run_pretrained_openfold.py: Change default paths of binary to be conda environment bin

README.md

@@ -171,7 +171,7 @@ python3 run_pretrained_openfold.py \
 
 where `data` is the same directory as in the previous step. If `jackhmmer`, 
 `hhblits`, `hhsearch` and `kalign` are available at the default path of 
-`/usr/bin`, their `binary_path` command-line arguments can be dropped.
+your conda environment's `bin` directory, their `binary_path` command-line arguments can be dropped.
 If you've already computed alignments for the query, you have the option to 
 skip the expensive alignment computation here with 
 `--use_precomputed_alignments`.

scripts/utils.py

 import argparse
 import ctypes
 from datetime import date
+import os
 import sys
+from pathlib import Path
 
 
+CONDA_ENV_BINARY_PATH= Path(os.environ['CONDA_PREFIX']) / 'bin'
+
 def add_data_args(parser: argparse.ArgumentParser):
     parser.add_argument(
         '--uniref90_database_path', type=str, default=None,
@@ -30,22 +34,22 @@ def add_data_args(parser: argparse.ArgumentParser):
         '--bfd_database_path', type=str, default=None,
     )
     parser.add_argument(
-        '--jackhmmer_binary_path', type=str, default='/usr/bin/jackhmmer'
+        '--jackhmmer_binary_path', type=Path, default=CONDA_ENV_BINARY_PATH / 'jackhmmer',
     )
     parser.add_argument(
-        '--hhblits_binary_path', type=str, default='/usr/bin/hhblits'
+        '--hhblits_binary_path', type=Path, default=CONDA_ENV_BINARY_PATH / 'hhblits',
     )
     parser.add_argument(
-        '--hhsearch_binary_path', type=str, default='/usr/bin/hhsearch'
+        '--hhsearch_binary_path', type=str, default=CONDA_ENV_BINARY_PATH / 'hhsearch',
     )
     parser.add_argument(
-        '--hmmsearch_binary_path', type=str, default='/usr/bin/hmmsearch'
+        '--hmmsearch_binary_path', type=str, default=CONDA_ENV_BINARY_PATH / 'hmmsearch',
     )
     parser.add_argument(
-        '--hmmbuild_binary_path', type=str, default='/usr/bin/hmmbuild'
+        '--hmmbuild_binary_path', type=str, default=CONDA_ENV_BINARY_PATH / 'hmmbuild',
     )
     parser.add_argument(
-        '--kalign_binary_path', type=str, default='/usr/bin/kalign'
+        '--kalign_binary_path', type=str, default=CONDA_ENV_BINARY_PATH / 'kalign',
     )
     parser.add_argument(
         '--max_template_date', type=str,