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From: "Andrew Ammerlaan" <andrewammerlaan@gentoo.org>
To: gentoo-commits@lists.gentoo.org
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Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" <andrewammerlaan@gentoo.org>
Message-ID: <1643116128.eb17f7ce1acf07564afb6b28f74777c3b2de1776.andrewammerlaan@gentoo>
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/sailfish/, sci-biology/sailfish/files/
X-VCS-Repository: proj/sci
X-VCS-Files: sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch sci-biology/sailfish/files/sailfish-allow-newer-boost.patch sci-biology/sailfish/files/sailfish-no-curl.patch sci-biology/sailfish/metadata.xml sci-biology/sailfish/sailfish-0.10.0.ebuild sci-biology/sailfish/sailfish-9999.ebuild
X-VCS-Directories: sci-biology/sailfish/ sci-biology/sailfish/files/
X-VCS-Committer: andrewammerlaan
X-VCS-Committer-Name: Andrew Ammerlaan
X-VCS-Revision: eb17f7ce1acf07564afb6b28f74777c3b2de1776
X-VCS-Branch: master
Date: Tue, 25 Jan 2022 13:09:14 +0000 (UTC)
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commit: eb17f7ce1acf07564afb6b28f74777c3b2de1776
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 13:08:48 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 13:08:48 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=eb17f7ce
sci-biology/sailfish: drop dead package
last update 2016
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../files/sailfish-0.9.2-no-boost-static.patch | 20 ----
.../files/sailfish-allow-newer-boost.patch | 13 ---
sci-biology/sailfish/files/sailfish-no-curl.patch | 121 ---------------------
sci-biology/sailfish/metadata.xml | 15 ---
sci-biology/sailfish/sailfish-0.10.0.ebuild | 83 --------------
sci-biology/sailfish/sailfish-9999.ebuild | 62 -----------
6 files changed, 314 deletions(-)
diff --git a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch b/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch
deleted file mode 100644
index 7ac3d0882..000000000
--- a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Do not force static and multithreaded boost libs, use what is available
-
-Patch by Michael Schubert
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH )
- set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
-
--##
--# We want static, multithreaded boost libraries
--##
--set (Boost_USE_STATIC_LIBS ON)
--set (Boost_USE_MULTITHREADED ON)
--#set (Boost_USE_STATIC_RUNTIME OFF)
--
- find_package (ZLIB)
- if (NOT ZLIB_FOUND)
- message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
diff --git a/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch b/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch
deleted file mode 100644
index 985f83f4a..000000000
--- a/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ee4b34c..3c58830 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -176,7 +176,7 @@ endif()
- ##
- # Set the latest version and look for what we need
- ##
--set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59")
-+set(Boost_ADDITIONAL_VERSIONS "1.72.0" "1.74.0" "1.75.0")
- find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
- message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
diff --git a/sci-biology/sailfish/files/sailfish-no-curl.patch b/sci-biology/sailfish/files/sailfish-no-curl.patch
deleted file mode 100644
index 2ec97808e..000000000
--- a/sci-biology/sailfish/files/sailfish-no-curl.patch
+++ /dev/null
@@ -1,121 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 1be4117..ee4b34c 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -230,9 +230,6 @@ elseif(FETCH_BOOST)
- message("Build system will fetch and build Boost")
- message("==================================================================")
- ExternalProject_Add(libboost
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.59.0/boost_1_59_0.tar.gz -o boost_1_59_0.tar.gz &&
-- tar xzf boost_1_59_0.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_59_0
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
-@@ -292,10 +289,6 @@ if (NOT JELLYFISH_FOUND)
- message("Build system will fetch and build Jellyfish")
- message("==================================================================")
- ExternalProject_Add(libjellyfish
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz -o jellyfish-2.2.5.tgz &&
-- rm -fr jellyfish-2.2.5 &&
-- tar -xzvf jellyfish-2.2.5.tgz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-@@ -335,11 +328,7 @@ if ("${TBB_COMPILER}" STREQUAL "gcc")
- endif()
-
- ExternalProject_Add(libtbb
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- URL http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz
-- DOWNLOAD_COMMAND curl -k -L http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz &&
-- tar -xzvf tbb_20140724oss_src.tgz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
-+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- PATCH_COMMAND "${TBB_PATCH_STEP}"
- CONFIGURE_COMMAND ""
-@@ -407,11 +396,6 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
- message("Build system will compile libgff")
- message("==================================================================")
- ExternalProject_Add(libgff
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
-- tar -xzvf libgff.tgz &&
-- rm -fr libgff &&
-- mv libgff-1.0 libgff
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -445,9 +429,6 @@ if (NOT HAVE_FAST_MALLOC)
- message("Build system will fetch and use JEMalloc")
- message("==================================================================")
- ExternalProject_Add(libjemalloc
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
-- tar -xzf jemalloc-3.6.0.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
- BUILD_IN_SOURCE TRUE
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -465,9 +446,6 @@ endif ()
- message("Build system will fetch and build SparseHash")
- message("==================================================================")
- ExternalProject_Add(libsparsehash
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
-- tar -xzf sparsehash-2.0.2.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
- BUILD_IN_SOURCE TRUE
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -487,7 +465,6 @@ ExternalProject_Add(libsparsehash
- #
- ####
- if(NOT FETCHED_RAPMAP)
-- exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchRapMap.sh)
- set(FETCHED_RAPMAP TRUE CACHE BOOL "Has RapMap been fetched?" FORCE)
- endif()
-
-diff --git a/scripts/fetchRapMap.sh b/scripts/fetchRapMap.sh
-deleted file mode 100755
-index cab05a1..0000000
---- a/scripts/fetchRapMap.sh
-+++ /dev/null
-@@ -1,37 +0,0 @@
--#!/bin/bash
--
--CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
--EXTERNAL_DIR=${CURR_DIR}/../external
--INSTALL_DIR=${CURR_DIR}/../external/install
--
--if [ -d ${EXTERNAL_DIR}/RapMap ] ; then
-- rm -fr ${EXTERNAL_DIR}/RapMap
--fi
--
--if [ -d ${INSTALL_DIR}/include/rapmap ] ; then
-- rm -fr ${INSTALL_DIR}/include/rapmap
--fi
--
--if [ -d ${INSTALL_DIR}/src/rapmap ] ; then
-- rm -fr ${INSTALL_DIR}/src/rapmap
--fi
--
--mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip -o ${EXTERNAL_DIR}/rapmap.zip
--rm -fr ${EXTERNAL_DIR}/RapMap
--unzip ${EXTERNAL_DIR}/rapmap.zip -d ${EXTERNAL_DIR}
--mv ${EXTERNAL_DIR}/RapMap-quasi-mph ${EXTERNAL_DIR}/RapMap
--
--mkdir -p ${INSTALL_DIR}/include/rapmap
--mkdir -p ${INSTALL_DIR}/src/rapmap
--
--rm ${EXTERNAL_DIR}/RapMap/src/xxhash.c
--rm ${EXTERNAL_DIR}/RapMap/include/xxhash.h
--
--cp -r ${EXTERNAL_DIR}/RapMap/external/libdivsufsort.zip ${EXTERNAL_DIR}
--cp -r ${EXTERNAL_DIR}/RapMap/src/*.c ${INSTALL_DIR}/src/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/src/*.cpp ${INSTALL_DIR}/src/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/tclap ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/*.h ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/*.hpp ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/emphf ${INSTALL_DIR}/include/rapmap
diff --git a/sci-biology/sailfish/metadata.xml b/sci-biology/sailfish/metadata.xml
deleted file mode 100644
index 530333987..000000000
--- a/sci-biology/sailfish/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <maintainer type="person">
- <email>mschu.dev@gmail.com</email>
- <name>Michael Schubert</name>
- </maintainer>
- <upstream>
- <remote-id type="github">kingsfordgroup/sailfish</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
deleted file mode 100644
index 9fa4060ca..000000000
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip
- https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz
- https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz
- https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz
-"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
- dev-libs/boost:0
- dev-libs/jemalloc
- dev-libs/libdivsufsort
- dev-cpp/tbb
- dev-cpp/sparsehash
- sci-biology/jellyfish:2
-"
-RDEPEND="${DEPEND}"
-BDEPEND="app-arch/unzip"
-# a C++-11 compliant compiler is needs, aka >=gcc-4.7
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.9.2-no-boost-static.patch"
- "${FILESDIR}/${PN}-no-curl.patch"
- "${FILESDIR}/${PN}-allow-newer-boost.patch"
-)
-
-src_unpack() {
- default
- mkdir -p "${S}/external"
- cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
- mv "${WORKDIR}/RapMap-quasi-mph" "${S}/external/RapMap" || die
- mv "${WORKDIR}/jellyfish-2.2.5" "${S}/external/jellyfish-2.2.5" || die
- mv "${WORKDIR}/sparsehash-sparsehash-2.0.2" "${S}/external/sparsehash-sparsehash-2.0.2" || die
- mv "${WORKDIR}/libgff-1.0" "${S}/external/libgff" || die
- mkdir -p "${S}/external/install/lib"
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
- mkdir -p "${S}/external/install/src/rapmap"
- cp "${S}/external/RapMap/src/"* "${S}/external/install/src/rapmap" || die
-}
-
-src_prepare() {
- cmake_src_prepare
- # use the dynamic library
- sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \
- -e 's/libdivsufsort64.a/libdivsufsort64.so/g' \
- -e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \
- src/CMakeLists.txt || die
-}
-
-src_configure() {
- JELLYFISH_INCLUDE_DIR="/usr/include/jellyfish2" cmake_src_configure
- # jellyfish2 instead of jellyfish
- find -type f -name "*.hpp" -exec sed -i -e 's/#include \"jellyfish\//#include \"jellyfish2\//g' {} + || die
- find -type f -name "*.hpp" -exec sed -i -e 's/#include <jellyfish\//#include <jellyfish2\//g' {} + || die
-}
-
-src_install() {
- cmake_src_install
- rm -r "${ED}"/usr/tests || die
- rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
deleted file mode 100644
index a76e8ee89..000000000
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake git-r3
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-EGIT_REPO_URI="https://github.com/kingsfordgroup/sailfish.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-PATCHES=( "${FILESDIR}/${PN}-0.9.2-no-boost-static.patch" )
-
-DEPEND="
- dev-libs/boost:0
- dev-libs/jemalloc
- dev-libs/libdivsufsort
- dev-cpp/tbb
- sci-biology/jellyfish:2
-"
-RDEPEND="${DEPEND}"
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-src_unpack() {
- default
- mkdir -p "${S}/external"
- cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
- mkdir -p "${S}/external/install/lib"
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
-}
-
-src_prepare() {
- cmake_src_prepare
- # use the dynamic library
- sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \
- -e 's/libdivsufsort64.a/libdivsufsort64.so/g' \
- -e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \
- src/CMakeLists.txt || die
-
- # jellyfish2 instead of jellyfish
- pushd external/install/include/rapmap
- find -type f -name "*.hpp" -exec sed -i -e 's/jellyfish/jellyfish2/g' {} + || die
- popd
-}
-
-src_install() {
- cmake_src_install
- rm -r "${ED}"/usr/tests || die
- rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}