diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9d40cc7865b733e1fde3e95323cb8dc31588bdfe..39f610cff12fb8efaa9a87e2b8a746f1708eb7a1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,12 @@
+Changes in Release 4.0.0
+=================================================================================
+
+* `run_af2` Python package:
+ * Rename command line option `--uniclust30-database-path` to
+ `--uniref30-database-path` according to the change in AF2 2.3.0
+ * Adapt `submit-af2` to newer SLURM version
+
+
Changes in Release 3.1.1
=================================================================================
diff --git a/run_af2/bin/submit-af2 b/run_af2/bin/submit-af2
index 1108268550d0ef516691276e68bbb7a8c3ff4874..b6a966864de09757383809c5a5d8c983dbc35926 100755
--- a/run_af2/bin/submit-af2
+++ b/run_af2/bin/submit-af2
@@ -66,7 +66,7 @@ shift
FASTAFILES=$@
sbatch --job-name=af2 \
- --workdir=$(pwd) \
+ -D $(pwd) \
--cpus-per-task=12 \
--mem=85G \
--qos=1week \
diff --git a/run_af2/pyproject.toml b/run_af2/pyproject.toml
index a4190d1f35c094bfc47b22a98ea85e7e976e763d..d550e432144c1f8f330d83c4049cee75509d983e 100644
--- a/run_af2/pyproject.toml
+++ b/run_af2/pyproject.toml
@@ -16,6 +16,8 @@ relative_to = ".."
write_to = "src/run_af2/version.py"
[build-system]
+# This works only with Python 3.6, for 3.7 this needs to be fixed. With
+# setuptools >=61, setup.cfg is gone (https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#configuring-setuptools-using-pyproject-toml-files)
requires = [
"setuptools==56",
"wheel",
diff --git a/run_af2/src/run_af2/_shared.py b/run_af2/src/run_af2/_shared.py
index 31a46a1bc1ea5a5ef044fce176b2cdc4262e8beb..9886788d18eb277a17ebcbf24b84ae0f05b51256 100644
--- a/run_af2/src/run_af2/_shared.py
+++ b/run_af2/src/run_af2/_shared.py
@@ -61,7 +61,7 @@ def parse_af2_arguments(parser):
`argparse.ArgumentParser.parse_args`.
"""
db_preset_choices = {
- "reduced_dbs": ["bfd_database_path", "uniclust30_database_path"],
+ "reduced_dbs": ["bfd_database_path", "uniref30_database_path"],
"full_dbs": ["small_bfd_database_path"],
}
@@ -155,7 +155,7 @@ def parse_af2_arguments(parser):
af2_group.add_argument(
"--uniref90-database-path",
type=str,
- help="Path to the Uniref90 database.",
+ help="Path to the UniRef90 database.",
metavar="<PATH>",
default=None,
)
@@ -182,9 +182,9 @@ def parse_af2_arguments(parser):
default=None,
)
af2_group.add_argument(
- "--uniclust30-database-path",
+ "--uniref30-database-path",
type=str,
- help="Path to the Uniclust30 database, prefix for the HHblits search.",
+ help="Path to the UniRef30 database, prefix for the HHblits search.",
metavar="<PATH/ PREFIX>",
default=None,
)
@@ -276,7 +276,7 @@ def parse_af2_arguments(parser):
# LocalWords: argparse ArgumentParser Namespace Bioinformatics Biozentrum af
# LocalWords: sublicense NONINFRINGEMENT sys cfg pylint toplevel ImportError
-# LocalWords: dbs bfd uniclust AlphaFold dir str metavar fasta nargs YYYY DL
+# LocalWords: dbs bfd uniref AlphaFold dir str metavar fasta nargs YYYY DL
# LocalWords: basenames gpu ensembling casp sciCORE prog params uniref pdb
# LocalWords: mgnify MGnify HHblits HHsearch mmcif pdbs args arg getattr
# LocalWords: stderr
diff --git a/run_af2/src/run_af2/run_singularity.py b/run_af2/src/run_af2/run_singularity.py
index e55a9b3022a3f70d1306400b0b789415955b8c6d..efd3efac60be9753473d7b94976e6e8dd7b969ce 100644
--- a/run_af2/src/run_af2/run_singularity.py
+++ b/run_af2/src/run_af2/run_singularity.py
@@ -232,8 +232,8 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
+ "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",
- uniclust30_database_path="/scicore/data/managed/Uniclust/"
- + "frozen_181015T170110/uniclust30_2018_08/uniclust30_2018_08",
+ 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",
@@ -331,9 +331,9 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
Corresponds to small_bfd_database_path in
AF2.
:type small_bfd_database_path: :class:`str`
- :param uniclust30_database_path: Uniclust30 database prefix. Corresponds to
- uniclust30_database_path in AF2.
- :type uniclust30_database_path: :class:`str`
+ :param uniref30_database_path: UniRef30 database prefix. Corresponds to
+ uniref30_database_path in AF2.
+ :type uniref30_database_path: :class:`str`
:param uniprot_database_path: UniProt sequence file. Corresponds to
uniprot_database_path in AF2. Needed for
model_preset == multimer.
@@ -387,7 +387,7 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
}
if db_preset == "full_dbs":
data_paths["bfd_database_path"] = bfd_database_path
- data_paths["uniclust30_database_path"] = uniclust30_database_path
+ data_paths["uniref30_database_path"] = uniref30_database_path
elif db_preset == "reduced_dbs":
data_paths["small_bfd_database_path"] = small_bfd_database_path
if model_preset == "multimer":
@@ -472,8 +472,8 @@ def main():
data_paths["bfd_database_path"] = opts.bfd_database_path
if opts.small_bfd_database_path is not None:
data_paths["small_bfd_database_path"] = opts.bfd_database_path
- if opts.uniclust30_database_path is not None:
- data_paths["uniclust30_database_path"] = opts.uniclust30_database_path
+ if opts.uniref30_database_path is not None:
+ data_paths["uniref30_database_path"] = opts.uniref30_database_path
if opts.uniprot_database_path is not None:
data_paths["uniprot_database_path"] = opts.uniprot_database_path
if opts.pdb70_database_path is not None:
@@ -509,5 +509,5 @@ def main():
# LocalWords: AlphaFold Slurm sciCORE param FASTA Basenames RuntimeException
# LocalWords: str dir snglrty tmpdir tmp argparse os ArgumentParser metavar
# LocalWords: RawDescriptionHelpFormatter nargs getenv startswith ValueError
-# LocalWords: RuntimeError bfd BFD dbs mgnify HHblits uniclust Uniclust pdb
+# LocalWords: RuntimeError bfd BFD dbs mgnify HHblits uniref Uniref pdb
# LocalWords: multimer seqres uniprot msas MSAs precomputed