From caf1e23eaa16051dcfff143e6283f07badb89ad8 Mon Sep 17 00:00:00 2001
From: Claire BURNY <cburny@e5-2670comp1.(none)>
Date: Tue, 21 Nov 2017 16:42:57 +0100
Subject: [PATCH] CDHIT/install_4.6.8.sh: script to install CDHIT
---
apps/CDHIT/install_4.6.8.sh | 54 +++++++++++++++++++++++++++++++++++++
1 file changed, 54 insertions(+)
create mode 100644 apps/CDHIT/install_4.6.8.sh
diff --git a/apps/CDHIT/install_4.6.8.sh b/apps/CDHIT/install_4.6.8.sh
new file mode 100644
index 0000000..8dee943
--- /dev/null
+++ b/apps/CDHIT/install_4.6.8.sh
@@ -0,0 +1,54 @@
+#!/bin/bash
+# Copyright claire burny for the LBMC UMR 5239 ©.
+# contributor(s) : claire burny (2017)
+#
+# claire.burny@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
+
+CDHIT_VERSION=4.6.8
+mkdir -p ${CDHIT_VERSION}/bin
+
+curl -k -L https://github.com/weizhongli/cdhit/releases/download/V${CDHIT_VERSION}/cd-hit-v${CDHIT_VERSION}-2017-0621-source.tar.gz -o cd-hit-v${CDHIT_VERSION}.tar.gz
+
+mkdir cd-hit-v${CDHIT_VERSION} && tar xzf cd-hit-v${CDHIT_VERSION}.tar.gz -C cd-hit-v${CDHIT_VERSION} --strip-components 1
+
+cd cd-hit-v${CDHIT_VERSION}
+make
+cd cd-hit-auxtools
+make
+cd ..
+cd ..
+
+rsync -av --exclude 'doc/' --exclude 'usecases/' --exclude 'README*' cd-hit-v${CDHIT_VERSION}/ ${CDHIT_VERSION}/bin/
+
+rm -Rf cd-hit-v${CDHIT_VERSION}*
--
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