From 255ac2d023ba62559ff34bf08b4df760ab47f661 Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Wed, 17 Jan 2024 10:12:01 -0600
Subject: [PATCH] Error out when attempting to use multithreading on MacOS

---
 pvactools/tools/pvacbind/run.py   | 4 ++++
 pvactools/tools/pvacfuse/run.py   | 3 +++
 pvactools/tools/pvacseq/run.py    | 4 ++++
 pvactools/tools/pvacvector/run.py | 5 ++++-
 4 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/pvactools/tools/pvacbind/run.py b/pvactools/tools/pvacbind/run.py
index b8ad94f50..7ba65b9c1 100644
--- a/pvactools/tools/pvacbind/run.py
+++ b/pvactools/tools/pvacbind/run.py
@@ -3,6 +3,7 @@
 import os
 import shutil
 import yaml
+import platform
 
 from pvactools.lib.prediction_class import *
 from pvactools.lib.pipeline import PvacbindPipeline
@@ -50,6 +51,9 @@ def main(args_input = sys.argv[1:]):
     if args.iedb_retries > 100:
         sys.exit("The number of IEDB retries must be less than or equal to 100")
 
+    if args.n_threads > 1 and platform.system() == "Darwin":
+        raise Exception("Multithreading is not supported on MacOS")
+
     input_file_type = 'fasta'
     base_output_dir = os.path.abspath(args.output_dir)
 
diff --git a/pvactools/tools/pvacfuse/run.py b/pvactools/tools/pvacfuse/run.py
index d7d179ee2..4ce94b527 100644
--- a/pvactools/tools/pvacfuse/run.py
+++ b/pvactools/tools/pvacfuse/run.py
@@ -2,6 +2,7 @@
 import argparse
 import os
 import shutil
+import platform
 
 from pvactools.lib.prediction_class import *
 from pvactools.lib.pipeline import PvacbindPipeline
@@ -124,6 +125,8 @@ def main(args_input = sys.argv[1:]):
     else:
         sys.exit("The downstream sequence length needs to be a positive integer or 'full'")
 
+    if args.n_threads > 1 and platform.system() == "Darwin":
+        raise Exception("Multithreading is not supported on MacOS")
 
     base_output_dir = os.path.abspath(args.output_dir)
 
diff --git a/pvactools/tools/pvacseq/run.py b/pvactools/tools/pvacseq/run.py
index 4500155bb..03265bd25 100644
--- a/pvactools/tools/pvacseq/run.py
+++ b/pvactools/tools/pvacseq/run.py
@@ -3,6 +3,7 @@
 import os
 import shutil
 import yaml
+import platform
 
 from pvactools.lib.prediction_class import *
 from pvactools.lib.pipeline import Pipeline
@@ -66,6 +67,9 @@ def main(args_input = sys.argv[1:]):
         elif args.tumor_purity < 0:
             raise Exception("--tumor-purity must be a float between 0 and 1. Value too small: {}".format(args.tumor_purity))
 
+    if args.n_threads > 1 and platform.system() == "Darwin":
+        raise Exception("Multithreading is not supported on MacOS")
+
     input_file_type = 'vcf'
     base_output_dir = os.path.abspath(args.output_dir)
 
diff --git a/pvactools/tools/pvacvector/run.py b/pvactools/tools/pvacvector/run.py
index df3c02344..72caed9c8 100644
--- a/pvactools/tools/pvacvector/run.py
+++ b/pvactools/tools/pvacvector/run.py
@@ -15,6 +15,7 @@
 from Bio.Alphabet import IUPAC
 import itertools
 import json
+import platform
 
 from pvactools.lib.optimal_peptide import OptimalPeptide
 from pvactools.lib.vector_visualization import VectorVisualization
@@ -411,7 +412,6 @@ def create_dna_backtranslation(results_file, dna_results_file):
     SeqIO.write([output_record], dna_results_file, 'fasta')
 
 def main(args_input=sys.argv[1:]):
-
     parser = define_parser()
     args = parser.parse_args(args_input)
 
@@ -433,6 +433,9 @@ def main(args_input=sys.argv[1:]):
     else:
         sys.exit("Input file type not as expected. Needs to be a .fa or a .tsv file")
 
+    if args.n_threads > 1 and platform.system() == "Darwin":
+        raise Exception("Multithreading is not supported on MacOS")
+
     (class_i_prediction_algorithms, class_ii_prediction_algorithms) = pvactools.lib.run_utils.split_algorithms(args.prediction_algorithms)
     if len(class_i_prediction_algorithms) == 0:
         print("No MHC class I prediction algorithms chosen. Skipping MHC class I predictions.")