From 66cb84e166285267678a7a9e409e892a67e3bdbd Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 24 Mar 2020 09:37:59 +0100
Subject: [PATCH] Docker: gatk3 fix arguments parsing

---
 src/.docker_modules/gatk/3.8.0/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/.docker_modules/gatk/3.8.0/Dockerfile b/src/.docker_modules/gatk/3.8.0/Dockerfile
index 8d1dbc91..41d27614 100644
--- a/src/.docker_modules/gatk/3.8.0/Dockerfile
+++ b/src/.docker_modules/gatk/3.8.0/Dockerfile
@@ -3,4 +3,5 @@ MAINTAINER Laurent Modolo
 
 ENV GATK_VERSION=3.8.0
 
-RUN echo "#\!/bin/sh\njava -jar /usr/GenomeAnalysisTK.jar \$0" > /bin/gatk3 
+RUN echo "#\!/bin/sh\njava -jar /usr/GenomeAnalysisTK.jar \$@" > /bin/gatk3 
+RUN chmod +x /bin/gatk3
-- 
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