From 8e82fe730bc10ae122c8cefe08b4481e2674b1df Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Mar 2019 17:12:42 +0100
Subject: [PATCH] picard: add singularity files
---
.../picard/2.18.11/build.sh | 3 ++
.../picard/2.18.11/picard.def | 30 +++++++++++++++++++
2 files changed, 33 insertions(+)
create mode 100755 src/singularity_modules/picard/2.18.11/build.sh
create mode 100644 src/singularity_modules/picard/2.18.11/picard.def
diff --git a/src/singularity_modules/picard/2.18.11/build.sh b/src/singularity_modules/picard/2.18.11/build.sh
new file mode 100755
index 00000000..aa29178c
--- /dev/null
+++ b/src/singularity_modules/picard/2.18.11/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/picard:2.18.11.sif src/singularity_modules/picard/2.18.11/picard.def
+singularity sign bin/picard:2.18.11.sif
diff --git a/src/singularity_modules/picard/2.18.11/picard.def b/src/singularity_modules/picard/2.18.11/picard.def
new file mode 100644
index 00000000..27a3e18a
--- /dev/null
+++ b/src/singularity_modules/picard/2.18.11/picard.def
@@ -0,0 +1,30 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%files
+src/singularity_modules/picard/2.18.11/PicardCommandLine /usr/bin/
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+PICARD_VERSION=2.18.11
+PACKAGES="default-jre \
+curl \
+ca-certificates"
+
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar -o picard.jar && \
+mkdir -p /usr/share/java/ && \
+mv picard.jar /usr/share/java/
+chmod +x /usr/bin/PicardCommandLine
+
+%environment
+export PICARD_VERSION=2.18.11
+
+%runscript
+exec /bin/bash "$@"
--
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