1 files changed, 59 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/sepp/package.py b/var/spack/repos/builtin/packages/sepp/package.py
new file mode 100644
index 0000000000..b855a97091
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sepp/package.py
@@ -0,0 +1,59 @@
+# Copyright 2013-2022 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.package import *
+
+
+class Sepp(Package):
+    """SEPP stands for SATe-enabled phylogenetic placement"""
+
+    homepage = "https://github.com/smirarab/sepp"
+
+    url = "https://github.com/smirarab/sepp/archive/refs/tags/4.5.1.tar.gz"
+    maintainers = ["snehring"]
+
+    version("4.5.1", sha256="51e052569ae89f586a1a94c804f09fe1b7910a3ffff7664e2005f18c7d3f717b")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+    depends_on("py-dendropy@4:", type=("build", "run"))
+
+    depends_on("java@1.8:", type="run")
+    depends_on("pasta@1:", type="run")
+    depends_on("blast-plus@2.10.1:", type="run")
+
+    extends("python")
+
+    def install(self, spec, prefix):
+        dirs = ["sepp", "tools"]
+        for d in dirs:
+            install_tree(d, join_path(prefix, d))
+        files = ["default.main.config", "*.py"]
+        for f in files:
+            install(f, prefix)
+        with working_dir(prefix):
+            prefix_string = "--prefix=" + prefix
+            python("setup.py", "config", "-c")
+            python("setup.py", "install", prefix_string)
+            python("setup.py", "upp", "-c")
+            for f in ["merge_script.py", "run_ensemble.py"]:
+                install(f, prefix.bin)
+                set_executable(join_path(prefix.bin, f))
+            remove_files = [
+                "merge_script.py",
+                "run_ensemble.py",
+                "run_sepp.py",
+                "run_upp.py",
+                "setup.py",
+                "split_sequences.py",
+                "distribute_setup.py",
+                "home.path",
+                "default.main.config",
+            ]
+            for f in remove_files:
+                force_remove(f)
+            dirs = ["sepp", "tools", "build", "dist", "__pycache__", "sepp.egg-info"]
+            for d in dirs:
+                remove_linked_tree(d)