From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 8401C1584AD for ; Tue, 06 May 2025 13:53:34 +0000 (UTC) Received: from lists.gentoo.org (bobolink.gentoo.org [140.211.166.189]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) (Authenticated sender: relay-lists.gentoo.org@gentoo.org) by smtp.gentoo.org (Postfix) with ESMTPSA id 70CAE3431B6 for ; Tue, 06 May 2025 13:53:34 +0000 (UTC) Received: from bobolink.gentoo.org (localhost [127.0.0.1]) by bobolink.gentoo.org (Postfix) with ESMTP id 6C32D1104BD; Tue, 06 May 2025 13:53:04 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by bobolink.gentoo.org (Postfix) with ESMTPS id 628091104B8 for ; Tue, 06 May 2025 13:53:04 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 175A1343112 for ; Tue, 06 May 2025 13:53:04 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 75F142837 for ; Tue, 06 May 2025 13:53:00 +0000 (UTC) From: "Alexander Puck Neuwirth" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Alexander Puck Neuwirth" Message-ID: <1746539533.9fcd962b2013fb8bf5ee1ddb8754815dbb6c47f8.alexander@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/tigmint/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/tigmint/metadata.xml sci-biology/tigmint/tigmint-1.2.4-r1.ebuild X-VCS-Directories: sci-biology/tigmint/ X-VCS-Committer: alexander X-VCS-Committer-Name: Alexander Puck Neuwirth X-VCS-Revision: 9fcd962b2013fb8bf5ee1ddb8754815dbb6c47f8 X-VCS-Branch: master Date: Tue, 06 May 2025 13:53:00 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 8d56070a-2261-4e5b-ab74-24f57ec9b054 X-Archives-Hash: 0082fa3f3a4e0f783eccf5b2b2f1c45e commit: 9fcd962b2013fb8bf5ee1ddb8754815dbb6c47f8 Author: Alexander Puck Neuwirth neuwirth-informatik de> AuthorDate: Tue May 6 00:10:45 2025 +0000 Commit: Alexander Puck Neuwirth neuwirth-informatik 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 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 @@ - - - - - mmokrejs@fold.natur.cuni.cz - Martin Mokrejs - - - sci-biology@gentoo.org - Gentoo Biology Project - - 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 -}