commit: ab02fb8c66c9c248f740e9b6997967153fdce4a1 Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Wed Jan 14 21:06:21 2026 +0000 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> CommitDate: Wed Jan 14 22:52:05 2026 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ab02fb8c
sci-biology/mothur: add 1.48.2 and fix build w/ boost-1.89 Closes: https://bugs.gentoo.org/965517 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> sci-biology/mothur/Manifest | 1 + .../mothur/files/mothur-1.48.2-boost-1.89.patch | 11 +++++ sci-biology/mothur/mothur-1.48.2.ebuild | 55 ++++++++++++++++++++++ 3 files changed, 67 insertions(+) diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest index ada6350ceeef..012b9574a8c3 100644 --- a/sci-biology/mothur/Manifest +++ b/sci-biology/mothur/Manifest @@ -1,2 +1,3 @@ DIST mothur-1.27.0.zip 7095054 BLAKE2B 96a6410d36f64ff50591955aa22bfddf6217c7568022c8c7f70ab70c65d57af2217477de56b6f9ceaf11237cdc5380bd354cf6564002357546539585d0f58221 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 DIST mothur-1.48.0.tar.gz 1652711 BLAKE2B 39e1d2a32a63d441267b4e0e739505bdcb3ab392c169c96d60e816dbd9fab6b92745e8a9eaae31062711f2de0130dae540bba34c6bd97e76a921711f58c11f65 SHA512 a43ef6a223238d40e51c15043360ba9cae86347affea2f1a4e365635fb0949981ad32001b88d4061a033b2a002e944df16923a0622a40bf061791f06143467e1 +DIST mothur-1.48.2.tar.gz 24702253 BLAKE2B 4342640e70f08763c4bc1605441a9526ef967bd5832d103db3095c470ea82c2c554dd03775e8ffdf02a983ee4dfdb43ba008dcf7ff19b99321a0204843f98710 SHA512 0c3496d08131d15db3933165eba832a135ca3bce8010e7a2b4a84802c91d6f5efa54711498148d7cc190420b75a94babf20d6c435a5e07c730924f1f3f966586 diff --git a/sci-biology/mothur/files/mothur-1.48.2-boost-1.89.patch b/sci-biology/mothur/files/mothur-1.48.2-boost-1.89.patch new file mode 100644 index 000000000000..26417a05992b --- /dev/null +++ b/sci-biology/mothur/files/mothur-1.48.2-boost-1.89.patch @@ -0,0 +1,11 @@ +--- a/Makefile ++++ b/Makefile +@@ -78,7 +78,7 @@ + + LDFLAGS += -L ${BOOST_LIBRARY_DIR} + +- LIBS += -lboost_iostreams -lboost_system -lboost_filesystem -lz ++ LIBS += -lboost_iostreams -lboost_filesystem -lz + CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR} + endif + diff --git a/sci-biology/mothur/mothur-1.48.2.ebuild b/sci-biology/mothur/mothur-1.48.2.ebuild new file mode 100644 index 000000000000..e9787ef8c9e2 --- /dev/null +++ b/sci-biology/mothur/mothur-1.48.2.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2026 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="A suite of algorithms for ecological bioinformatics" +HOMEPAGE="https://mothur.org/"; +SRC_URI="https://github.com/mothur/mothur/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="amd64 ~x86" +IUSE="boost gsl hdf5 mpi +readline" + +RDEPEND=" + sci-biology/uchime + boost? ( dev-libs/boost:=[zlib] ) + gsl? ( sci-libs/gsl:= ) + hdf5? ( sci-libs/hdf5:=[cxx] ) + mpi? ( virtual/mpi ) +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-1.48.0-build.patch + "${FILESDIR}"/${P}-boost-1.89.patch # bug 965517 +) + +src_configure() { + use mpi && export CXX=mpicxx || tc-export CXX + use amd64 && append-cppflags -DBIT_VERSION +} + +src_compile() { + # bug #862273 + append-flags -fno-strict-aliasing + filter-lto + + # USEBOOST - link with boost libraries. Must install boost. Allows the make.contigs command to read .gz files. + # USEHDF5 - link with HDF5cpp libraries. Must install HDF5. Allows the biom.info command to read Biom format 2.0. + # USEGSL - link with GNU Scientific libraries. Must install GSL. Allows the estimiator.single command to find diversity estimates. + emake \ + USEBOOST=$(usex boost) \ + USEHDF5=$(usex hdf5) \ + USEGSL=$(usex gsl) \ + USEMPI=$(usex mpi) \ + USEREADLINE=$(usex readline) \ + OPTIMIZE=no +} + +src_install() { + dobin mothur +}
