From b0ec2788ab57d418a7193ea7bd1a0a57342ccaf0 Mon Sep 17 00:00:00 2001
From: ilbiondo <61497728+ilbiondo@users.noreply.github.com>
Date: Thu, 16 Apr 2020 12:19:20 +0200
Subject: HAL: added new package at v2.1 (#16085)

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
---
 var/spack/repos/builtin/packages/hal/package.py | 102 ++++++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/hal/package.py

diff --git a/var/spack/repos/builtin/packages/hal/package.py b/var/spack/repos/builtin/packages/hal/package.py
new file mode 100644
index 0000000000..752feab1d8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hal/package.py
@@ -0,0 +1,102 @@
+# 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 Hal(MakefilePackage):
+    """HAL is a structure to efficiently store and index multiple
+    genome alignments and ancestral reconstructions.
+
+    HAL is a graph-based representation which provides several advantages
+    over matrix/block-based formats such as MAF, such as
+    improved scalability and the ability to perform queries with
+    respect to an arbitrary reference or subtree."""
+
+    homepage = "https://github.com/ComparativeGenomicsToolkit/hal"
+    url      = "https://github.com/ComparativeGenomicsToolkit/hal/archive/release-V2.1.tar.gz"
+
+    version('2.1', '540255be1af55abf390359fe034b82d7e61bdf6c3277df3cc01259cd450994e5')
+
+    maintainers = ['ilbiondo']
+
+    # HAL expects to be compiled alongside sonlib so we need both the
+    # source version and python library version
+
+    depends_on('hdf5+cxx~mpi')
+    depends_on('sonlib',    type='build')
+    depends_on('python',    type='run')
+    depends_on('py-sonlib', type='run')
+
+    # As we install sonlib seperately the include.mk needs
+    # editing to comment out an include
+
+    def patch(self):
+        includemk = FileFilter('include.mk')
+        includemk.filter(r'^include  \$\{sonLibRootDir\}/include\.mk',
+                         '# include  ${sonLibRootDir}/include.mk')
+
+    def setup_build_environment(self, env):
+        env.set('sonLibRootDir', self.spec['sonlib'].prefix)
+
+    def install(self, spec, prefix):
+
+        # First the easy bit
+
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
+
+        # Copy the rest of the "toolkit" as to a directory named hal
+        # in order that the python libraries can be found and used
+
+        haldirs = ['alignmentDepth',
+                   'analysis',
+                   'api',
+                   'assemblyHub',
+                   'benchmarks',
+                   'blockViz',
+                   'doc',
+                   'extra',
+                   'extract',
+                   'fasta',
+                   'liftover',
+                   'lod',
+                   'maf',
+                   'modify',
+                   'mutations',
+                   'objs',
+                   'phyloP',
+                   'randgen',
+                   'stats',
+                   'synteny',
+                   'testdata',
+                   'validate']
+
+        for folder in haldirs:
+
+            install_tree(folder, join_path(self.prefix, 'hal', folder))
+
+        install('__init__.py', join_path(self.prefix, 'hal'))
+
+        # Now in order to make things useful we copy some python tools to bin
+
+        halpyfiles = ['analysis/halContiguousRegions.py',
+                      'assemblyHub/hal2assemblyHub.py',
+                      'liftover/halLiftoverStatus.py',
+                      'lod/halLodBenchmark.py',
+                      'lod/halLodInterpolate.py',
+                      'maf/hal2mafMP.py',
+                      'phyloP/halPhyloPMP.py']
+
+        for pyfile in halpyfiles:
+
+            install(pyfile, self.prefix.bin)
+
+    # The hal directory is a python library so we set the path
+    # to be the installation root
+
+    def setup_run_environment(self, env):
+        env.prepend_path('PYTHONPATH', self.prefix)
-- 
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