add fastp

apps/bedtools/.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

+*/

apps/multiqc/.gitignore

+*/

apps/salmon/.gitignore

+*/

apps/trimmomatic/.gitignore

+*/

apps/urqt/.gitignore

+*/

modulefiles/fastp/0.19.7.lua

+--[=====[
+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"))