From b3aee97229d94aa4838f02dda99135b58c4bff80 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 11 Jun 2019 15:16:14 +0200
Subject: [PATCH] subread singularity: fix sps and pbs path

---
 src/singularity_modules/subread/1.6.4/build.sh    |  2 +-
 src/singularity_modules/subread/1.6.4/subread.def | 15 +++++++++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)
 create mode 100644 src/singularity_modules/subread/1.6.4/subread.def

diff --git a/src/singularity_modules/subread/1.6.4/build.sh b/src/singularity_modules/subread/1.6.4/build.sh
index 455172af..4a758ee5 100755
--- a/src/singularity_modules/subread/1.6.4/build.sh
+++ b/src/singularity_modules/subread/1.6.4/build.sh
@@ -1,3 +1,3 @@
 #/bin/sh
-sudo singularity build --force bin/subread:1.6.4.img docker://quay.io/biocontainers/subread:1.6.4--h84994c4_1 && \
+sudo singularity build --force bin/subread:1.6.4.img src/singularity_modules/subread/1.6.4/subread.def && \
 singularity sign bin/subread:1.6.4.img
diff --git a/src/singularity_modules/subread/1.6.4/subread.def b/src/singularity_modules/subread/1.6.4/subread.def
new file mode 100644
index 00000000..db8f00c2
--- /dev/null
+++ b/src/singularity_modules/subread/1.6.4/subread.def
@@ -0,0 +1,15 @@
+Bootstrap: docker
+From: quay.io/biocontainers/subread:1.6.4--h84994c4_1
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+mkdir -p /sps /pbs /scratch
+SUBREF_VERSION=1.6.4
+
+%environment
+export SUBREF_VERSION=1.6.4
+
+%runscript
+exec /bin/bash "$@"
-- 
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