install bowtie2/2.3.2

.gitignore

 apps/SAMtools/1.5/
 apps/RSEM/1.3.0/
+apps/Bowtie2/2.3.2/

apps/Bowtie2/install_2.3.2.sh

+#!/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
+
+BOWTIE2_VERSION=2.3.2
+
+curl -k -L  https://sourceforge.net/projects/bowtie-bio/files/bowtie2/${BOWTIE2_VERSION}/bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip/download -o bowtie2-${BOWTIE2_VERSION}.zip
+unzip bowtie2-${BOWTIE2_VERSION}.zip
+mkdir -p ${BOWTIE2_VERSION}/bin
+cp bowtie2-${BOWTIE2_VERSION}/bowtie2* ${BOWTIE2_VERSION}/bin/
+rm -Rf bowtie2*

modulefiles/Bowtie2/2.3.2

+#%Module1.0####################################################################
+# 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.
+##
+##
+###############################################################################
+# for Tcl script use only
+set     version         2.3.2
+set     modname         Bowtie2
+set     osarch          "Debian 7"
+set     modroot         /Xnfs/site/lbmcdb/communs_data/modules/apps/Bowtie2/2.3.2
+
+setenv  LAST_MODULE     $modname/$version
+
+###############################################################################
+proc ModulesHelp { } {
+        global modname version osarch
+        puts stderr "\nThis set the environment variables for $modname $version - $osarch."
+}
+
+
+module-whatis   "loads $modname $version ($osarch) environment"
+###############################################################################
+
+# conflict
+conflict $modname
+
+if [ module-info mode load ] {
+  prereq Base/psmn
+}
+
+prepend-path    PATH            $modroot/bin
+setenv          RSEM_PATH       $modroot/bin