[gentoo-commits] proj/sci:master commit in: sci-biology/tigmint/

["Alexander Puck Neuwirth" <alexander@neuwirth-informatik.de>]

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>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</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
-}