We can use multiple threads when converting cram to bam files

galaxyproject · Dec 8, 2017 · 64deb4f · 64deb4f
1 parent 07158e0
commit 64deb4f
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/lib/galaxy/datatypes/converters/cram_to_bam.py b/lib/galaxy/datatypes/converters/cram_to_bam.py
@@ -5,6 +5,7 @@
 usage: %prog in_file out_file
 """
 import optparse
+import os
 
 import pysam
 
@@ -14,7 +15,8 @@ def main():
     parser = optparse.OptionParser()
     (options, args) = parser.parse_args()
     input_fname, output_fname = args
-    pysam.sort('-o', output_fname, '-O', 'bam', '-T', '.', input_fname)
+    slots = os.getenv('GALAXY_SLOTS', 1)
+    pysam.sort("-@%s" % slots, '-o', output_fname, '-O', 'bam', '-T', '.', input_fname)
 
 
 if __name__ == "__main__":