From 3f9cff2aa2cb7ce260321086f07eb32b0ce24810 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 27 Jun 2017 16:10:04 +0200
Subject: [PATCH] install Kallisto/0.42.1
---
.gitignore | 1 +
apps/Kallisto/install_0.43.1.sh | 43 ++++++++++++++++++++++
modulefiles/Kallisto/0.43.1 | 64 +++++++++++++++++++++++++++++++++
3 files changed, 108 insertions(+)
create mode 100644 apps/Kallisto/install_0.43.1.sh
create mode 100644 modulefiles/Kallisto/0.43.1
diff --git a/.gitignore b/.gitignore
index 09526e9..e9e2d1b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
apps/SAMtools/1.5/
apps/RSEM/1.3.0/
apps/Bowtie2/2.3.2/
+apps/Kallisto/0.43.1/
diff --git a/apps/Kallisto/install_0.43.1.sh b/apps/Kallisto/install_0.43.1.sh
new file mode 100644
index 0000000..030c6ff
--- /dev/null
+++ b/apps/Kallisto/install_0.43.1.sh
@@ -0,0 +1,43 @@
+#!/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
+
+KALLISTO_VERSION=0.43.1
+curl -k -L https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz
+tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz
+mkdir -p ${KALLISTO_VERSION}/bin
+cp kallisto_linux-v${KALLISTO_VERSION}/kallisto ${KALLISTO_VERSION}/bin
+rm -Rf kallisto_linux-v${KALLISTO_VERSION}*
diff --git a/modulefiles/Kallisto/0.43.1 b/modulefiles/Kallisto/0.43.1
new file mode 100644
index 0000000..8dcdd64
--- /dev/null
+++ b/modulefiles/Kallisto/0.43.1
@@ -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 0.43.1
+set modname kallisto
+set osarch "Debian 7"
+set modroot /Xnfs/site/lbmcdb/communs_data/modules/apps/kallisto/0.43.1
+
+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 KALLISTO_PATH $modroot/bin
--
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