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
-}
