Commit f48baa2f authored by Laurent Modolo's avatar Laurent Modolo
Browse files

try to fix multiqc

parent c39bdc84
......@@ -34,7 +34,7 @@
# knowledge of the CeCILL license and that you accept its terms.
source ../build_env.sh
module load python/2.7
module load Python/2.7.13
MULTIQC_VERSION=1.0
MARKUPSAFE_VERSION=1.0
......@@ -52,7 +52,7 @@ python setup.py install --single-version-externally-managed --prefix ${MULTIQC_R
cd ..
rm -Rf markupsafe
pip install --install-option="--prefix=$MULTIQC_ROOT" multiqc==${MULTIQC_VERSION}
pip install --ignore-installed --prefix=$MULTIQC_ROOT multiqc==${MULTIQC_VERSION}
#git clone https://github.com/pallets/click.git
#cd click
......
#%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 0.9
set modname MultiQC
set osarch "Python2.7/Debian7"
set modroot /Xnfs/site/lbmcdb/common/modules/apps/MultiQC/0.9
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
module load python/2.7
prereq python/2.7
}
if [ module-info mode remove ] {
module unload python/2.7
}
prepend-path PYTHONPATH $modroot/lib/python2.7/site-packages/
prepend-path PATH $modroot/bin
setenv HTSEQ_PATH $modroot/bin
--[=====[
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/multiqc/0.9"
conflict("multiqc")
conflict("Python/3.6.1")
load("Python/2.7.13")
prereq_any("Python/2.7.13")
prepend_path{"PATH", pathJoin(root, "/lib/python2.7/site-packages/")}
prepend_path{"PYTHONPATH", pathJoin(root, "/bin/"), delim=":", priority="0"}
setenv("MULTIQC_PATH", pathJoin(root, "/bin/"))
......@@ -41,5 +41,5 @@ load("Python/2.7.13")
prereq_any("Python/2.7.13")
prepend_path{"PATH", pathJoin(root, "/lib/python2.7/site-packages/")}
prepend_path{"PYTHONPATH", pathJoin(root, "/lib/python2.7/site-packages/"), delim=":", priority="0"}
setenv("MULTIQC_PATH", pathJoin(root, "/lib/python2.7/site-packages/"))
prepend_path{"PYTHONPATH", pathJoin(root, "/bin/"), delim=":", priority="0"}
setenv("MULTIQC_PATH", pathJoin(root, "/bin/"))
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment