From 54834540b88d9855d8aee66694b6612562ded418 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Mar 2019 17:23:22 +0100
Subject: [PATCH] rsem: add singularity files

---
 src/singularity_modules/rsem/1.3.0/build.sh |  3 ++
 src/singularity_modules/rsem/1.3.0/rsem.def | 36 +++++++++++++++++++++
 2 files changed, 39 insertions(+)
 create mode 100755 src/singularity_modules/rsem/1.3.0/build.sh
 create mode 100644 src/singularity_modules/rsem/1.3.0/rsem.def

diff --git a/src/singularity_modules/rsem/1.3.0/build.sh b/src/singularity_modules/rsem/1.3.0/build.sh
new file mode 100755
index 00000000..88e2e4e2
--- /dev/null
+++ b/src/singularity_modules/rsem/1.3.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/rsem:1.3.0.sif src/singularity_modules/rsem/1.3.0/rsem.def
+singularity sign bin/rsem:1.3.0.sif
diff --git a/src/singularity_modules/rsem/1.3.0/rsem.def b/src/singularity_modules/rsem/1.3.0/rsem.def
new file mode 100644
index 00000000..2e615b0d
--- /dev/null
+++ b/src/singularity_modules/rsem/1.3.0/rsem.def
@@ -0,0 +1,36 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+RSEM_VERSION=1.3.0
+BOWTIE2_VERSION=2.3.4.1
+SAMTOOLS_VERSION=1.7
+PACKAGES="git \
+build-essential \
+ca-certificates \
+zlib1g-dev \
+bowtie2=${BOWTIE2_VERSION}* \
+samtools=${SAMTOOLS_VERSION}*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+git clone https://github.com/deweylab/RSEM.git RSEM_${RSEM_VERSION} && \
+cd RSEM_${RSEM_VERSION} && \
+git checkout tags/v${RSEM_VERSION} && \
+make && \
+cd .. && \
+mv RSEM_${RSEM_VERSION}/rsem-* RSEM_${RSEM_VERSION}/rsem_* RSEM_${RSEM_VERSION}/convert-* RSEM_${RSEM_VERSION}/extract-* /usr/bin/ && \
+rm -Rf RSEM_${RSEM_VERSION}
+
+%environment
+export RSEM_VERSION=1.3.0
+export BOWTIE2_VERSION=2.3.4.1
+export SAMTOOLS_VERSION=1.7
+
+%runscript
+exec /bin/bash "$@"
-- 
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