From 262de647926c877ecbe60518eee14c0023190fb3 Mon Sep 17 00:00:00 2001
From: Yifan Zhu <ifanzhu@foxmail.com>
Date: Sat, 12 May 2018 01:22:45 -0500
Subject: shoremap: new package (#7343)

---
 var/spack/repos/builtin/packages/dislin/package.py | 23 +++++++++
 var/spack/repos/builtin/packages/libxt/package.py  |  6 +++
 .../repos/builtin/packages/shoremap/package.py     | 54 ++++++++++++++++++++++
 3 files changed, 83 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/shoremap/package.py

diff --git a/var/spack/repos/builtin/packages/dislin/package.py b/var/spack/repos/builtin/packages/dislin/package.py
index 05f8cfa153..f662f0b4fc 100644
--- a/var/spack/repos/builtin/packages/dislin/package.py
+++ b/var/spack/repos/builtin/packages/dislin/package.py
@@ -33,11 +33,31 @@ class Dislin(Package):
     homepage = "http://www.mps.mpg.de/dislin"
     url      = "ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.tar.gz"
 
+    version('11.1.linux.i586_64', '34218c257efedaf706f058bdf111ce9d')
     version('11.0.linux.i586_64', '6fb099b54f41db009cafc702eebb5bc6')
 
     depends_on('motif')
     depends_on('mesa')
 
+    @property
+    def libs(self):
+        query_parameters = self.spec.last_query.extra_parameters
+        query2libraries = {
+            tuple(): ['libdislin'],
+            ('d',): ['libdislin_d'],
+            ('c', ): ['libdislnc'],
+            ('cd',): ['libdislnc_d'],
+            ('cxx',): ['libdiscpp'],
+            ('java',): ['libdisjava']
+        }
+
+        key = tuple(query_parameters)
+        libraries = query2libraries[key]
+
+        return find_libraries(
+            libraries, root=self.prefix, shared=True, recursive=True
+        )
+
     def setup_environment(self, spack_env, run_env):
         spack_env.set('DISLIN', self.prefix)
         run_env.set('DISLIN', self.prefix)
@@ -46,6 +66,9 @@ class Dislin(Package):
         run_env.prepend_path('LD_LIBRARY_PATH', self.spec['motif'].prefix.lib)
         run_env.prepend_path('LD_LIBRARY_PATH', self.spec['mesa'].prefix.lib)
 
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        run_env.prepend_path('LD_LIBRARY_PATH', self.prefix)
+
     def install(self, spec, prefix):
         INSTALL = Executable('./INSTALL')
         INSTALL()
diff --git a/var/spack/repos/builtin/packages/libxt/package.py b/var/spack/repos/builtin/packages/libxt/package.py
index b50871fe9f..2b09c57de4 100644
--- a/var/spack/repos/builtin/packages/libxt/package.py
+++ b/var/spack/repos/builtin/packages/libxt/package.py
@@ -41,3 +41,9 @@ class Libxt(AutotoolsPackage):
     depends_on('kbproto', type='build')
     depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
+
+    @property
+    def libs(self):
+        return find_libraries(
+            'libXt', root=self.prefix, shared=True, recursive=True
+        )
diff --git a/var/spack/repos/builtin/packages/shoremap/package.py b/var/spack/repos/builtin/packages/shoremap/package.py
new file mode 100644
index 0000000000..663c2d48f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shoremap/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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 Shoremap(MakefilePackage):
+    """SHOREmap is a computational tool implementing a method that enables
+       simple and straightforward mapping-by-sequencing analysis.
+
+       Whole genome resequencing of pools of recombinant mutant genomes allows
+       directly linking phenotypic traits to causal mutations. Such an
+       analysis, called mapping-by-sequencing, combines classical genetic
+       mapping and next generation sequencing by relying on selection-induced
+       patterns within genome-wide allele frequency in pooled genomes."""
+
+    homepage = "http://bioinfo.mpipz.mpg.de/shoremap/"
+    url      = "http://bioinfo.mpipz.mpg.de/shoremap/SHOREmap_v3.6.tar.gz"
+
+    version('3.6', 'ccc9331189705a139d50f2c161178cb1')
+
+    depends_on('dislin')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('makefile')
+        makefile.filter(r'-L/usr/lib/',
+                        self.spec['libxt'].libs.search_flags)
+        makefile.filter(r'-L\./dislin.* -ldislin_d',
+                        self.spec['dislin:d'].libs.ld_flags)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('SHOREmap', prefix.bin)
-- 
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