Merge pull request #499 from fulcrumgenomics/fix_parallellism_on_osx

fix parallelism for osx
fritzsedlazeck · Aug 13, 2024 · a4af992 · a4af992
2 parents 7f71d13 + b89b496
commit a4af992
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/src/sniffles/sniffles b/src/sniffles/sniffles
@@ -10,6 +10,7 @@
 #
 import logging
 import logging.config
+import multiprocessing
 from typing import Optional
 
 from sniffles.utils.resmon import ResourceMonitor
@@ -70,6 +71,10 @@ def Sniffles2_Main(processes: list[parallel.SnifflesWorker]):
 
     input_ext = [f.split(".")[-1].lower() for f in config.input]
 
+    # needed for running on osx
+    if sys.platform == "darwin":
+        multiprocessing.set_start_method("fork")
+
     if len(set(input_ext)) > 1:
         util.fatal_error_main(f"Please specify either: A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input. (supplied were: {list(set(input_ext))})")