From 18e9f912e1468172974bd99ee1d7e91f5512fdfa Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Mar 2019 15:30:36 +0100
Subject: [PATCH] sambamba: add singularity files
---
.../sambamba/0.6.7/build.sh | 2 ++
.../sambamba/0.6.7/sambamba.def | 27 +++++++++++++++++++
2 files changed, 29 insertions(+)
create mode 100755 src/singularity_modules/sambamba/0.6.7/build.sh
create mode 100644 src/singularity_modules/sambamba/0.6.7/sambamba.def
diff --git a/src/singularity_modules/sambamba/0.6.7/build.sh b/src/singularity_modules/sambamba/0.6.7/build.sh
new file mode 100755
index 0000000..008e43f
--- /dev/null
+++ b/src/singularity_modules/sambamba/0.6.7/build.sh
@@ -0,0 +1,2 @@
+#/bin/sh
+sudo singularity build --force /bin/sambamba:0.6.7.sif src/singularity_modules/sambamba/0.6.7/sambamba.def
diff --git a/src/singularity_modules/sambamba/0.6.7/sambamba.def b/src/singularity_modules/sambamba/0.6.7/sambamba.def
new file mode 100644
index 0000000..f94a1b8
--- /dev/null
+++ b/src/singularity_modules/sambamba/0.6.7/sambamba.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+SAMBAMBA_VERSION=0.6.7
+PACKAGES="curl=7.58.0* \
+ca-certificates=20180409 \
+build-essential=12.4* \
+zlib1g-dev=1:1.2.11*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+mv sambamba /usr/bin/ && \
+rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
+
+%environment
+export SAMBAMBA_VERSION=0.6.7
+
+%runscript
+exec /bin/bash "$@"
--
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