package.py

# 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 RRhtslib(RPackage):
    """HTSlib high-throughput sequencing library as an R package.

    This package provides version 1.7 of the 'HTSlib' C library for high-
    throughput sequence analysis. The package is primarily useful to
    developers of other R packages who wish to make use of HTSlib.
    Motivation and instructions for use of this package are in the vignette,
    vignette(package="Rhtslib", "Rhtslib")."""

    bioc = "Rhtslib"

    # There is a problem with the git repository where the commit for
    # version 1.28.0 pulls changes to a file that blocks checking out the
    # commit. Use the branch instead.
    # error: Your local changes to the following files would be overwritten by
    # checkout:
    #             src/htslib-1.15.1/htscodecs/tests/names/tok3/nv.names.1
    #             Please, commit your changes or stash them before you can switch
    #             branches.
    #             Aborting
    # version("1.28.0", commit='214fde2218bdbca89f1e12a30d2e081e76915aef')
    version("2.0.0", commit="1757333eb88625158505e5fa47840081110cf8a4")
    version("1.28.0", branch="RELEASE_3_15")
    version("1.26.0", commit="f5b20e97b283942877529f750b28398782552655")
    version("1.22.0", commit="899b79faa54d42c7c9b9a2bc49972109637d367f")
    version("1.18.1", commit="751a2ebaed43b7991204b27bd6c7870645001d82")
    version("1.16.3", commit="3ed0b5db2ee3cf0df1c6096fde8855c8485eebd4")
    version("1.14.1", commit="4be260720f845a34d0ac838278fce1363f645230")
    version("1.12.1", commit="e3487b1355995d09b28fde5d0a7504a3e79a7203")
    version("1.10.0", commit="53dcf7dfe35d735283956c77c011a97ca3f4eb26")
    version("1.8.0", commit="3b5493473bed42958614091c58c739932ffcfa79")

    depends_on("r-zlibbioc", type=("build", "run"))
    depends_on("bzip2", type=("build", "link", "run"))
    depends_on("xz", type=("build", "link", "run"))
    depends_on("curl", type=("build", "link", "run"))
    depends_on("gmake", type="build")

    # Some versions of this package will leave the temporary installation
    # directory in the htslib shared object. R will fix this if patchelf is
    # available
    depends_on("patchelf", type="build", when="@1.12:1.14")

    patch("use_spack_Makeconf.patch", when="@1.12:1.28.0")
    patch("find_deps-1.12.patch", when="@1.12:1.14")
    patch("find_deps-1.16.patch", when="@1.16:1.28.0")

    @when("@1.12:")
    def setup_build_environment(self, env):
        env.set("BZIP2_INCLUDE", self.spec["bzip2"].headers.include_flags)
        env.set("XZ_INCLUDE", self.spec["xz"].headers.include_flags)
        env.set("BZIP2_LIB", self.spec["bzip2"].libs.search_flags)
        env.set("XZ_LIB", self.spec["xz"].libs.search_flags)