diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/mothur/package.py | 83 |
1 files changed, 63 insertions, 20 deletions
diff --git a/var/spack/repos/builtin/packages/mothur/package.py b/var/spack/repos/builtin/packages/mothur/package.py index 2d546c7958..3e88378a5d 100644 --- a/var/spack/repos/builtin/packages/mothur/package.py +++ b/var/spack/repos/builtin/packages/mothur/package.py @@ -4,7 +4,6 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack.package import * -from spack.pkg.builtin.boost import Boost class Mothur(MakefilePackage): @@ -15,37 +14,81 @@ class Mothur(MakefilePackage): homepage = "https://github.com/mothur/mothur" url = "https://github.com/mothur/mothur/archive/v1.39.5.tar.gz" + version("1.48.0", sha256="9494406abd8d14b821782ab9db811f045ded9424f28f01234ee6764d4e78941d") version("1.46.1", sha256="29b500b3c92d726cde34922f697f2e47f0b7127d76d9a6fb167cc2b8ba3d00fd") version("1.43.0", sha256="12ccd95a85bec3bb1564b8feabd244ea85413973740754803d01fc71ecb0a2c1") version("1.42.1", sha256="6b61591dda289ac2d8361f9c1547ffbeeba3b9fbdff877dd286bad850bbd5539") version("1.40.5", sha256="a0fbdfa68b966d7adc4560e3787506a0dad8b47b4b996c2663cd6c0b416d101a") version("1.39.5", sha256="9f1cd691e9631a2ab7647b19eb59cd21ea643f29b22cde73d7f343372dfee342") + maintainers = ["snehring"] - variant("vsearch", default=False, description="Use vsearch") + variant( + "boost", + default=True, + description="Build with boost support (allow make.contigs to read gz files).", + ) + variant("hdf5", default=False, description="Build with hdf5 support", when="@1.41.0:") + variant( + "gsl", default=False, description="Build with the gnu scientific libaries", when="@1.43.0:" + ) - # TODO: replace this with an explicit list of components of Boost, - # for instance depends_on('boost +filesystem') - # See https://github.com/spack/spack/pull/22303 for reference - depends_on(Boost.with_default_variants) + depends_on("boost+iostreams+filesystem+system", when="+boost") + depends_on("gsl", when="+gsl") + depends_on("hdf5+cxx", when="+hdf5") depends_on("readline") - depends_on("vsearch@2.13.3", when="+vsearch", type="run") + depends_on("vsearch@2.13.5:", type="run") + depends_on("usearch", type="run") + depends_on("zlib", when="+boost") def edit(self, spec, prefix): - makefile = FileFilter("Makefile") - makefile.filter( - 'BOOST_LIBRARY_DIR="\\"Enter_your_boost_library_path' '_here\\""', - "BOOST_LIBRARY_DIR=%s" % self.spec["boost"].prefix.lib, - ) - makefile.filter( - 'BOOST_INCLUDE_DIR="\\"Enter_your_boost_include_path' '_here\\""', - "BOOST_INCLUDE_DIR=%s" % self.spec["boost"].prefix.include, - ) - makefile.filter( - 'MOTHUR_FILES="\\"Enter_your_default_path_' 'here\\""', "MOTHUR_FILES=%s" % prefix - ) + filter_file(r"^.*DMOTHUR_TOOLS.*$", "", "Makefile") + filter_file(r"^.*DMOTHUR_FILES.*$", "", "Makefile") + filter_file(r"(\$\(skipUchime\))", r"\1, source/", "Makefile") + if spec.satisfies("@1.40.5"): + filter_file( + r"^(#define writer_h)", "\\1 \n#include<memory>", join_path("source", "writer.h") + ) + # this includes the public domain uchime, which needs work to + # compile on newer compilers we'll use what's in usearch + filter_file(" uchime", "", "Makefile") + if spec.satisfies("+boost"): + filter_file(r"USEBOOST \?=.*$", "USEBOOST = yes", "Makefile") + filter_file( + r"^BOOST_LIBRARY_DIR .*$", + "BOOST_LIBRARY_DIR=%s" % self.spec["boost"].prefix.lib, + "Makefile", + ) + filter_file( + r"BOOST_INCLUDE_DIR .*$", + "BOOST_INCLUDE_DIR=%s" % self.spec["boost"].prefix.include, + "Makefile", + ) + if spec.satisfies("+hdf5"): + filter_file(r"USEHDF5 \?=.*$", "USEHDF5 = yes", "Makefile") + filter_file( + r"^HDF5_LIBRARY_DIR \?=.*$", + "HDF5_LIBRARY_DIR = " + spec["hdf5"].prefix.lib, + "Makefile", + ) + filter_file( + r"^HDF5_INCLUDE_DIR \?=.*$", + "HDF5_INCLUDE_DIR = " + spec["hdf5"].prefix.include, + "Makefile", + ) + if spec.satisfies("+gsl"): + filter_file(r"^USEGSL \?=.*$", "USEGSL = yes", "Makefile") + filter_file( + r"GSL_LIBRARY_DIR \?=.*$", + "GSL_LIBRARY_DIR = " + spec["gsl"].prefix.lib, + "Makefile", + ) + filter_file( + r"GSL_INCLUDE_DIR \?=.*$", + "GSL_INCLUDE_DIR = " + spec["gsl"].prefix.include, + "Makefile", + ) def install(self, spec, prefix): mkdirp(prefix.bin) install("mothur", prefix.bin) - install("uchime", prefix.bin) install_tree("source", prefix.include) |