From 26554d46dad97177fcc870038c65a70f1151c296 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 28 Jun 2017 15:08:41 +0200
Subject: [PATCH] install /FastQC/0.11.5
---
.gitignore | 1 +
apps/FastQC/install_0.11.5.sh | 45 ++++++++++++++++++++++++
modulefiles/FastQC/0.11.5 | 64 +++++++++++++++++++++++++++++++++++
modulefiles/UrQt/d62c1f8 | 2 +-
4 files changed, 111 insertions(+), 1 deletion(-)
create mode 100644 apps/FastQC/install_0.11.5.sh
create mode 100644 modulefiles/FastQC/0.11.5
diff --git a/.gitignore b/.gitignore
index 47cc759..218306a 100644
--- a/.gitignore
+++ b/.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/
diff --git a/apps/FastQC/install_0.11.5.sh b/apps/FastQC/install_0.11.5.sh
new file mode 100644
index 0000000..accbd94
--- /dev/null
+++ b/apps/FastQC/install_0.11.5.sh
@@ -0,0 +1,45 @@
+#!/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
diff --git a/modulefiles/FastQC/0.11.5 b/modulefiles/FastQC/0.11.5
new file mode 100644
index 0000000..dd105bd
--- /dev/null
+++ b/modulefiles/FastQC/0.11.5
@@ -0,0 +1,64 @@
+#%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
diff --git a/modulefiles/UrQt/d62c1f8 b/modulefiles/UrQt/d62c1f8
index 5110ee9..3fc10e8 100644
--- a/modulefiles/UrQt/d62c1f8
+++ b/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
--
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