diff --git a/.gitignore b/.gitignore index 47cc759fcb510b776563a37577f428239e18af03..218306a529d891c551c913c5b81d3b3a8fbba0d4 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ apps/HTSeq/0.8.0/ apps/MultiQC/0.9/ apps/MultiQC/1.0/ apps/UrQt/d62c1f8/ +apps/FastQC/0.11.5/ diff --git a/apps/FastQC/install_0.11.5.sh b/apps/FastQC/install_0.11.5.sh new file mode 100644 index 0000000000000000000000000000000000000000..accbd942120d30552238098f309a2bf8ef41d4d9 --- /dev/null +++ b/apps/FastQC/install_0.11.5.sh @@ -0,0 +1,45 @@ +#!/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 + +FASTQC_VERSION=0.11.5 +mkdir -p ${FASTQC_VERSION}/bin + +curl -k -L http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${FASTQC_VERSION}.zip -o fastqc_v${FASTQC_VERSION}.zip +unzip fastqc_v${FASTQC_VERSION}.zip +mv FastQC/* ${FASTQC_VERSION}/bin/ + +rm -Rf FastQC fastqc_v${FASTQC_VERSION}.zip diff --git a/modulefiles/FastQC/0.11.5 b/modulefiles/FastQC/0.11.5 new file mode 100644 index 0000000000000000000000000000000000000000..dd105bddb1870bbe4adf464424b740adbdf0510d --- /dev/null +++ b/modulefiles/FastQC/0.11.5 @@ -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 0.11.5 +set modname FastQC +set osarch "Debian 7" +set modroot /Xnfs/site/lbmcdb/communs_data/modules/apps/FastQC/0.11.5 + +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 FASTQC_PATH $modroot/bin diff --git a/modulefiles/UrQt/d62c1f8 b/modulefiles/UrQt/d62c1f8 index 5110ee9b99f9fa889cec26ad873aa7147a447b87..3fc10e846119a8bb75789743e76e6e10d92a758b 100644 --- a/modulefiles/UrQt/d62c1f8 +++ b/modulefiles/UrQt/d62c1f8 @@ -61,4 +61,4 @@ if [ module-info mode load ] { } prepend-path PATH $modroot/bin -setenv SALMON_PATH $modroot/bin +setenv URQT_PATH $modroot/bin