From c9849dd41d3b774acabeddc5d8099ee2e6b123e5 Mon Sep 17 00:00:00 2001
From: snehring <7978778+snehring@users.noreply.github.com>
Date: Mon, 15 May 2023 12:14:58 -0500
Subject: [PATCH] tmalign: new version 20220412 (#37645)

---
 .../repos/builtin/packages/tmalign/package.py | 29 +++++++++++++++++--
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/var/spack/repos/builtin/packages/tmalign/package.py b/var/spack/repos/builtin/packages/tmalign/package.py
index 48b517ed2ba..c27a79a3d89 100644
--- a/var/spack/repos/builtin/packages/tmalign/package.py
+++ b/var/spack/repos/builtin/packages/tmalign/package.py
@@ -10,12 +10,35 @@ class Tmalign(Package):
     """TM-align is an algorithm for sequence-order independent protein
     structure comparisons."""
 
-    homepage = "https://zhanglab.ccmb.med.umich.edu/TM-align"
-    url = "http://zhanglab.ccmb.med.umich.edu/TM-align/TM-align-C/TMalignc.tar.gz"
+    homepage = "https://zhanggroup.org/TM-align/"
+    url = "https://zhanggroup.org/TM-align/TMalign.cpp"
+
+    maintainers("snehring")
 
     version(
-        "2016-05-25", sha256="ce7f68289f3766d525afb0a58e3acfc28ae05f538d152bd33d57f8708c60e2af"
+        "20220412",
+        sha256="09227c46705ca8cf7c922a6e1672c34d7ed4daba32e5c7c484306808db54117a",
+        expand=False,
     )
+    version(
+        "2016-05-25",
+        sha256="ce7f68289f3766d525afb0a58e3acfc28ae05f538d152bd33d57f8708c60e2af",
+        url="http://zhanglab.ccmb.med.umich.edu/TM-align/TM-align-C/TMalignc.tar.gz",
+        deprecated=True,
+    )
+
+    variant("fast-math", default=False, when="@20220412:")
+
+    with when("@20220412:"):
+        phases = ["build", "install"]
+
+    def build(self, spec, prefix):
+        cxx = Executable(self.compiler.cxx)
+        args = ["-O3"]
+        if spec.satisfies("+fast-math"):
+            args.append("-ffast-math")
+        args.extend(["-lm", "-o", "TMalign", "TMalign.cpp"])
+        cxx(*args)
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)