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| 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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this shouldn't be removed, this is a test example
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| --bind $INPUT_FASTA_FILE_DIR:/fasta \ | ||
| --bind $OUTPUT_DATA_DIR:/dimer_models \ | ||
| --bind /scratch/rhaas/SUP-5301/database:/database \ | ||
| /scratch/rhaas/SUP-5301/alphafold.sif \ |
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would be good to keep in sync with the original binding folders and use env variables for the container and database ($AF_CONTAINER and $AF_DB respectively)
| --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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there are two configurations for tests (depends on what's available), thus would be good to preserve both of them
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@mtitov This PR is out of date now. |
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