diff --git a/apps/Bowtie2/install_2.3.4.1.sh b/apps/Bowtie2/install_2.3.4.1.sh new file mode 100644 index 0000000000000000000000000000000000000000..f2ff3e739408e14b4267f8c273a37ba9e9f13ee4 --- /dev/null +++ b/apps/Bowtie2/install_2.3.4.1.sh @@ -0,0 +1,44 @@ +#!/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=2.3.4.1 + +curl -k -L https://freefr.dl.sourceforge.net/project/bowtie-bio/bowtie2/${BOWTIE2_VERSION}/bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip -o bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip +unzip bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip +mkdir -p ${BOWTIE3_VERSION}/bin +cp bowtie2-${BOWTIE2_VERSION}-linux-x86_64/bowtie2* ${BOWTIE2_VERSION}/bin/ +rm -Rf bowtie2* diff --git a/modulefiles/Bowtie2/2.3.4.1.lua b/modulefiles/Bowtie2/2.3.4.1.lua new file mode 100644 index 0000000000000000000000000000000000000000..cfdd1d158e6c76309fd155236799a8fa3b316498 --- /dev/null +++ b/modulefiles/Bowtie2/2.3.4.1.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/Bowtie2/2.3.4.1" + +conflict("Bowtie2") + +whatis([===[loads Bowtie2 2.3.4.1 (Debian 9) environment ]===]) +prepend_path{"PATH", pathJoin(root, "bin")} +setenv("BOWTIE2_PATH", pathJoin(root, "bin"))