From 087f35f9d9bfb8404ab798e561fda300ab8b4b9f Mon Sep 17 00:00:00 2001
From: Bo Li <bli25@berkeley.edu>
Date: Mon, 9 Jan 2017 17:23:45 -0800
Subject: [PATCH] Enabled multi-threading option for building Bowtie2 indices

---
 rsem-prepare-reference | 1 +
 1 file changed, 1 insertion(+)

diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index e7b638f..515ed58 100755
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -156,6 +156,7 @@ if ($bowtie) {
 
 if ($bowtie2) { 
     $command = $bowtie2_path."bowtie2-build -f";
+    if ($star_nthreads > 1) { $command .= " --threads $star_nthreads"; }
     if ($quiet) { $command .= " -q"; }
     $command .= " $ARGV[1].idx.fa $ARGV[1]";