From 8a86db97eb89833a88b1ee876880cb1c07ce8565 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 10 May 2019 11:47:54 +0200
Subject: [PATCH] update sambamba to 0.6.9
---
apps/sambamba/install_0.6.9.sh | 43 ++++++++++++++++++++++++++++++++++
modulefiles/sambamba/0.6.9.lua | 43 ++++++++++++++++++++++++++++++++++
2 files changed, 86 insertions(+)
create mode 100755 apps/sambamba/install_0.6.9.sh
create mode 100644 modulefiles/sambamba/0.6.9.lua
diff --git a/apps/sambamba/install_0.6.9.sh b/apps/sambamba/install_0.6.9.sh
new file mode 100755
index 0000000..2ce7444
--- /dev/null
+++ b/apps/sambamba/install_0.6.9.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+# Copyright laurent modolo for the LBMC UMR 5239 ©.
+# contributor(s) : laurent modolo (2017)
+#
+# laurent.modolo@ens-lyon.fr
+#
+# This software is a computer program whose purpose is to manage dated file
+# names in complience with the bioinformatic good practices used in the LBMC.
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+#
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+source ../build_env.sh
+
+SAMBAMBA_VERSION=0.6.9
+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 && \
+mkdir -p ${SAMBAMBA_VERSION}/bin && \
+cp sambamba ${SAMBAMBA_VERSION}/bin/ && \
+rm -Rf sambamba_v${SAMBAMBA_VERSION}_linux* sambamba
diff --git a/modulefiles/sambamba/0.6.9.lua b/modulefiles/sambamba/0.6.9.lua
new file mode 100644
index 0000000..404dbc4
--- /dev/null
+++ b/modulefiles/sambamba/0.6.9.lua
@@ -0,0 +1,43 @@
+--[=====[
+Copyright laurent modolo for the LBMC UMR 5239 ©.
+contributor(s) : laurent modolo (2017)
+
+laurent.modolo@ens-lyon.fr
+
+This software is a computer program whose purpose is to manage dated file
+names in complience with the bioinformatic good practices used in the LBMC.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+--]=====]
+
+local root = "/Xnfs/lbmcdb/common/modules/apps/sambamba/0.6.9/"
+
+conflict("samblaster")
+
+whatis([===[loads sambamba 0.6.9 (Debian 9) environment ]===])
+prepend_path{"PATH", pathJoin(root, "bin")}
+setenv("SRATOOLKIT_PATH", pathJoin(root, "bin"))
--
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