paintor: new package @3.0 (#40359)

* paintor: new package @3.0
* Update var/spack/repos/builtin/packages/paintor/package.py
---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

1 files changed, 37 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/paintor/package.py b/var/spack/repos/builtin/packages/paintor/package.py
new file mode 100644
index 0000000000..421a92cb11
--- /dev/null
+++ b/var/spack/repos/builtin/packages/paintor/package.py
@@ -0,0 +1,37 @@
+# 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 Paintor(MakefilePackage):
+    """Probabilistic Annotation integrator. Fast, integrative fine mapping with functional
+    data"""
+
+    homepage = "https://github.com/gkichaev/PAINTOR_V3.0"
+    url = "https://github.com/gkichaev/PAINTOR_V3.0/archive/refs/tags/3.0.tar.gz"
+
+    version("3.0", sha256="cc39d3c334cc6d787e4f04847192c9d0185025a2ca46910bd38901b6679d198f")
+
+    depends_on("nlopt")
+    depends_on("eigen")
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter("Makefile")
+        makefile.filter("CC = g\\+\\+", f"CC = {spack_cxx}")
+        makefile.filter(
+            r"(.*)-I/\$\(curr\)/eigen/Eigen(.*)",
+            r"\1-I{}/eigen3/Eigen\2".format(spec["eigen"].prefix.include),
+        )
+        makefile.filter(r"(.*)-L/\$\{curr}/lib(.*)", r"\1-L{}\2".format(spec["nlopt"].prefix.lib))
+        makefile.filter(
+            r"(.*)-I/\${curr}/include(.*)", r"\1-I{}\2".format(spec["nlopt"].prefix.include)
+        )
+
+    @run_after("install")
+    def mv_binary(self):
+        mkdirp(self.prefix.bin)
+        with working_dir(self.build_directory):
+            install("PAINTOR", self.prefix.bin)