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config.yaml
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config.yaml
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# table with sample --> fasta_file information
samples_file: tests/data/multi-mcr.tsv
# output location
output_dir: tests/output/multi-mcr/
# temporary file directory (your username will be added automatically)
tmp_dir: /ebio/abt3_scratch/
# params (change as needed)
params:
ionice: -c 3
use_gpu: true
af_msa_num_cpu: 8
max_template_date: "2022-01-01"
db_preset: full_dbs #reduced_dbs
model_preset: multimer #monomer
is_prokaryote: true
mTM_align:
run_intra: true
run_inter: true
# databases
## all databases should be within the `base_path`
databases:
base_path: /ebio/abt3_scratch/alphafold/v2/data/
uniref90: uniref90/uniref90.fasta
uniprot: uniprot/uniprot.fasta
mgnify: mgnify/mgy_clusters_2018_12.fa
bfd: bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
small_bfd: small_bfd/bfd-first_non_consensus_sequences.fasta
uniclust30: uniclust30/uniclust30_2018_08/uniclust30_2018_08
pdb70: pdb70/pdb70
pdb_seqres: pdb_seqres/pdb_seqres.txt
template_mmcif: pdb_mmcif/mmcif_files
obsolete_pdbs: pdb_mmcif/obsolete.dat
# snakemake pipeline
pipeline:
snakemake_folder: ./
script_folder: ./bin/scripts/
export_conda: True
name: alphafold_sm