CONTRIBUTING.md

@@ -8,7 +8,7 @@ To install your forked version of the LBMC modules repository on the PSMN run fo
 
 ```
 git clone git@gitlab.biologie.ens-lyon.fr:<your_login>/modules.git ~/privatemodules_dev
-module use ~/privatemodules_dev
+module use ~/privatemodules_dev/modulefiles/
 ```
 
 If you don’t have a `.ssh/config` file and if you like typing your password, you can instead use the following clone command, after defining your [Gitlab password](https://gitlab.biologie.ens-lyon.fr/profile/password/edit).

apps/bcftools/.gitignore

+*/

apps/bcftools/install_1.7.sh

+#!/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
+
+BCFTOOLS_VERSION=1.7
+git clone git://github.com/samtools/htslib.git
+cd htslib
+git checkout tags/${BCFTOOLS_VERSION}
+cd ..
+git clone git://github.com/samtools/bcftools.git
+cd bcftools
+git checkout tags/${BCFTOOLS_VERSION}
+make
+cd ..
+mkdir -p ${BCFTOOLS_VERSION}/bin
+cp bcftools/bcftools ${BCFTOOLS_VERSION}/bin/
+rm -Rf htslib bcftools

apps/bedtools/.gitignore

+*/

apps/bioawk/.gitignore

+*/

apps/bioawk/install_1.0.sh

+#!/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
+
+BIOAWK_VERSION=1.0
+
+git clone https://github.com/lh3/bioawk.git && \
+cd bioawk && \
+git checkout tags/v${BIOAWK_VERSION} && \
+make && \
+cd .. && \
+mkdir -p ${BIOAWK_VERSION}/bin && \
+mv bioawk/bioawk ${BIOAWK_VERSION}/bin/ && \
+rm -Rf bioawk

apps/bowtie2/.gitignore

+*/

apps/canu/.gitignore

+*/

apps/cutadapt/.gitignore

+*/

apps/cutadapt/install_1.14.sh

+#!/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=1.14
+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 1.14/
+rm -Rf cutadapt

apps/cutadapt/install_2.1.sh

+#!/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

apps/deeptools/.gitignore

+*/

apps/fastp/.gitignore

+*/

apps/fastp/install_0.19.7.sh

+#!/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

apps/fastqc/.gitignore

+*/