commit: 9fcd962b2013fb8bf5ee1ddb8754815dbb6c47f8 Author: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de> AuthorDate: Tue May 6 00:10:45 2025 +0000 Commit: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de> CommitDate: Tue May 6 13:52:13 2025 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9fcd962b
sci-biology/tigmint: treeclean Signed-off-by: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik.de> sci-biology/tigmint/metadata.xml | 12 ----- sci-biology/tigmint/tigmint-1.2.4-r1.ebuild | 69 ----------------------------- 2 files changed, 81 deletions(-) diff --git a/sci-biology/tigmint/metadata.xml b/sci-biology/tigmint/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/tigmint/metadata.xml +++ /dev/null @@ -1,12 +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> -</pkgmetadata> diff --git a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild deleted file mode 100644 index c0ba566bd..000000000 --- a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) -DISTUTILS_USE_SETUPTOOLS=no - -inherit distutils-r1 - -DESCRIPTION="Correct misassemblies using linked reads from 10x Genomics Chromium" -HOMEPAGE="https://github.com/bcgsc/tigmint https://bcgsc.github.io/tigmint/"; -SRC_URI="https://github.com/bcgsc/tigmint/releases/download/v${PV}/${P}.tar.gz"; - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RESTRICT="test" -PROPERTIES="test_network" - -RDEPEND=" - dev-python/intervaltree[${PYTHON_USEDEP}] - dev-python/pybedtools[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}] - app-arch/pigz - app-shells/zsh - sci-biology/samtools - sci-biology/minimap2 - sci-biology/seqtk -" - -distutils_enable_tests pytest - -src_prepare(){ - # install the executable into /usr/bin - sed -i Makefile -e 's#prefix=/usr/local#prefix=/usr#' - default -} - -src_configure(){ - python_setup - default -} - -# do not run src_compile step as it runs git, makefile2graph, gsed, tred - -python_install() { - # This is a bit unorthodox, but it allows us to get both a symlink from - # /usr/bin to our script using the correct python implementation - # *and* to import it from the python shell - python_domodule bin/*.py - python_domodule bin/tigmint-arcs-tsv - python_domodule bin/tigmint-cut - - python_doscript bin/*.py - python_doscript bin/tigmint-arcs-tsv - python_doscript bin/tigmint-cut -} - -python_install_all() { - dobin bin/tigmint - dobin bin/tigmint-make -} - -src_test(){ - default - distutils-r1_src_test -}
