From f2fdb0d9d634989a9c86ef25b98f98439f07cc27 Mon Sep 17 00:00:00 2001 From: Laurent Modolo <laurent.modolo@ens-lyon.fr> Date: Thu, 31 May 2018 14:03:42 +0200 Subject: [PATCH] HTSeq: fix 0.8.0 and add 0.9.0 --- apps/HTSeq/install_0.8.0.sh | 5 ++-- apps/HTSeq/install_0.9.1.sh | 57 +++++++++++++++++++++++++++++++++++++ modulefiles/HTSeq/0.8.0.lua | 2 +- modulefiles/HTSeq/0.9.0.lua | 43 ++++++++++++++++++++++++++++ 4 files changed, 104 insertions(+), 3 deletions(-) create mode 100644 apps/HTSeq/install_0.9.1.sh create mode 100644 modulefiles/HTSeq/0.9.0.lua diff --git a/apps/HTSeq/install_0.8.0.sh b/apps/HTSeq/install_0.8.0.sh index 44eafcd..dce8bf6 100644 --- a/apps/HTSeq/install_0.8.0.sh +++ b/apps/HTSeq/install_0.8.0.sh @@ -34,11 +34,11 @@ # knowledge of the CeCILL license and that you accept its terms. source ../build_env.sh -module load python/2.7.13 +module load Python/2.7.13 HTSEQ_VERSION=0.8.0 PYSAM_VERSION=0.11.2.2 -HTSEQ_ROOT=/Xnfs/lbmcdb/common/modules/apps/HTSeq/${HTSEQ_VERSION} +HTSEQ_ROOT=/Xnfs/lbmcdb/common/modules/apps/HTSeq/${HTSEQ_VERSION}/ mkdir -p ${HTSEQ_VERSION}/lib/python2.7/dist-packages/ PYTHONPATH=$PYTHONPATH:${HTSEQ_ROOT}/lib/python2.7/dist-packages/ @@ -52,5 +52,6 @@ git clone https://github.com/simon-anders/htseq.git cd htseq git checkout tags/release_${HTSEQ_VERSION} python setup.py install --single-version-externally-managed --prefix ${HTSEQ_ROOT} --record htseq_install.txt +cd .. rm -Rf htseq pysam diff --git a/apps/HTSeq/install_0.9.1.sh b/apps/HTSeq/install_0.9.1.sh new file mode 100644 index 0000000..b2658af --- /dev/null +++ b/apps/HTSeq/install_0.9.1.sh @@ -0,0 +1,57 @@ +#!/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 +module load Python/2.7.13 + +HTSEQ_VERSION=0.9.1 +PYSAM_VERSION=0.11.2.2 +HTSEQ_ROOT=/Xnfs/lbmcdb/common/modules/apps/HTSeq/${HTSEQ_VERSION}/ +mkdir -p ${HTSEQ_VERSION}/lib/python2.7/dist-packages/ +PYTHONPATH=$PYTHONPATH:${HTSEQ_ROOT}/lib/python2.7/dist-packages/ + +git clone https://github.com/pysam-developers/pysam.git +cd pysam +git checkout tags/v${PYSAM_VERSION} +python setup.py install --single-version-externally-managed --prefix ${HTSEQ_ROOT} --record pysam_install.txt +cd .. + +git clone https://github.com/simon-anders/htseq.git +cd htseq +git checkout tags/release_${HTSEQ_VERSION} +python setup.py install --single-version-externally-managed --prefix ${HTSEQ_ROOT} --record htseq_install.txt +cd .. + +rm -Rf htseq pysam diff --git a/modulefiles/HTSeq/0.8.0.lua b/modulefiles/HTSeq/0.8.0.lua index bb522b9..bb68730 100644 --- a/modulefiles/HTSeq/0.8.0.lua +++ b/modulefiles/HTSeq/0.8.0.lua @@ -35,7 +35,7 @@ knowledge of the CeCILL license and that you accept its terms. --]=====] local root = "/Xnfs/lbmcdb/common/modules/apps/HTSeq/0.8.0" -conflict("file_handle") +conflict("HTSeq") conflict("Python/3.6.1") load("Python/2.7.13") prereq_any("Python/2.7.13") diff --git a/modulefiles/HTSeq/0.9.0.lua b/modulefiles/HTSeq/0.9.0.lua new file mode 100644 index 0000000..0febb04 --- /dev/null +++ b/modulefiles/HTSeq/0.9.0.lua @@ -0,0 +1,43 @@ +--[=====[ +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/HTSeq/0.9.0" +conflict("HTSeq") +conflict("Python/3.6.1") +load("Python/2.7.13") +prereq_any("Python/2.7.13") +prepend_path{"PATH", pathJoin(root, "bin")} +setenv("HTSEQ_PATH", pathJoin(root, "bin")) -- GitLab