From 2bf54bd2b92da3d373fb50d1fc1f5ed2792b6308 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 27 Jul 2018 15:21:28 +0200
Subject: [PATCH] Picard/2.18.11: add Dockerfiles
---
src/docker_modules/picard/2.18.11/Dockerfile | 19 +++++++++++++++++++
.../picard/2.18.11/PicardCommandLine | 15 +++++++++++++++
.../picard/2.18.11/docker_init.sh | 2 ++
3 files changed, 36 insertions(+)
create mode 100644 src/docker_modules/picard/2.18.11/Dockerfile
create mode 100644 src/docker_modules/picard/2.18.11/PicardCommandLine
create mode 100755 src/docker_modules/picard/2.18.11/docker_init.sh
diff --git a/src/docker_modules/picard/2.18.11/Dockerfile b/src/docker_modules/picard/2.18.11/Dockerfile
new file mode 100644
index 0000000..6a358e5
--- /dev/null
+++ b/src/docker_modules/picard/2.18.11/Dockerfile
@@ -0,0 +1,19 @@
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV PICARD_VERSION=2.18.11
+ENV PACKAGES default-jre=2:1.1* \
+ curl=7.58.0* \
+ ca-certificates=20180409
+
+
+RUN apt-get update && \
+ apt-get install -y --no-install-recommends ${PACKAGES} && \
+ apt-get clean
+
+RUN curl -k -L https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar -o picard.jar && \
+ mkdir -p /usr/share/java/ && \
+ mv picard.jar /usr/share/java/
+
+COPY PicardCommandLine /usr/bin/
+RUN chmod +x /usr/bin/PicardCommandLine
diff --git a/src/docker_modules/picard/2.18.11/PicardCommandLine b/src/docker_modules/picard/2.18.11/PicardCommandLine
new file mode 100644
index 0000000..ce06736
--- /dev/null
+++ b/src/docker_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 ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
diff --git a/src/docker_modules/picard/2.18.11/docker_init.sh b/src/docker_modules/picard/2.18.11/docker_init.sh
new file mode 100755
index 0000000..7546e34
--- /dev/null
+++ b/src/docker_modules/picard/2.18.11/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/picard/2.18.11 -t 'picard:2.18.11'
--
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