LigandMPNN step won't run if workdir is not set to default

[bifxcore]

workdir == where I want to write the output == /data/boltzd_run3

Boltz design step completes and writes output to workdir. All good.

LigandMPNN crashes because it expects workdir to be the location of the Boltzdesign1 repository, but it's reading the workdir instead:

Boltz design step completed!
Starting LigandMPNN redesign step...
Traceback (most recent call last):
File "/data/packages/BoltzDesign1/boltzdesign.py", line 792, in
main()
File "/data/packages/BoltzDesign1/boltzdesign.py", line 786, in main
results = run_pipeline_steps(args, config, boltz_model, yaml_dir, output_dir)
File "/data/packages/BoltzDesign1/boltzdesign.py", line 731, in run_pipeline_steps
run_ligandmpnn_step(
File "/data/packages/BoltzDesign1/boltzdesign.py", line 410, in run_ligandmpnn_step
with open(yaml_path, "r") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/data/boltzd_run3/LigandMPNN/run_ligandmpnn_logits_config.yaml'

It should have looked into the Boltzdesign1 repository: /data/packages/BoltzDesign1/LigandMPNN/run_ligandmpnn_logits_config.yaml

It looks like run_ligandmpnn_step may need to have script_dir passed to find the yaml_path?

script_dir = os.path.dirname(os.path.abspath(__file__))
# **boltzdesign.py line 408**
# Setup LigandMPNN config
original_yaml_path = f"(script_dir}/LigandMPNN/run_ligandmpnn_logits_config.yaml"
# copy yaml file to workdir
# open workdir yaml file

Same goes for the run_alphafold_step() lines 560 and 570.

[bifxcore]

I have now tested the hacks modifications I needed to get boltzdesign to complete if workdir is set to a custom value. These edits worked for me:

$> diff boltzdesign.py original_boltzdesign.py
408,413d407
< 
<     print(f"main_dir: {main_dir}")
<     print(f"ligandmpnn_dir: {ligandmpnn_dir}")
<     print(f"yaml_dir: {yaml_dir}")
<     script_dir = os.path.dirname(os.path.abspath(__file__))
<     original_yaml_path = f"{script_dir}/LigandMPNN/run_ligandmpnn_logits_config.yaml"
415c409,410
<     with open(original_yaml_path, "r") as f:
---
>     yaml_path = f"{work_dir}/LigandMPNN/run_ligandmpnn_logits_config.yaml"
>     with open(yaml_path, "r") as f:
420c415
<             mpnn_config[key] = value.replace("${CWD}", script_dir)
---
>             mpnn_config[key] = value.replace("${CWD}", work_dir)
425,427d419
<     os.makedirs(f"{work_dir}/LigandMPNN")
<     shutil.copy(original_yaml_path, f"{work_dir}/LigandMPNN")
<     yaml_path = f"{work_dir}/LigandMPNN/run_ligandmpnn_logits_config.yaml"
567d558
<     script_dir = os.path.dirname(os.path.abspath(__file__))
569c560
<         f'{script_dir}/boltzdesign/alphafold.sh',
---
>         f'{work_dir}/boltzdesign/alphafold.sh',
579c570
<         f'{script_dir}/boltzdesign/alphafold.sh',
---
>         f'{work_dir}/boltzdesign/alphafold.sh',