From a8472a831040a9365e8bca0b6a0ff263fc61895b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Mar 2019 17:13:03 +0100
Subject: [PATCH] picard: add PicardCommandLine for singularity
---
.../picard/2.18.11/PicardCommandLine | 15 +++++++++++++++
1 file changed, 15 insertions(+)
create mode 100644 src/singularity_modules/picard/2.18.11/PicardCommandLine
diff --git a/src/singularity_modules/picard/2.18.11/PicardCommandLine b/src/singularity_modules/picard/2.18.11/PicardCommandLine
new file mode 100644
index 00000000..ce067365
--- /dev/null
+++ b/src/singularity_modules/picard/2.18.11/PicardCommandLine
@@ -0,0 +1,15 @@
+#!/bin/sh
+set -eu
+PRG="$(basename -- "$0")"
+case "$PRG" in
+picard-tools)
+ echo 1>&2 'Warning: picard-tools is deprecated and should be replaced by PicardCommandLine'
+ ;;
+PicardCommandLine)
+ ;;
+*)
+ set -- "$PRG" "$@"
+ ;;
+esac
+
+exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
--
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