commit: 82b8e8223692b1e63dfc2f865252db711c08ec7d Author: Alexander Puck Neuwirth <apn-pucky <AT> gentoo <DOT> org> AuthorDate: Wed Nov 19 08:28:16 2025 +0000 Commit: Alexander Puck Neuwirth <apn-pucky <AT> gentoo <DOT> org> CommitDate: Mon Feb 2 11:17:32 2026 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=82b8e822
sci-biology/sga: treeclean Signed-off-by: Alexander Puck Neuwirth <apn-pucky <AT> gentoo.org> Part-of: https://github.com/gentoo/sci/pull/1386 sci-biology/sga/metadata.xml | 18 ------------- sci-biology/sga/sga-9999.ebuild | 58 ----------------------------------------- 2 files changed, 76 deletions(-) diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml deleted file mode 100644 index 51beb3925..000000000 --- a/sci-biology/sga/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="jemalloc">Use <pkg>dev-libs/jemalloc</pkg></flag> - </use> - <upstream> - <remote-id type="github">jts/sga</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild deleted file mode 100644 index ac1e208ac..000000000 --- a/sci-biology/sga/sga-9999.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2025 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit git-r3 autotools - -DESCRIPTION="String Graph OLC Assembler for short reads (overlap-layout-consensus)" -HOMEPAGE="https://github.com/jts/sga"; -EGIT_REPO_URI="https://github.com/jts/sga"; - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="jemalloc python" - -DEPEND=" - dev-cpp/sparsehash - sci-biology/bamtools - virtual/zlib:= - jemalloc? ( dev-libs/jemalloc ) -" -RDEPEND="${DEPEND} - sci-biology/abyss - python? ( sci-biology/pysam - sci-biology/ruffus )" - -S="${WORKDIR}/${P}/src" - -src_prepare() { - default - eautoreconf -} - -# http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/sga.htm -src_configure(){ - econf --with-bamtools="${EPREFIX}"/usr --with-sparsehash="${EPREFIX}"/usr -} - -src_compile(){ - # https://github.com/AlgoLab/FastStringGraph/issues/1#issuecomment-345999596 - # https://github.com/jts/sga/issues/106 - # https://github.com/jts/sga/pull/110 - # https://github.com/jts/sga/issues/108 - # - # other unreviewed patches: - # https://github.com/jts/sga/issues/96 - default -} - -src_install(){ - dodoc README - emake install DESTDIR="${D}" - insinto /usr/share/sga/examples - doins -r examples/* - cd .. || - dodoc README.md -}
