eagle: new package at v1.1.2 (#15409)

1 files changed, 46 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/eagle/package.py b/var/spack/repos/builtin/packages/eagle/package.py
new file mode 100644
index 0000000000..81e0be6f90
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eagle/package.py
@@ -0,0 +1,46 @@
+# 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 Eagle(MakefilePackage):
+    """EAGLE: Explicit Alternative Genome Likelihood Evaluator"""
+
+    homepage = "https://github.com/tony-kuo/eagle"
+    url      = "https://github.com/tony-kuo/eagle/archive/v1.1.2.tar.gz"
+
+    version('1.1.2', sha256='afe967560d1f8fdbd0caf4b93b5f2a86830e9e4d399fee4a526140431343045e')
+
+    depends_on('curl')
+    depends_on('zlib')
+    depends_on('lzma')
+    depends_on('htslib')
+
+    def edit(self, spec, prefix):
+        # remove unused gcc flags
+        filter_file('$(LFLAGS) $(INCLUDES)', '', 'Makefile', string=True)
+
+        # drop static link to htslib
+        filter_file('$(LIBS)', '', 'Makefile', string=True)
+
+        # don't try to build htslib.
+        filter_file('all: UTIL HTSLIB', 'all: UTIL',
+                    'Makefile', string=True)
+
+        # add htslib link to ldflags
+        filter_file('-lcurl', '-lcurl -lhts', 'Makefile', string=True)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        bins = [
+            'eagle',
+            'eagle-rc',
+            'eagle-nm',
+        ]
+
+        for b in bins:
+            install(b, prefix.bin)