install /FastQC/0.11.5

.gitignore

@@ -8,3 +8,4 @@ apps/HTSeq/0.8.0/
 apps/MultiQC/0.9/
 apps/MultiQC/1.0/
 apps/UrQt/d62c1f8/
+apps/FastQC/0.11.5/

apps/FastQC/install_0.11.5.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
+
+FASTQC_VERSION=0.11.5
+mkdir -p ${FASTQC_VERSION}/bin
+
+curl -k -L http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${FASTQC_VERSION}.zip -o fastqc_v${FASTQC_VERSION}.zip
+unzip fastqc_v${FASTQC_VERSION}.zip
+mv FastQC/* ${FASTQC_VERSION}/bin/
+
+rm -Rf FastQC fastqc_v${FASTQC_VERSION}.zip

modulefiles/FastQC/0.11.5

+#%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         0.11.5
+set     modname         FastQC
+set     osarch          "Debian 7"
+set     modroot         /Xnfs/site/lbmcdb/communs_data/modules/apps/FastQC/0.11.5
+
+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
+}
+
+prepend-path    PATH            $modroot/bin
+setenv          FASTQC_PATH   $modroot/bin

modulefiles/UrQt/d62c1f8

@@ -61,4 +61,4 @@ if [ module-info mode load ] {
 }
 
 prepend-path    PATH            $modroot/bin
-setenv          SALMON_PATH   $modroot/bin
+setenv          URQT_PATH   $modroot/bin