From 4d7898a669d41073138e97892435f5664e99edbd Mon Sep 17 00:00:00 2001
From: George Young <A-N-Other@users.noreply.github.com>
Date: Tue, 13 Feb 2024 02:20:33 +0000
Subject: [PATCH] psipred: new package @4.02 (#42529)

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
---
 .../repos/builtin/packages/psipred/package.py | 71 +++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/psipred/package.py

diff --git a/var/spack/repos/builtin/packages/psipred/package.py b/var/spack/repos/builtin/packages/psipred/package.py
new file mode 100644
index 00000000000000..e8f83999da111d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/psipred/package.py
@@ -0,0 +1,71 @@
+# 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)
+
+from spack.package import *
+
+
+class Psipred(MakefilePackage):
+    """PSIPRED is a simple and accurate secondary structure prediction method, incorporating
+    two feed-forward neural networks which perform an analysis on output obtained from
+    PSI-BLAST (Position Specific Iterated - BLAST). Using a very stringent cross validation
+    method to evaluate the methods performance"""
+
+    homepage = "http://bioinf.cs.ucl.ac.uk/psipred/"
+    url = "http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred.4.02.tar.gz"
+
+    license_url = "http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/LICENSE"
+
+    version("4.02", sha256="b4009b6a5f8b76c6d60ac91c4a743512d844864cf015c492fb6d1dc0d092c467")
+
+    variant("blast-plus", default=False, description="Use blast-plus in place of blast-legacy")
+
+    depends_on("blast-legacy", type="run", when="~blast-plus")
+    depends_on("blast-plus", type="run", when="+blast-plus")
+
+    build_directory = "src"
+
+    # patch to fix segfault on input lines >256 chars
+    # https://github.com/psipred/psipred/pull/8
+    patch(
+        "https://github.com/psipred/psipred/commit/cee0f2c.patch?full_index=1",
+        sha256="ef75999f688eaf7984e17f663c17c13e4eaba98912a904be128f562a7eaf8315",
+        when="@:1.10.1%gcc@13:",
+        level=1,
+    )
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            filter_file(r"CC\s+= cc", f"CC = {spack_cc}", "Makefile")
+
+    def build(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make("all")
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        with working_dir(self.build_directory):
+            for f in ("psipred", "psipass2", "chkparse", "seq2mtx"):
+                install(f, prefix.bin)
+
+    @run_after("install")
+    def configure(self):
+        # install data sources
+        install_tree("data", prefix.data)
+        # modify and install the relevant helper script examples
+        mkdir(self.prefix.scripts)
+        if self.spec.satisfies("~blast-plus"):
+            script = FileFilter("runpsipred")
+            blast_location = self.spec["blast-legacy"].prefix.bin
+        else:  # +blast-plus
+            script = FileFilter(join_path("BLAST+", "runpsipredplus"))
+            blast_location = self.spec["blast-plus"].prefix.bin
+        script.filter("set dbname .*", "set dbname = ")
+        script.filter("set ncbidir .*", f"set ncbidir = {blast_location}")
+        script.filter("set execdir .*", f"set execdir = {self.prefix.bin}")
+        script.filter("set datadir .*", f"set datadir = {self.prefix.data}")
+        if self.spec.satisfies("~blast-plus"):
+            install("runpsipred", self.prefix.scripts)
+        else:  # +blast-plus
+            install(join_path("BLAST+", "runpsipredplus"), self.prefix.scripts)