From 1fa22125437c4102b87b77661672690a18120026 Mon Sep 17 00:00:00 2001
From: lingnanyuan <1297162327@qq.com>
Date: Thu, 5 Jul 2018 21:34:38 -0500
Subject: [PATCH] ncbitoolkit: Create new package. (#8591)

* ncbitoolkit: Create new package.

* Fix Flake8 Error.

* Add version constraints and change format.

* Fix version constraints.
---
 .../builtin/packages/ncbi-toolkit/package.py  | 65 +++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ncbi-toolkit/package.py

diff --git a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py
new file mode 100644
index 0000000000..876b9ac80d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py
@@ -0,0 +1,65 @@
+##############################################################################
+# 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/llnl/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 NcbiToolkit(AutotoolsPackage):
+    """NCBI C++ Toolkit"""
+
+    homepage = "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/"
+    url      = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--21_0_0.tar.gz"
+
+    version('21_0_0', '14e021e08b1a78ac9cde98d0cab92098')
+
+    depends_on('boost@1.35.0:')
+    depends_on('bzip2')
+    depends_on('libjpeg')
+    depends_on('libpng')
+    depends_on('libtiff')
+    depends_on('libxml2')
+    depends_on('libxslt@1.1.14:')
+    depends_on('lzo')
+    depends_on('pcre')
+    depends_on('giflib')
+    depends_on('sqlite@3.6.6:')
+    depends_on('zlib')
+    depends_on('samtools')
+    depends_on('bamtools')
+
+    def configure_args(self):
+        return ['--without-sybase', '--without-fastcgi']
+
+    def patch(self):
+        with working_dir(join_path('src', 'util', 'image')):
+            filter_file(r'jpeg_start_compress(&cinfo, true)',
+                        'jpeg_start_compress(&cinfo, TRUE)',
+                        'image_io_jpeg.cpp', string=True)
+
+    def build(self, spec, prefix):
+        CompilerVersion = self.compiler.version.joined
+
+        with working_dir(join_path(
+                'GCC{0}-DebugMT64'.format(CompilerVersion), 'build')):
+            make('all_r')