diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f7fa4120f05c24bc62ba67f5f4485f1bbe55159c..5b05123d022715c187d6b19c8cad995b77b51979 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,3 +1,7 @@
+# IMPORTANT: running the pipeline for testing, keep in mind, re-building an
+# existing package version fails! For testing, build for an old tag which does
+# not have a package in the registry, yet. Delete the package after testing.
+
build-package:
stage: deploy
image: python:3.6
diff --git a/README.md b/README.md
index 1ff7ec7c9e513d843c1634cb2489bac2cb99d099..04ca64eb2514ea71406a9cdc420d405ca9108317 100644
--- a/README.md
+++ b/README.md
@@ -111,6 +111,56 @@ output files ...), here are some things to consider:
- if running on CPUs without GPU, avoid the `lii` nodes (`--exclude=lii[02-28]`)
+## Custom AF2 pipeline
+
+`run_af2` executes the default AlphaFold 2 pipeline. That is, in the end a
+script [`run_alphafold.py`](
+https://github.com/deepmind/alphafold/blob/main/run_alphafold.py) is run. For
+some studies, you may want to go by a modified version of `run_alphafold.py`.
+While `run_af2` is based on containerised software in its backyard, injecting
+your custom script inside the Singularity container is not terribly complicated.
+In the shell, you want to run your command in, simply create an environment
+variable `SINGULARITY_BINDPATH` with the mapping of your script to the original
+script inside the container:
+
+```terminal
+$ export SINGULARITY_BINDPATH="/PATH/TO/SCRIPT/run_alphafold.py:/app/alphafold/run_alphafold.py""
+```
+
+Where `/PATH/TO/SCRIPT/run_alphafold.py` points to your modified
+`run_alphafold.py`. After that, just run `run_af2` as described in
+[Default AF2 pipeline](#default-af2-pipeline).
+
+Please note, this method of altering the app executed by a container defies the
+main purpose of containers providing unaltered apps ready to go, out of the box.
+Also note, since this method relies on internals of the pipeline beyond the
+scope of af2@scicore, future updates of AF2 may break it.
+
+
+## Custom container
+
+`run_af2` uses the AlphaFold 2 pipeline as provided by DeepMind. That is, we
+build the vanilla Docker container as described in their [documentation](
+https://github.com/deepmind/alphafold). Simply run
+
+```terminal
+$ docker build -f docker/Dockerfile -t alphafold:2022-01-11 .
+```
+
+inside a checkout of the AF2 Git repository. That creates the container tagged
+with `2022-01-11`, which is the way `run_af2` indicates versions. It's simply
+the date of creation of the container from a fresh checkout of the Git repository.
+
+This Docker container is then turned into a Singularity container:
+
+```terminal
+$ singularity build alphafold-2022-01-11.sif docker-daemon://alphafold:2022-01-11
+```
+
+`alphafold-2022-01-11.sif` can then be used with the `--singularity-image` of
+`run_af2`.
+
+
## Interactive IPython notebook
As an expert mode, we provide a notebook version of the default AF2 pipeline
@@ -193,5 +243,5 @@ highly secure *my_password*.
<!-- LocalWords: AlphaFold sciCORE IPython ipynb GitLab PyPI af FASTA py rtx
-->
-<!-- LocalWords: alphafold sbatch
+<!-- LocalWords: alphafold sbatch DeepMind
-->
diff --git a/run_af2/src/run_af2/_shared.py b/run_af2/src/run_af2/_shared.py
index 27aa8e1ce24b726aa2b13e957b844950464e5797..f2affaaddcbfddc4799fb4ce76ce1fa1baf0dda1 100644
--- a/run_af2/src/run_af2/_shared.py
+++ b/run_af2/src/run_af2/_shared.py
@@ -212,7 +212,7 @@ def parse_af2_arguments(parser):
metavar="<FILE>",
default=None,
)
- opts = parser.parse_args()
+ opts, extra_opts = parser.parse_known_args()
# check that the db_preset setting makes sense
for arg in db_preset_choices[opts.db_preset]:
@@ -253,7 +253,7 @@ def parse_af2_arguments(parser):
)
sys.exit(1)
- return opts
+ return opts, extra_opts
# LocalWords: argparse ArgumentParser Namespace Bioinformatics Biozentrum af
diff --git a/run_af2/src/run_af2/run_singularity.py b/run_af2/src/run_af2/run_singularity.py
index 0e35bac2b10116eab6fa467d7f3cb59b1568d796..9b04f8d4aa18c2ac12d5b217b32ce7d7cdf5d12f 100644
--- a/run_af2/src/run_af2/run_singularity.py
+++ b/run_af2/src/run_af2/run_singularity.py
@@ -118,6 +118,7 @@ def _assemble_singularity_call( # pylint: disable=too-many-arguments
model_preset,
is_prokaryote_list,
data_paths,
+ extra_arg_list,
):
"""Assemble the command to run AF2 from the Singularity image."""
# Since the number of arguments to this function is already high, we allow
@@ -158,6 +159,9 @@ def _assemble_singularity_call( # pylint: disable=too-many-arguments
for flag, path in data_paths.items():
snglrty_cmd.append(f"--{flag}={path}")
+ # append extra arguments
+ snglrty_cmd.extend(extra_arg_list)
+
return snglrty_cmd
@@ -199,6 +203,7 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
af2_image_dir="/scicore/home/schwede/GROUP/alphafold_data/",
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/",
uniref90_database_path="/scicore/data/managed/UniProt/latest/uniref/"
@@ -274,6 +279,10 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
:param tmpdir_var: An environment variable defining tmp space, that is not
necessarily "/tmp" on some systems.
:type tmpdir_var: :class:`str`
+ :param extra_arg_list: List of extra arguments appended to the Singularity
+ call. That is for adding extra arguments in a
+ modified version of run_alphafold.py.
+ :type extra_arg_list: :class:`list`
:param data_dir: Holds the params sub directory with model parameters.
Corresponds to DOWNLOAD_DIR in AF2.
:type data_dir: :class:`str`
@@ -321,6 +330,8 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
# Since the number of arguments to this function is already high, we allow
# more local variables than defined by PEP8.
# pylint: disable=too-many-locals
+ if extra_arg_list is None:
+ extra_arg_list = []
tmpdir = os.getenv(tmpdir_var)
if tmpdir is None:
raise ValueError(f"tmpdir_var {tmpdir_var} must not be empty.")
@@ -382,6 +393,7 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
model_preset,
is_prokaryote_list,
data_paths,
+ extra_arg_list,
)
# set up environment
@@ -412,7 +424,7 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments
def main():
"""Execute as script"""
- opts = _parse_cmdline()
+ opts, extra_arg_list = _parse_cmdline()
# Collect data paths into a dictionary so we can deal with default path on
# the sciCORE cluster more easily.
@@ -449,7 +461,8 @@ def main():
opts.db_preset,
opts.model_preset,
opts.is_prokaryote_list,
- af2_image_file=opts.singularity_image,
+ opts.singularity_image,
+ extra_arg_list=extra_arg_list,
**data_paths,
)
except RuntimeError as rte: