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Commit ae770d67 authored by Laurent Modolo's avatar Laurent Modolo
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install Salmon/0.8.2

parent 3f9cff2a
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......@@ -2,3 +2,4 @@ apps/SAMtools/1.5/
apps/RSEM/1.3.0/
apps/Bowtie2/2.3.2/
apps/Kallisto/0.43.1/
apps/Salmon/0.8.2/
#!/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
SALMON_VERSION=0.8.2
mkdir -p ${SALMON_VERSION}
curl -k -L https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz -o Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz
tar xzf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz
mv Salmon-${SALMON_VERSION}_linux_x86_64 ${SALMON_VERSION}
rm -Rf Salmon-${SALMON_VERSION}*
#%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 0.8.2
set modname Salmon
set osarch "Debian 7"
set modroot /Xnfs/site/lbmcdb/communs_data/modules/apps/Salmon/0.8.2
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
prepend-path LD_LIBRARY_PATH $modroot/lib
setenv SALMON_PATH $modroot/bin
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