From bbe94a62b59616c6b67eea7f1f345e929a3721b0 Mon Sep 17 00:00:00 2001 From: Laurent Modolo <laurent@modolo.fr> Date: Thu, 21 Mar 2019 16:12:42 +0100 Subject: [PATCH] add local changes --- apps/BCFtools/install_1.7.sh | 2 +- apps/nextflow/install_19.01.0.sh | 51 ++++++++++++++++++++++++++++++++ modulefiles/nextflow/19.01.0.lua | 45 ++++++++++++++++++++++++++++ 3 files changed, 97 insertions(+), 1 deletion(-) create mode 100755 apps/nextflow/install_19.01.0.sh create mode 100644 modulefiles/nextflow/19.01.0.lua diff --git a/apps/BCFtools/install_1.7.sh b/apps/BCFtools/install_1.7.sh index 0477544..83dda4d 100755 --- a/apps/BCFtools/install_1.7.sh +++ b/apps/BCFtools/install_1.7.sh @@ -45,6 +45,6 @@ cd bcftools git checkout tags/${BCFTOOLS_VERSION} make cd .. -mkdir ${BCFTOOLS_VERSION}/bin +mkdir -p ${BCFTOOLS_VERSION}/bin cp bcftools/bcftools ${BCFTOOLS_VERSION}/bin/ rm -Rf htslib bcftools diff --git a/apps/nextflow/install_19.01.0.sh b/apps/nextflow/install_19.01.0.sh new file mode 100755 index 0000000..deba517 --- /dev/null +++ b/apps/nextflow/install_19.01.0.sh @@ -0,0 +1,51 @@ +#!/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 +ml Java/1.8.0_151 + +NF_VERSION=19.01.0 +mkdir -p ${NF_VERSION}/bin + +git clone https://github.com/nextflow-io/nextflow.git +cd nextflow +git checkout tags/v${NF_VERSION} +make compile +make pack +./nextflow + +cd .. +cp nextflow/nextflow ${NF_VERSION}/bin/ +rm -Rf nextflow diff --git a/modulefiles/nextflow/19.01.0.lua b/modulefiles/nextflow/19.01.0.lua new file mode 100644 index 0000000..327bb87 --- /dev/null +++ b/modulefiles/nextflow/19.01.0.lua @@ -0,0 +1,45 @@ +--[=====[ +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/nextflow/19.01.0" + +conflict("nextflow") +load("Java/1.8.0_151") +prereq_any("Java/1.8.0_151") + +whatis([===[loads nextflow 19.01.0 (Debian 9) environment ]===]) +prepend_path{"PATH", pathJoin(root, "bin")} +setenv("NEXTFLOW_PATH", pathJoin(root, "bin")) -- GitLab