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Commit 2b451a97 authored by Bienchen's avatar Bienchen
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Switch pre-defined data paths to sciCORE

parent a2b90ec3
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...@@ -222,27 +222,36 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments ...@@ -222,27 +222,36 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
snglrty_bin="/usr/bin/singularity", snglrty_bin="/usr/bin/singularity",
tmpdir_var="TMPDIR", tmpdir_var="TMPDIR",
extra_arg_list=None, extra_arg_list=None,
# data_dir="/scicore/data/managed/AF2params/frozen_210805T171956/", data_dir="/scicore/data/managed/AF2params/frozen_230815T000000/",
data_dir="/scicore/home/schwede/GROUP/alphafold_data/",
uniref90_database_path="/scicore/data/managed/UniProt/latest/uniref/" uniref90_database_path="/scicore/data/managed/UniProt/latest/uniref/"
+ "uniref90/uniref90.fasta", + "uniref90/uniref90.fasta",
mgnify_database_path="/scicore/data/managed/MGnify/frozen_210805T103002/" mgnify_database_path="/scicore/data/managed/MGnify/frozen_230815T000000/"
+ "mgy_clusters_2018_12.fa", + "mgnify/mgy_clusters_2022_05.fa",
bfd_database_path="/scicore/data/managed/BFD/frozen_210805T085238/" bfd_database_path="/scicore/data/managed/BFD/frozen_210805T085238/"
+ "bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt", + "bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt",
small_bfd_database_path="/scicore/data/managed/BFD_small/" small_bfd_database_path="/scicore/data/managed/BFD_small/"
+ "frozen_210812T135116/bfd-first_non_consensus_sequences.fasta", + "frozen_210812T135116/bfd-first_non_consensus_sequences.fasta",
uniref30_database_path="/scicore/home/schwede/GROUP/alphafold_data/" uniref30_database_path="/scicore/data/managed/AF_UniProt/"
+ "uniref30/UniRef30_2021_03", + "frozen_221115T101000/uniref/uniref30/UniRef30_2021_03",
uniprot_database_path="/scicore/home/schwede/GROUP/alphafold_data/uniprot/" uniprot_database_path="/scicore/data/managed/UniProt/latest/knowledgebase/"
+ "uniprot.fasta", + "complete/uniprot.fasta",
pdb70_database_path="/scicore/data/managed/PDB70/frozen_210805T142857/pdb70", pdb70_database_path="/scicore/data/managed/PDB70/frozen_210805T142857/"
pdb_seqres_database_path="/scicore/home/schwede/GROUP/alphafold_data/" + "pdb70",
+ "pdb_seqres/pdb_seqres.txt", 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/" template_mmcif_dir="/scicore/data/managed/PDB/latest/data/structures/all/"
+ "mmcif_files/", + "mmcif_files/",
obsolete_pdbs_path="/scicore/data/managed/PDB/latest/data/status/" obsolete_pdbs_path="/scicore/data/managed/PDB/latest/data/status/"
+ "obsolete.dat", + "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/" # template_mmcif_dir="/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif/"
# + "mmcif_files/", # + "mmcif_files/",
# obsolete_pdbs_path="/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif/" # obsolete_pdbs_path="/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif/"
......
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