From 80f49b2a5cd5fed8023feffecb51f828bb728b33 Mon Sep 17 00:00:00 2001
From: Santiago Lacalle <33420220+slacalle@users.noreply.github.com>
Date: Fri, 20 Aug 2021 10:18:10 +0100
Subject: [PATCH] samtools check updated to work in Batch mode

"samtools view" will fail in non interactive shells.
---
 midas/utility.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/midas/utility.py b/midas/utility.py
index ed8d628..708b2c7 100644
--- a/midas/utility.py
+++ b/midas/utility.py
@@ -126,7 +126,7 @@ def add_executables(args):
 
 	import subprocess as sp
 
-	process = sp.Popen("%s view" % args['samtools'], shell=True, stdout=sp.PIPE, stderr=sp.PIPE)
+	process = sp.Popen("%s --help" % args['samtools'], shell=True, stdout=sp.PIPE, stderr=sp.PIPE)
 	process.wait()
 	if process.returncode != 0:
 		err = "\nError: could not execute samtools binary: %s\n" % args['samtools']