1 files changed, 37 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/snphylo/package.py b/var/spack/repos/builtin/packages/snphylo/package.py
new file mode 100644
index 0000000000..d249af2e65
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snphylo/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 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 Snphylo(Package):
+    """A pipeline to generate a phylogenetic tree from huge SNP data"""
+
+    homepage = "http://chibba.pgml.uga.edu/snphylo/"
+    url      = "http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz"
+
+    version('2016-02-04', '467660814965bc9bed6c020c05c0d3a6')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('r', type=('build', 'run'))
+    depends_on('r-phangorn', type=('build', 'run'))
+    depends_on('r-gdsfmt', type=('build', 'run'))
+    depends_on('r-snprelate', type=('build', 'run'))
+    depends_on('r-getopt', type=('build', 'run'))
+    depends_on('muscle')
+    depends_on('phylip')
+
+    def install(self, spec, prefix):
+        install_answer = ['y', 'y', 'y', 'y']
+        install_answer_input = 'spack-config.in'
+        with open(install_answer_input, 'w') as f:
+            f.writelines(install_answer)
+        with open(install_answer_input, 'r') as f:
+            bash = which('bash')
+            bash('./setup.sh', input=f)
+            install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix)