From d846664165a1d78d5fa7549b42f939613c54ccfa Mon Sep 17 00:00:00 2001 From: George Young Date: Mon, 9 Oct 2023 17:54:44 +0100 Subject: 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 Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> --- .../repos/builtin/packages/paintor/package.py | 37 ++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 var/spack/repos/builtin/packages/paintor/package.py (limited to 'var') 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) -- cgit v1.2.3-60-g2f50