diff --git a/apps/bedtools/.gitignore b/apps/bedtools/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..355164c126511e7d9f9896171414647f098dd30e --- /dev/null +++ b/apps/bedtools/.gitignore @@ -0,0 +1 @@ +*/ diff --git a/apps/fastp/.gitignore b/apps/fastp/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..355164c126511e7d9f9896171414647f098dd30e --- /dev/null +++ b/apps/fastp/.gitignore @@ -0,0 +1 @@ +*/ diff --git a/apps/fastp/install_0.19.7.sh b/apps/fastp/install_0.19.7.sh new file mode 100644 index 0000000000000000000000000000000000000000..86c2d3227468510e7beb7775034d5073b47a1219 --- /dev/null +++ b/apps/fastp/install_0.19.7.sh @@ -0,0 +1,48 @@ +#!/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 + +FASTP_VERSION=0.19.7 +mkdir -p ${FASTP_VERSION}/bin + +git clone https://github.com/OpenGene/fastp.git +cd fastp +git checkout v${FASTP_VERSION} +make +cd .. +mv fastp/fastp ${FASTP_VERSION}/bin/ + +rm -Rf fastp diff --git a/apps/fastqc/.gitignore b/apps/fastqc/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..355164c126511e7d9f9896171414647f098dd30e --- /dev/null +++ b/apps/fastqc/.gitignore @@ -0,0 +1 @@ +*/ diff --git a/apps/multiqc/.gitignore b/apps/multiqc/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..355164c126511e7d9f9896171414647f098dd30e --- /dev/null +++ b/apps/multiqc/.gitignore @@ -0,0 +1 @@ +*/ diff --git a/apps/salmon/.gitignore b/apps/salmon/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..355164c126511e7d9f9896171414647f098dd30e --- /dev/null +++ b/apps/salmon/.gitignore @@ -0,0 +1 @@ +*/ diff --git a/apps/trimmomatic/.gitignore b/apps/trimmomatic/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..355164c126511e7d9f9896171414647f098dd30e --- /dev/null +++ b/apps/trimmomatic/.gitignore @@ -0,0 +1 @@ +*/ diff --git a/apps/urqt/.gitignore b/apps/urqt/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..355164c126511e7d9f9896171414647f098dd30e --- /dev/null +++ b/apps/urqt/.gitignore @@ -0,0 +1 @@ +*/ diff --git a/modulefiles/fastp/0.19.7.lua b/modulefiles/fastp/0.19.7.lua new file mode 100644 index 0000000000000000000000000000000000000000..68ef27fc1bf35a1783f7b5f2a65f511fea4aada9 --- /dev/null +++ b/modulefiles/fastp/0.19.7.lua @@ -0,0 +1,42 @@ +--[=====[ +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/fastp/0.19.7" +setenv("LAST_MODULE","fastp/0.19.7") +whatis([===[loads fastp 0.19.7 (Debian 7) environment ]===]) +conflict("fastp") +prepend_path{"PATH",pathJoin(root, "/bin"),delim=":",priority="0"} +setenv("FASTP_PATH",pathJoin(root, "/bin"))