From 341132a87fa9d32d45c81627d8cc290d40046fe5 Mon Sep 17 00:00:00 2001
From: 健美猞猁 <weijianwen@gmail.com>
Date: Tue, 15 May 2018 00:07:00 +0800
Subject: A new pacakge: Kaiju. (#8111)

* A new package: kaiju.

* Replace ftp:// with https://.
---
 var/spack/repos/builtin/packages/kaiju/package.py | 48 +++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/kaiju/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/kaiju/package.py b/var/spack/repos/builtin/packages/kaiju/package.py
new file mode 100644
index 0000000000..e77e3f529d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kaiju/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Kaiju(MakefilePackage):
+    """Kaiju is a program for the taxonomic classification
+    of high-throughput sequencing reads."""
+
+    homepage = "https://github.com/bioinformatics-centre/kaiju"
+    url      = "https://github.com/bioinformatics-centre/kaiju/archive/v1.6.2.zip"
+
+    version('1.6.2', '0bd85368954837aa31f3de8b87ea410b')
+
+    build_directory = 'src'
+
+    depends_on('perl-io-compress', type='run')
+    depends_on('py-htseq', type='run')
+
+    def edit(self, spec, prefix):
+        # Replace ftp:// with https://
+        makedb = FileFilter('util/makeDB.sh')
+        makedb.filter('ftp://', 'https://', string=True)
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
-- 
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