From 2b451a97546700a6a80a93ae6255c07874ac4a53 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 17 Aug 2023 09:34:01 +0200
Subject: [PATCH] Switch pre-defined data paths to sciCORE
---
run_af2/src/run_af2/run_singularity.py | 31 +++++++++++++++++---------
1 file changed, 20 insertions(+), 11 deletions(-)
diff --git a/run_af2/src/run_af2/run_singularity.py b/run_af2/src/run_af2/run_singularity.py
index 3c6115a..7d1f963 100644
--- a/run_af2/src/run_af2/run_singularity.py
+++ b/run_af2/src/run_af2/run_singularity.py
@@ -222,27 +222,36 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
snglrty_bin="/usr/bin/singularity",
tmpdir_var="TMPDIR",
extra_arg_list=None,
- # data_dir="/scicore/data/managed/AF2params/frozen_210805T171956/",
- data_dir="/scicore/home/schwede/GROUP/alphafold_data/",
+ data_dir="/scicore/data/managed/AF2params/frozen_230815T000000/",
uniref90_database_path="/scicore/data/managed/UniProt/latest/uniref/"
+ "uniref90/uniref90.fasta",
- mgnify_database_path="/scicore/data/managed/MGnify/frozen_210805T103002/"
- + "mgy_clusters_2018_12.fa",
+ mgnify_database_path="/scicore/data/managed/MGnify/frozen_230815T000000/"
+ + "mgnify/mgy_clusters_2022_05.fa",
bfd_database_path="/scicore/data/managed/BFD/frozen_210805T085238/"
+ "bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt",
small_bfd_database_path="/scicore/data/managed/BFD_small/"
+ "frozen_210812T135116/bfd-first_non_consensus_sequences.fasta",
- uniref30_database_path="/scicore/home/schwede/GROUP/alphafold_data/"
- + "uniref30/UniRef30_2021_03",
- 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/GROUP/alphafold_data/"
- + "pdb_seqres/pdb_seqres.txt",
+ uniref30_database_path="/scicore/data/managed/AF_UniProt/"
+ + "frozen_221115T101000/uniref/uniref30/UniRef30_2021_03",
+ uniprot_database_path="/scicore/data/managed/UniProt/latest/knowledgebase/"
+ + "complete/uniprot.fasta",
+ pdb70_database_path="/scicore/data/managed/PDB70/frozen_210805T142857/"
+ + "pdb70",
+ pdb_seqres_database_path="/scicore/data/managed/PDB/latest/derived_data/"
+ + "pdb_seqres.txt",
template_mmcif_dir="/scicore/data/managed/PDB/latest/data/structures/all/"
+ "mmcif_files/",
obsolete_pdbs_path="/scicore/data/managed/PDB/latest/data/status/"
+ "obsolete.dat",
+ # data_dir="/scicore/home/schwede/GROUP/alphafold_data/",
+ #mgnify_database_path="/scicore/data/managed/MGnify/frozen_210805T103002/"
+ #+ "mgy_clusters_2018_12.fa",
+ # uniref30_database_path="/scicore/home/schwede/GROUP/alphafold_data/"
+ # + "uniref30/UniRef30_2021_03",
+ # pdb_seqres_database_path="/scicore/home/schwede/GROUP/alphafold_data/"
+ # + "pdb_seqres/pdb_seqres.txt",
+ # uniprot_database_path="/scicore/home/schwede/GROUP/alphafold_data/uniprot/"
+ # + "uniprot.fasta",
# template_mmcif_dir="/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif/"
# + "mmcif_files/",
# obsolete_pdbs_path="/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif/"
--
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