s4pred: add new package (#42520)

var/spack/repos/builtin/packages/s4pred/package.py

@@ -0,0 +1,45 @@
+# Copyright 2013-2024 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)
+
+import os
+
+from spack.package import *
+
+
+class S4pred(Package):
+    """A tool for accurate prediction of a protein's secondary structure from only its amino
+    acid sequence with no evolutionary information"""
+
+    homepage = "http://bioinf.cs.ucl.ac.uk/psipred/"
+    url = "https://github.com/psipred/s4pred/archive/refs/tags/v1.2.0.tar.gz"
+
+    license("GPL-3.0-only", checked_by="A-N-Other")
+
+    version("1.2.0", sha256="133d4710cef8c58fa603bdedcd41dbd060d9afc029dd181a5bd43f6539783a89")
+
+    depends_on("python", type="run")
+
+    depends_on("py-torch@1.5.1:", type="run")
+    depends_on("py-biopython@1.78:", type="run")
+
+    resource(
+        name="weights",
+        url="http://bioinfadmin.cs.ucl.ac.uk/downloads/s4pred/weights.tar.gz",
+        sha256="6a91e887c01bac41b11249ae098fe0d43bcb9e3e15c746758a24a3299fe20283",
+    )
+
+    def install(self, spec, prefix):
+        # This package has no setup.py, so...
+        mkdirp(prefix.bin)
+        # unpack resources and correct hardcoded location
+        install_tree("weights", prefix.weights)
+        filter_file("/weights/", "/../weights/", "run_model.py")
+        # add shebang and ensure +x for the main script
+        sed = Executable("sed")
+        sed("-i", rf'1 i\#! {self.spec["python"].command.path}\n', "run_model.py")
+        os.chmod("run_model.py", 0o755)
+        # install files and make convenience symlink
+        install("*.py", prefix.bin)
+        os.symlink(join_path(prefix.bin, "run_model.py"), join_path(prefix.bin, "s4pred"))