wise2: adding new package wise2 (#40341)

1 files changed, 58 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/wise2/package.py b/var/spack/repos/builtin/packages/wise2/package.py
new file mode 100644
index 0000000000..153305896b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wise2/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2023 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 Wise2(MakefilePackage):
+    """The Wise2 package is now a rather stately bioinformatics package that
+    has be around for a while. Its key programs are genewise, a program
+    for aligning proteins or protein HMMs to DNA, and dynamite a rather
+    cranky "macro language" which automates the production of dynamic
+    programming."""
+
+    homepage = "https://www.ebi.ac.uk/~birney/wise2/"
+    url = "https://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz"
+
+    maintainers("snehring")
+
+    version("2.4.1", sha256="240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1")
+
+    depends_on("gettext")
+    depends_on("glib")
+    depends_on("libiconv")
+    depends_on("pcre2")
+
+    build_directory = "src"
+
+    build_targets = ["all"]
+
+    def edit(self, spec, prefix):
+        glib_include_include = join_path(
+            spec["glib"].prefix.include, "glib-" + str(spec["glib"].version[0]) + ".0"
+        )
+        glib_lib_include = join_path(
+            spec["glib"].prefix.lib, "glib-" + str(spec["glib"].version[0]) + ".0", "include"
+        )
+        glib_lib = spec["glib"].prefix.lib
+        glib_config_files = ["src/makefile", "src/network/makefile", "src/models/makefile"]
+        for f in glib_config_files:
+            filter_file(
+                "`glib-config --cflags`",
+                f"-I{glib_include_include} -I{glib_lib_include}",
+                f,
+                string=True,
+            )
+            filter_file("`glib-config --libs`", f"-L{glib_lib} -lglib-2.0", f, string=True)
+        filter_file('"glib.h"', "<glib.h>", "src/dynlibsrc/subseqhash.h", string=True)
+        filter_file("getline", "getlineseq", "src/HMMer2/sqio.c", string=True)
+        filter_file("isnumber", "isdigit", "src/models/phasemodel.c", string=True)
+        filter_file(r".*welcome.csh.*", "", "src/makefile")
+
+    def install(self, spec, prefix):
+        with working_dir("src"):
+            install_tree("bin", prefix.bin)
+        mkdirp(prefix.share.wise2)
+        install_tree("wisecfg", prefix.share.wise2)