diff --git a/run_af2/src/run_af2/run_singularity.py b/run_af2/src/run_af2/run_singularity.py index de18bb1f407c9fbaa4bd69a1ee07fe4980e79679..837ae2bb9ba33ddf274ab8c273bd508652936655 100644 --- a/run_af2/src/run_af2/run_singularity.py +++ b/run_af2/src/run_af2/run_singularity.py @@ -195,11 +195,12 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments model_preset="monomer", is_prokaryote_list=None, af2_image_file=None, - # "/export/soft/singularity-containers/alphafold", + # af2_image_dir="/export/soft/singularity-containers/alphafold", af2_image_dir="/scicore/home/schwede/GROUP/alphafold_data/", snglrty_bin="/usr/bin/singularity", tmpdir_var="TMPDIR", - data_dir="/scicore/data/managed/AF2params/frozen_210805T171956/", + # data_dir="/scicore/data/managed/AF2params/frozen_210805T171956/", + data_dir="/scicore/home/schwede/GROUP/alphafold_data/", uniref90_database_path="/scicore/data/managed/UniProt/latest/uniref/" + "uniref90/uniref90.fasta", mgnify_database_path="/scicore/data/managed/MGnify/frozen_210805T103002/" @@ -210,13 +211,14 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments + "frozen_210812T135116/bfd-first_non_consensus_sequences.fasta", uniclust30_database_path="/scicore/data/managed/Uniclust/" + "frozen_181015T170110/uniclust30_2018_08/uniclust30_2018_08", - uniprot_database_path="/scicore/home/schwede/scicore/home/schwede/GROUP/" - + "alphafold_data/uniprot/uniprot.fasta", + uniprot_database_path="/scicore/home/schwede/GROUP/alphafold_data/uniprot/" + + "uniprot.fasta", pdb70_database_path="/scicore/data/managed/PDB70/frozen_210805T142857/pdb70", - pdb_seqres_database_path="/scicore/home/schwede/scicore/home/schwede/GROUP/" - + "alphafold_data/pdb_seqres/pdb_seqres.txt", - template_mmcif_dir="/scicore/data/managed/PDB/latest/data/structures/all/" - + "mmcif_files/", + pdb_seqres_database_path="/scicore/home/schwede/GROUP/alphafold_data/" + + "pdb_seqres/pdb_seqres.txt", + # template_mmcif_dir="/scicore/data/managed/PDB/latest/data/structures/all/" + # + "mmcif_files/", + template_mmcif_dir="/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif", obsolete_pdbs_path="/scicore/data/managed/PDB/latest/data/status/" + "obsolete.dat", ):