From 0c034f5bbeb8e91cecc04466b74654503a94ac7c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 9 Apr 2019 11:18:52 +0200
Subject: [PATCH] cutadapt: add v2.1
---
apps/cutadapt/install_2.1.sh | 52 ++++++++++++++++++++++++++++++++++++
modulefiles/cutadapt/2.1.lua | 44 ++++++++++++++++++++++++++++++
2 files changed, 96 insertions(+)
create mode 100755 apps/cutadapt/install_2.1.sh
create mode 100644 modulefiles/cutadapt/2.1.lua
diff --git a/apps/cutadapt/install_2.1.sh b/apps/cutadapt/install_2.1.sh
new file mode 100755
index 0000000..3f504a2
--- /dev/null
+++ b/apps/cutadapt/install_2.1.sh
@@ -0,0 +1,52 @@
+#!/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
+module load Python/3.6.1
+
+CUTADAPT_VERSION=2.1
+CUTADAPT_ROOT=/Xnfs/lbmcdb/common/modules/apps/cutadapt/${CUTADAPT_VERSION}
+mkdir -p ${CUTADAPT_VERSION}/lib/python2.7/dist-packages/
+PYTHONPATH=${CUTADAPT_ROOT}lib/python2.7/dist-packages/:$PYTHONPATH
+
+
+git clone https://github.com/marcelm/cutadapt.git
+cd cutadapt
+git checkout tags/v${CUTADAPT_VERSION}
+python setup.py install --single-version-externally-managed --prefix ${CUTADAPT_ROOT} --record markupsafe_install.txt
+cd ..
+rm -Rf markupsafe
+mv bin lib 2.1/
+rm -Rf cutadapt
diff --git a/modulefiles/cutadapt/2.1.lua b/modulefiles/cutadapt/2.1.lua
new file mode 100644
index 0000000..2508e1b
--- /dev/null
+++ b/modulefiles/cutadapt/2.1.lua
@@ -0,0 +1,44 @@
+--[=====[
+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/cutadapt/2.1"
+conflict("cutadapt")
+conflict("Python/2.7.13")
+load("Python/3.6.1")
+prereq_any("Python/3.6.1")
+prepend_path{"PYTHONPATH","/Xnfs/lbmcdb/common/modules/apps/cutadapt/2.1/lib/python3.6/site-packages/",delim=":",priority="0"}
+prepend_path{"PATH","/Xnfs/lbmcdb/common/modules/apps/cutadapt/2.1/bin",delim=":",priority="0"}
+setenv("HTSEQ_PATH","/Xnfs/lbmcdb/common/modules/apps/cutadapt/2.1/bin")
--
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