From e8fe1028919ea9adcb3aef28618c68da8d461454 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Mar 2019 15:41:59 +0100
Subject: [PATCH] hisat2: add singularity files
---
src/singularity_modules/hisat2/2.0.0/build.sh | 3 ++
.../hisat2/2.0.0/hisat2.def | 32 +++++++++++++++++++
2 files changed, 35 insertions(+)
create mode 100755 src/singularity_modules/hisat2/2.0.0/build.sh
create mode 100644 src/singularity_modules/hisat2/2.0.0/hisat2.def
diff --git a/src/singularity_modules/hisat2/2.0.0/build.sh b/src/singularity_modules/hisat2/2.0.0/build.sh
new file mode 100755
index 0000000..3335ba3
--- /dev/null
+++ b/src/singularity_modules/hisat2/2.0.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/hisat2:2.0.0.sif src/singularity_modules/hisat2/2.0.0/hisat2.def
+singularity sign bin/hisat2:2.0.0.sif
diff --git a/src/singularity_modules/hisat2/2.0.0/hisat2.def b/src/singularity_modules/hisat2/2.0.0/hisat2.def
new file mode 100644
index 0000000..a3941bf
--- /dev/null
+++ b/src/singularity_modules/hisat2/2.0.0/hisat2.def
@@ -0,0 +1,32 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Nicolas Fontrodona
+
+%post
+HISAT2_VERSION=2.0.0
+PACKAGES="unzip \
+gcc \
+g++ \
+make \
+curl \
+ca-certificates"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
+unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
+cd hisat2-${HISAT2_VERSION}-beta && \
+make && \
+cp hisat2 /usr/bin && \
+cp hisat2-* /usr/bin && \
+rm -Rf hisat2-${HISAT2_VERSION}-beta
+
+%environment
+export HISAT2_VERSION=2.0.0
+
+%runscript
+exec /bin/bash "$@"
--
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