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*/

*/

*/

*/

*/

*/

module load Python/3.6.1

CUTADAPT_VERSION=1.14

CUTADAPT_ROOT=/Xnfs/lbmcdb/common/modules/apps/cutadapt/${MULTIQC_VERSION}

CUTADAPT_ROOT=/Xnfs/lbmcdb/common/modules/apps/cutadapt/${CUTADAPT_VERSION}

mkdir -p ${CUTADAPT_VERSION}/lib/python2.7/dist-packages/

PYTHONPATH=${CUTADAPT_ROOT}lib/python2.7/dist-packages/:$PYTHONPATH

rm -Rf markupsafe

mv bin lib 1.14/

rm -Rf cutadapt

#!/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/3.6.1

CUTADAPT_VERSION=2.1

CUTADAPT_ROOT=/Xnfs/lbmcdb/common/modules/apps/cutadapt/${CUTADAPT_VERSION}

mkdir -p ${CUTADAPT_VERSION}/lib/python2.7/dist-packages/

PYTHONPATH=${CUTADAPT_ROOT}lib/python2.7/dist-packages/:$PYTHONPATH

git clone https://github.com/marcelm/cutadapt.git

cd cutadapt

git checkout tags/v${CUTADAPT_VERSION}

python setup.py install --single-version-externally-managed --prefix ${CUTADAPT_ROOT} --record markupsafe_install.txt

cd ..

rm -Rf markupsafe

mv bin lib 2.1/

rm -Rf cutadapt

*/

*/

#!/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

*/

*/

*/

*/

#!/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

HISAT2_VERSION=2.0.0

curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip

unzip hisat2_linux-v${HISAT2_VERSION}.zip

mkdir ${HISAT2_VERSION}

mkdir ${HISAT2_VERSION}/bin

cd hisat2-${HISAT2_VERSION}-beta

make

cp hisat2 ../${HISAT2_VERSION}/bin && \

cp hisat2-* ../${HISAT2_VERSION}/bin && \

rm -Rf hisat2-${HISAT2_VERSION}-beta

rm -Rf hisat2-${HISAT2_VERSION}-beta.zip

#!/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

HISAT2_VERSION=2.1.0

curl -k -L http://ccb.jhu.edu/software/hisat2/dl/hisat2-${HISAT2_VERSION}-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip

unzip hisat2_linux-v${HISAT2_VERSION}.zip

mkdir ${HISAT2_VERSION}

mkdir ${HISAT2_VERSION}/bin

cd hisat2-${HISAT2_VERSION}

make

cp hisat2 ../${HISAT2_VERSION}/bin && \

cp hisat2-* ../${HISAT2_VERSION}/bin && \

rm -Rf hisat2-${HISAT2_VERSION}

rm -Rf hisat2-${HISAT2_VERSION}.zip

*/

#%Module1.0#####################################################################

#!/bin/bash

# Copyright laurent modolo for the LBMC UMR 5239 ©.

# contributor(s) : laurent modolo (2017)

#

#

# 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

source ../build_env.sh

module load Python/2.7.13

###############################################################################

proc ModulesHelp { } {

        global modname version osarch

        puts stderr "\nThis set the environment variables for $modname $version - $osarch."

}

HTSEQ_VERSION=0.11.2

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/

module-whatis   "loads $modname $version ($osarch) environment"

###############################################################################

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 ..

# conflict

conflict $modname

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 ..

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

rm -Rf htseq pysam

*/

*/

# 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

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

#!/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

MULTIQC_VERSION=1.7

MARKUPSAFE_VERSION=1.7

#CLICK_VERSION=6.7

#LZSTRING_VERSION=6840ae522a099de53313b93fa13289beaac119f2

#FUTURE_VERSION=3.1.1

MULTIQC_ROOT=/Xnfs/lbmcdb/common/modules/apps/MultiQC/${MULTIQC_VERSION}

mkdir -p ${MULTIQC_VERSION}/lib/python2.7/dist-packages/

PYTHONPATH=${MULTIQC_ROOT}lib/python2.7/dist-packages/:$PYTHONPATH

git clone https://github.com/pallets/markupsafe.git

cd markupsafe

git checkout tags/${MARKUPSAFE_VERSION}

python setup.py install --single-version-externally-managed --prefix ${MULTIQC_ROOT} --record markupsafe_install.txt

cd ..

rm -Rf markupsafe

pip install --install-option="--prefix=$MULTIQC_ROOT" multiqc==${MULTIQC_VERSION}

#git clone https://github.com/pallets/click.git

#cd click

#git checkout tags/${CLICK_VERSION}

#python setup.py install --single-version-externally-managed --prefix ${MULTIQC_ROOT} --record click_install.txt

#cd ..

#

#git clone https://github.com/gkovacs/lz-string-python.git

#cd lz-string-python

#git checkout tags/${LZSTRING_VERSION}

#python setup.py install --single-version-externally-managed --prefix ${MULTIQC_ROOT} --record lz-string_install.txt

#cd ..

#

#git clone https://github.com/agronholm/pythonfutures.git

#cd pythonfutures

#git checkout tags/${FUTURE_VERSION}

#python setup.py install --single-version-externally-managed --prefix ${MULTIQC_ROOT} --record future_install.txt

#cd ..

#

#git clone https://github.com/ewels/MultiQC.git

#cd MultiQC

#git checkout tags/v${MULTIQC_VERSION}

#python setup.py install --single-version-externally-managed --prefix ${MULTIQC_ROOT} --record multiqc_install.txt

#cd ..

##

#rm -Rf click lz-string-python MultiQC

*/

*/

*/

*/

*/

*/

*/

*/

#!/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

SAMBAMBA_VERSION=0.6.9

curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \

tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \

mkdir -p ${SAMBAMBA_VERSION}/bin && \

cp sambamba ${SAMBAMBA_VERSION}/bin/ && \

rm -Rf sambamba_v${SAMBAMBA_VERSION}_linux* sambamba

*/

*/

*/

*/

*/

local root = "/Xnfs/lbmcdb/common/modules/apps/bioawk/1.0"

setenv("LAST_MODULE","bioawk/1.0")

whatis([===[loads bioawk 1.0 (Debian 7) environment ]===])

conflict("UrQt")

conflict("urqt")

prepend_path{"PATH",pathJoin(root, "/bin"),delim=":",priority="0"}

setenv("URQT_PATH",pathJoin(root, "/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/cutadapt/2.1"

conflict("cutadapt")

conflict("Python/2.7.13")

load("Python/3.6.1")

prereq_any("Python/3.6.1")

prepend_path{"PYTHONPATH","/Xnfs/lbmcdb/common/modules/apps/cutadapt/2.1/lib/python3.6/site-packages/",delim=":",priority="0"}

prepend_path{"PATH","/Xnfs/lbmcdb/common/modules/apps/cutadapt/2.1/bin",delim=":",priority="0"}

setenv("HTSEQ_PATH","/Xnfs/lbmcdb/common/modules/apps/cutadapt/2.1/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/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"))

--[=====[

Copyright nicolas fontrodona for the LBMC UMR 5239 ©.

contributor(s) : nicolas fontrodona (2018)

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/hisat2/2.0.0"

conflict("hisat2")

prepend_path{"PATH", pathJoin(root, "bin")}

setenv("HSAT2_PATH", pathJoin(root, "bin"))

--[=====[

Copyright nicolas fontrodona for the LBMC UMR 5239 ©.

contributor(s) : nicolas fontrodona (2018)

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/hisat2/2.1.0"

conflict("hisat2")

prepend_path{"PATH", pathJoin(root, "bin")}

setenv("HSAT2_PATH", pathJoin(root, "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/htseq/0.11.2"

conflict("htseq")

conflict("Python/3.6.1")

load("Python/2.7.13")

prereq_any("Python/2.7.13")

prepend_path{"PATH", pathJoin(root, "bin")}

prepend_path{"PYTHONPATH", pathJoin(root, "/lib/python2.7/site-packages/"), delim=":", priority="0"}

setenv("HTSEQ_PATH", pathJoin(root, "bin"))