From 5067b956f45187686a10592b1c25037b5881c086 Mon Sep 17 00:00:00 2001
From: ilbiondo <61497728+ilbiondo@users.noreply.github.com>
Date: Thu, 23 Jul 2020 13:22:58 +0200
Subject: [PATCH] Shapeit4: added new package at v4.1.3 (#17674)

---
 .../builtin/packages/shapeit4/package.py      | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/shapeit4/package.py

diff --git a/var/spack/repos/builtin/packages/shapeit4/package.py b/var/spack/repos/builtin/packages/shapeit4/package.py
new file mode 100644
index 0000000000..009e5084bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shapeit4/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Shapeit4(MakefilePackage):
+    """SHAPEIT4 is a fast and accurate method for estimation of haplotypes
+    (aka phasing) for SNP array and high coverage sequencing data."""
+
+    homepage = "https://odelaneau.github.io/shapeit4/"
+    url      = "https://github.com/odelaneau/shapeit4/archive/v4.1.3.tar.gz"
+
+    version('4.1.3', sha256='d209731277b00bca1e3478b7e0a0cbe40fbe23826c3d640ad12e0dd6033cbbb8')
+
+    maintainers = ['ilbiondo']
+
+    depends_on('htslib')
+    depends_on('boost')
+    depends_on('bzip2')
+    depends_on('xz')
+
+    def edit(self, spec, prefix):
+
+        makefile = FileFilter('makefile')
+        makefile.filter('CXX=.*', 'CXX = c++')
+
+        makefile.filter('CXXFLAG=.*', 'CXXFLAG = -O3')
+        makefile.filter('LDFLAG=.*', 'LDFLAG = -O3')
+
+        makefile.filter('HTSLIB_INC=.*', 'HTSLIB_INC = '
+                        + self.spec['htslib'].prefix.include)
+
+        makefile.filter('HTSLIB_LIB=.*', 'HTSLIB_LIB = '
+                        + self.spec['htslib'].prefix.lib + '/libhts.so')
+
+        makefile.filter('BOOST_INC=.*', 'BOOST_INC = '
+                        + self.spec['boost'].prefix.include)
+
+        makefile.filter('BOOST_LIB_IO=.*', 'BOOST_LIB_IO = '
+                        + self.spec['boost'].prefix.lib
+                        + "/libboost_iostreams.so")
+
+        makefile.filter('BOOST_LIB_PO=.*', 'BOOST_LIB_PO = '
+                        + self.spec['boost'].prefix.lib
+                        + "/libboost_program_options.so")
+
+    def install(self, spec, prefix):
+
+        install_tree('bin', prefix.bin)
+        install_tree('test', join_path(self.prefix, 'test'))
+        install_tree('docs', join_path(self.prefix, 'docs'))
+        install_tree('maps', join_path(self.prefix, 'maps'))