Switch pre-defined data paths to sciCORE

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/"