From 0fc97384a0e2f403badf7579556e6ebd3221ec80 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 22 Mar 2019 15:17:38 +0100
Subject: [PATCH] add umitools and fix cutadapt
---
apps/cutadapt/install_1.14.sh | 3 +-
apps/umitools/.gitignore | 1 +
apps/umitools/install_0.3.4.sh | 51 ++++++++++++++++++++++++++++++++++
modulefiles/umitools/0.3.4.lua | 44 +++++++++++++++++++++++++++++
4 files changed, 97 insertions(+), 2 deletions(-)
create mode 100644 apps/umitools/.gitignore
create mode 100644 apps/umitools/install_0.3.4.sh
create mode 100644 modulefiles/umitools/0.3.4.lua
diff --git a/apps/cutadapt/install_1.14.sh b/apps/cutadapt/install_1.14.sh
index 0110c3d..df65dbd 100755
--- a/apps/cutadapt/install_1.14.sh
+++ b/apps/cutadapt/install_1.14.sh
@@ -37,7 +37,7 @@ source ../build_env.sh
module load Python/3.6.1
CUTADAPT_VERSION=1.14
-CUTADAPT_ROOT=/Xnfs/lbmcdb/common/modules/apps/cutadapt/${MULTIQC_VERSION}
+CUTADAPT_ROOT=/Xnfs/lbmcdb/common/modules/apps/cutadapt/${CUTADAPT_VERSION}
mkdir -p ${CUTADAPT_VERSION}/lib/python2.7/dist-packages/
PYTHONPATH=${CUTADAPT_ROOT}lib/python2.7/dist-packages/:$PYTHONPATH
@@ -50,4 +50,3 @@ cd ..
rm -Rf markupsafe
mv bin lib 1.14/
rm -Rf cutadapt
-
diff --git a/apps/umitools/.gitignore b/apps/umitools/.gitignore
new file mode 100644
index 0000000..355164c
--- /dev/null
+++ b/apps/umitools/.gitignore
@@ -0,0 +1 @@
+*/
diff --git a/apps/umitools/install_0.3.4.sh b/apps/umitools/install_0.3.4.sh
new file mode 100644
index 0000000..9963293
--- /dev/null
+++ b/apps/umitools/install_0.3.4.sh
@@ -0,0 +1,51 @@
+#!/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
+
+UMITOOLS_VERSION=0.3.4
+UMITOOLS_ROOT=/Xnfs/lbmcdb/common/modules/apps/UMITOOLS/${UMITOOLS_VERSION}
+mkdir -p ${UMITOOLS_VERSION}/lib/python3.6/dist-packages/
+PYTHONPATH=${UMITOOLS_ROOT}lib/python3.6/dist-packages/:$PYTHONPATH
+
+
+git clone https://github.com/weng-lab/umitools.git
+cd umitools
+python setup.py install --single-version-externally-managed --prefix ${UMITOOLS_ROOT} --record markupsafe_install.txt
+cd ..
+rm -Rf markupsafe
+mv bin lib ${UMITOOLS_VERSION}/
+rm -Rf UMITOOLS
diff --git a/modulefiles/umitools/0.3.4.lua b/modulefiles/umitools/0.3.4.lua
new file mode 100644
index 0000000..8c0a40c
--- /dev/null
+++ b/modulefiles/umitools/0.3.4.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/umitools/0.3.4"
+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/umitools/0.3.4/lib/python3.6/site-packages/",delim=":",priority="0"}
+prepend_path{"PATH","/Xnfs/lbmcdb/common/modules/apps/umitools/0.3.4/bin",delim=":",priority="0"}
+setenv("HTSEQ_PATH","/Xnfs/lbmcdb/common/modules/apps/umitools/0.3.4/bin")
--
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