diff --git a/.gitignore b/.gitignore index 09526e9cb1c008b8070f4dfaefb88d3816d0438c..e9e2d1be3fed831476c81001e929120900ef947c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ apps/SAMtools/1.5/ apps/RSEM/1.3.0/ apps/Bowtie2/2.3.2/ +apps/Kallisto/0.43.1/ diff --git a/apps/Kallisto/install_0.43.1.sh b/apps/Kallisto/install_0.43.1.sh new file mode 100644 index 0000000000000000000000000000000000000000..030c6ffe0a420e02a9d2cfbfba3072f983508bde --- /dev/null +++ b/apps/Kallisto/install_0.43.1.sh @@ -0,0 +1,43 @@ +#!/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 + +KALLISTO_VERSION=0.43.1 +curl -k -L https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz +tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz +mkdir -p ${KALLISTO_VERSION}/bin +cp kallisto_linux-v${KALLISTO_VERSION}/kallisto ${KALLISTO_VERSION}/bin +rm -Rf kallisto_linux-v${KALLISTO_VERSION}* diff --git a/modulefiles/Kallisto/0.43.1 b/modulefiles/Kallisto/0.43.1 new file mode 100644 index 0000000000000000000000000000000000000000..8dcdd645890b70ae7ec6b71f92677255ddf4d7a7 --- /dev/null +++ b/modulefiles/Kallisto/0.43.1 @@ -0,0 +1,64 @@ +#%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 0.43.1 +set modname kallisto +set osarch "Debian 7" +set modroot /Xnfs/site/lbmcdb/communs_data/modules/apps/kallisto/0.43.1 + +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 KALLISTO_PATH $modroot/bin