commit: cab50758802747210942702dceb6cf7ec8732e3e Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Tue Jan 25 13:06:18 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Tue Jan 25 13:06:18 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cab50758
sci-biology/pufferfish: drop dead package Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> .../pufferfish/files/pufferfish-do-not-fetch.patch | 31 ------------------- sci-biology/pufferfish/metadata.xml | 11 ------- sci-biology/pufferfish/pufferfish-1.4.0.ebuild | 35 ---------------------- 3 files changed, 77 deletions(-) diff --git a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch b/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch deleted file mode 100644 index c86fe847f..000000000 --- a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch +++ /dev/null @@ -1,31 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 7f1516a..90f7cdd 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -282,12 +282,9 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}") - - - ExternalProject_Add(libseqlib --GIT_REPOSITORY https://github.com/COMBINE-lab/SeqLib.git --GIT_TAG master - UPDATE_COMMAND "" - UPDATE_DISCONNECTED 1 - BUILD_IN_SOURCE TRUE --DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - CONFIGURE_COMMAND ./configure -@@ -300,13 +297,10 @@ INSTALL_COMMAND mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include & - ) - - ExternalProject_Add(libSetCover -- GIT_REPOSITORY https://github.com/martin-steinegger/setcover.git -- GIT_TAG master - UPDATE_COMMAND "" - CONFIGURE_COMMAND "" - UPDATE_DISCONNECTED 1 - BUILD_IN_SOURCE TRUE -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - BUILD_COMMAND make -j8 diff --git a/sci-biology/pufferfish/metadata.xml b/sci-biology/pufferfish/metadata.xml deleted file mode 100644 index 7b582e896..000000000 --- a/sci-biology/pufferfish/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">COMBINE-lab/pufferfish</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild b/sci-biology/pufferfish/pufferfish-1.4.0.ebuild deleted file mode 100644 index 588970e06..000000000 --- a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -SC_COMMIT="b1de7919c0a4d0e65c5cd0b6d78963516e44be25" -SL_COMMIT="340dad36dff67ca96815bd412fe65587d4d64479" -HL_COMMIT="be22a2a1082f6e570718439b9ace2db17a609eae" - -DESCRIPTION="Index for the colored, compacted, de Bruijn graph" -HOMEPAGE="https://github.com/COMBINE-lab/pufferfish" -SRC_URI="https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/martin-steinegger/setcover/archive/${SC_COMMIT}.tar.gz -> setcover-${P}.tar.gz - https://github.com/COMBINE-lab/SeqLib/archive/${SL_COMMIT}.tar.gz -> seqlib-${P}.tar.gz - https://github.com/samtools/htslib/archive/${HL_COMMIT}.tar.gz -> htslib-${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" - -DEPEND="dev-cpp/tbb" - -S="${WORKDIR}/${PN}-salmon-v${PV}" - -PATCHES=( "${FILESDIR}/${PN}-do-not-fetch.patch" ) - -src_prepare() { - mkdir -p external/{setcover,seqlib} - mv "../setcover-${SC_COMMIT}"/* external/setcover || die - mv "../SeqLib-${SL_COMMIT}"/* external/seqlib || die - mv "../htslib-${HL_COMMIT}"/* external/seqlib/htslib || die - cmake_src_prepare -}