2021_03 \
--max_template_date=2020-12-01 \
--use_gpu_relax=True

INPUT_FASTA_FILE_DIR=$1
INPUT_FASTA_FILE_NAME=$2
OUTPUT_DATA_DIR=$3

apptainer run --nv \
--bind $INPUT_FASTA_FILE_DIR:/fasta \
--bind $OUTPUT_DATA_DIR:/dimer_models \
--bind /scratch/rhaas/SUP-5301/database:/database \
/scratch/rhaas/SUP-5301/alphafold.sif \
Comment on lines +98 to +101
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would be good to keep in sync with the original binding folders and use env variables for the container and database ($AF_CONTAINER and $AF_DB respectively)

--data_dir=/database \
--uniref90_database_path=/database/uniref90/uniref90.fasta \
--mgnify_database_path=/database/mgnify/mgy_clusters_2022_05.fa \
--template_mmcif_dir=/database/pdb_mmcif/mmcif_files/ \
--obsolete_pdbs_path=/database/pdb_mmcif/obsolete.dat \
--fasta_paths=/fasta/$INPUT_FASTA_FILE_NAME \
--output_dir=/dimer_models \
--model_preset=multimer \
--db_preset=reduced_dbs \
--small_bfd_database_path=/database/small_bfd/bfd-first_non_consensus_sequences.fasta \
--uniprot_database_path=/database/uniprot/uniprot.fasta \
--pdb_seqres_database_path=/database/pdb_seqres/pdb_seqres.txt \
--max_template_date=2020-12-01 \
--use_gpu_relax=True
```

---
**NOTE**

To use the `Apptainer` or `Singularity` AlphaFold2 container with `RADICAL-Pilot`, you need to create an environment at the pilot level and pass it to the container task as follows:

```python
pilot.prepare_env('bs0', {'type' : 'shell'})
# create a new task description, and fill it.
td = rp.TaskDescription()
td.pre_exec = ['module load cuda/12.3.0']
td.executable = '/bin/bash'
td.arguments = ['/scratch/bblj/alsaadi1/AF-SUP-5301/apptainer-overlay.sh']
td.named_env = 'bs0'
```
Failure to specify `td.named_env = 'bs0'` will result in a container internal error due to a mismatch in Python libraries.

---

### PyRosetta

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