sci-biology/kallisto: Bump to 0.46.2

Bug: https://bugs.gentoo.org/696504
Bug: https://bugs.gentoo.org/708658
Bug: https://bugs.gentoo.org/788427
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: David Seifert <soap@gentoo.org>

6 files changed, 325 insertions, 0 deletions

diff --git a/sci-biology/kallisto/Manifest b/sci-biology/kallisto/Manifest
index 720b078417b1..85d85197b1cc 100644
--- a/sci-biology/kallisto/Manifest
+++ b/sci-biology/kallisto/Manifest
@@ -1 +1,2 @@
 DIST kallisto-0.43.1.tar.gz 1067076 BLAKE2B 15a2fc65f0c9db431d9be6b2c8434b582ff7bf95fb659a9838d287feb3486744bca6201563d0f318be47c0f8532b805148a2eabfda633075d6b55bad1c3a406a SHA512 c7725a2d649cf96fcd24a20d542b409777cfd9fe97c09f0f459a5ec2981e0a4f5f0ea03d76d3ec3edf0e498c799fc7d074d442d5e35ddb4043d1f7634619dda8
+DIST kallisto-0.46.2.tar.gz 2693869 BLAKE2B 73d725e74133d64b9f7910f69a5fff85eac05b93ad6891807a6fd4e16a1fa16a55306058db3fcb4e0fbfeb0719d3a9d3c8da7d2b76b64dde5a2fea51b0254b99 SHA512 6aca29afa0abe1c6896d27745fd2436c9b9aaf298d70276baf877dbf0aaaba94df54b9a42829c8f8f7c02e7262ecd1837b8a021625c3066a10c0cc0551179093
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
new file mode 100644
index 000000000000..7566966c1c68
--- /dev/null
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
@@ -0,0 +1,38 @@
+--- a/unit_tests/main.cpp
++++ b/unit_tests/main.cpp
+@@ -1,2 +1,2 @@
+ #define CATCH_CONFIG_MAIN
+-#include "catch.hpp"
++#include <catch2/catch.hpp>
+--- a/unit_tests/test_index.cpp
++++ b/unit_tests/test_index.cpp
+@@ -1,4 +1,4 @@
+-#include "catch.hpp"
++#include <catch2/catch.hpp>
+ 
+ #include "common.h"
+ #include "KmerIndex.h"
+--- a/unit_tests/test_kmerhashtable.cpp
++++ b/unit_tests/test_kmerhashtable.cpp
+@@ -1,4 +1,4 @@
+-#include "catch.hpp"
++#include <catch2/catch.hpp>
+ 
+ #include <random>
+ #include <string>
+--- a/unit_tests/test_multinomial.cpp
++++ b/unit_tests/test_multinomial.cpp
+@@ -1,4 +1,4 @@
+-#include "catch.hpp"
++#include <catch2/catch.hpp>
+ 
+ #include <iostream>
+ #include <vector>
+--- a/unit_tests/test_weights.cpp
++++ b/unit_tests/test_weights.cpp
+@@ -1,4 +1,4 @@
+-#include "catch.hpp"
++#include <catch2/catch.hpp>
+ 
+ #include <vector>
+ 
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch
new file mode 100644
index 000000000000..ba6114a9164f
--- /dev/null
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch
@@ -0,0 +1,149 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -11,9 +11,6 @@
+     add_compile_definitions("USE_HDF5=ON")
+ endif(USE_HDF5)
+ 
+-set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext)
+-set(CMAKE_CXX_FLAGS_PROFILE "-g")
+-
+ # Set Release type for builds where CMAKE_BUILD_TYPE is unset
+ # This is usually a good default as this implictly enables
+ #
+@@ -33,44 +30,12 @@
+     set(CMAKE_CXX_EXTENSIONS OFF)
+ endif()
+ 
+-#add_compile_options(-Wall -Wno-unused-function)
+-
+-if(LINK MATCHES static)
+-    message("static build")
+-ELSE(LINK MATCHES shared)
+-    message("shared build")
+-ENDIF(LINK MATCHES static)
+-
+-
+-include(ExternalProject)
+-ExternalProject_Add(htslib
+-    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
+-    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
+-    BUILD_IN_SOURCE 1
+-    CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure 
+-        --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
+-    BUILD_COMMAND make lib-static
+-    INSTALL_COMMAND ""
+-)
+-
+-include_directories(${htslib_PREFIX}/src/htslib)
+-
+-
+-
+-# add_compile_options(-Wdeprecated-register)
+-
+ add_subdirectory(src)
+-include_directories(${EXT_PROJECTS_DIR})
+ 
+ option(BUILD_TESTING "Build unit tests." OFF)
+ include(CTest)
+ 
+ if (BUILD_TESTING)
+-    add_subdirectory(${EXT_PROJECTS_DIR}/catch)
+-
+-    # Includes Catch in the project:
+-    include_directories(${CATCH_INCLUDE_DIR} ${COMMON_INCLUDES})
+-
+     add_subdirectory(unit_tests)
+ endif(BUILD_TESTING)
+ 
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -3,30 +3,17 @@
+ 
+ list(REMOVE_ITEM sources main.cpp)
+ 
+-include_directories(../ext/htslib)
+-
+ add_library(kallisto_core ${sources} ${headers})
+ target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+ 
+ add_executable(kallisto main.cpp)
+ 
+-find_package( Threads REQUIRED )
+-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
+-
+-if(LINK MATCHES static)
+-    set(BUILD_SHARED_LIBS OFF)
+-    set(HDF5_USE_STATIC_LIBRARIES 1)
+-
+-    if (UNIX AND NOT APPLE)
+-        #set(CMAKE_EXE_LINKER_FLAGS  "-static -static-libgcc -static-libstdc++")
+-        set(CMAKE_EXE_LINKER_FLAGS  "-static -static-libstdc++")
+-        SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+-        set(CMAKE_EXE_LINKER_FLAGS  "-static -static-libgcc -static-libstdc++")
+-    endif(UNIX AND NOT APPLE)
+-
+-    SET_TARGET_PROPERTIES(kallisto kallisto_core PROPERTIES LINK_SEARCH_END_STATIC 1)
+-endif(LINK MATCHES static)
++find_package( PkgConfig REQUIRED )
++pkg_check_modules( HTSLIB REQUIRED htslib )
+ 
++find_package( Threads REQUIRED )
++target_include_directories(kallisto PRIVATE ${HTSLIB_CFLAGS})
++target_link_libraries(kallisto PRIVATE kallisto_core Threads::Threads ${HTSLIB_LDFLAGS})
+ 
+ if(USE_HDF5)
+     find_package( HDF5 REQUIRED )
+@@ -36,7 +23,7 @@
+ 
+ if ( ZLIB_FOUND )
+     include_directories( ${ZLIB_INCLUDE_DIRS} )
+-    target_link_libraries(kallisto kallisto_core ${ZLIB_LIBRARIES})
++    target_link_libraries(kallisto PRIVATE kallisto_core ${ZLIB_LIBRARIES})
+ else()
+     message(FATAL_ERROR "zlib not found. Required for to output files" )
+ endif( ZLIB_FOUND )
+@@ -44,22 +31,17 @@
+ if(USE_HDF5)
+     if(HDF5_FOUND)
+         include_directories( ${HDF5_INCLUDE_DIRS} )
+-        target_link_libraries( kallisto_core ${HDF5_LIBRARIES} )
+-        target_link_libraries( kallisto ${HDF5_LIBRARIES} )
++        target_link_libraries( kallisto_core PRIVATE ${HDF5_LIBRARIES} )
++        target_link_libraries( kallisto PRIVATE ${HDF5_LIBRARIES} )
+     else()
+         message(FATAL_ERROR "HDF5 not found. Required to output files")
+     endif()
+ endif(USE_HDF5)
+ 
+-if(LINK MATCHES static)
+-    if (UNIX AND NOT APPLE)
+-        target_link_libraries(kallisto librt.a)
+-    endif()
+-else()
+-    if (UNIX AND NOT APPLE)
+-        target_link_libraries(kallisto rt)
+-    endif()
+-endif(LINK MATCHES static)
+-
++target_compile_options( kallisto_core PRIVATE ${HTSLIB_CFLAGS} )
++target_link_libraries( kallisto_core PRIVATE ${HTSLIB_LDFLAGS} )
+ 
+-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
+\ No newline at end of file
++install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
++if ( BUILD_SHARED_LIBS )
++    install(TARGETS kallisto_core DESTINATION "${CMAKE_INSTALL_LIBDIR}")
++endif()
+--- a/unit_tests/CMakeLists.txt
++++ b/unit_tests/CMakeLists.txt
+@@ -8,6 +8,10 @@
+ add_executable(tests ${sources})
+ add_test(unittest tests)
+ 
++find_package( Catch2 REQUIRED )
++include_directories( ${Catch2_INCLUDE_DIRS} )
++target_link_libraries( tests ${Catch2_LIBRARIES} )
++
+ find_package( ZLIB REQUIRED )
+ if ( ZLIB_FOUND )
+     include_directories( ${ZLIB_INCLUDE_DIRS} )
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch b/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch
new file mode 100644
index 000000000000..19594f067776
--- /dev/null
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch
@@ -0,0 +1,21 @@
+From 1d63e9d731bada64f6038818e27f06da63007d73 Mon Sep 17 00:00:00 2001
+From: Nilesh Patra <npatra974@gmail.com>
+Date: Thu, 4 Mar 2021 23:38:30 +0530
+Subject: [PATCH] Fix GCC-11 Build Failure: include limits lib
+
+---
+ src/MinCollector.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/MinCollector.h b/src/MinCollector.h
+index a905f1f..c4460fb 100644
+--- a/src/MinCollector.h
++++ b/src/MinCollector.h
+@@ -7,6 +7,7 @@
+ #include <sstream>
+ #include <vector>
+ #include <unordered_map>
++#include <limits>
+ 
+ #include "KmerIndex.h"
+ #include "weights.h"
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch b/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch
new file mode 100644
index 000000000000..0e926136261c
--- /dev/null
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch
@@ -0,0 +1,52 @@
+--- a/src/KmerIndex.cpp
++++ b/src/KmerIndex.cpp
+@@ -4,7 +4,7 @@
+ #include <ctype.h>
+ #include <zlib.h>
+ #include <unordered_set>
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ 
+ #ifndef KSEQ_INIT_READY
+ #define KSEQ_INIT_READY
+--- a/src/ProcessReads.cpp
++++ b/src/ProcessReads.cpp
+@@ -1,6 +1,6 @@
+ /*
+ #include <zlib.h>
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ #include <string>
+ #include <vector>
+ #include <unordered_map>
+@@ -20,7 +20,7 @@
+ #include <iomanip>
+ 
+ #include "ProcessReads.h"
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ #include "PseudoBam.h"
+ #include "Fusion.hpp"
+ #include "BUSData.h"
+--- a/src/ProcessReads.h
++++ b/src/ProcessReads.h
+@@ -2,7 +2,7 @@
+ #define KALLISTO_PROCESSREADS_H
+ 
+ #include <zlib.h>
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ #include <string>
+ #include <vector>
+ #include <unordered_map>
+--- a/unit_tests/test_kmerhashtable.cpp
++++ b/unit_tests/test_kmerhashtable.cpp
+@@ -13,7 +13,7 @@
+ #include "KmerHashTable.h"
+ 
+ #include <zlib.h>
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ 
+ #ifndef KSEQ_INIT_READY
+ #define KSEQ_INIT_READY
diff --git a/sci-biology/kallisto/kallisto-0.46.2.ebuild b/sci-biology/kallisto/kallisto-0.46.2.ebuild
new file mode 100644
index 000000000000..293cf9f76ed0
--- /dev/null
+++ b/sci-biology/kallisto/kallisto-0.46.2.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="Near-optimal RNA-Seq quantification"
+HOMEPAGE="http://pachterlab.github.io/kallisto/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
+else
+	SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="hdf5 test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	sci-libs/htslib:=
+	sys-libs/zlib:=
+	hdf5? ( sci-libs/hdf5:= )"
+DEPEND="
+	${RDEPEND}
+	test? (
+		dev-cpp/catch:0
+		sci-libs/hdf5
+	)"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-cmake.patch
+	"${FILESDIR}"/${P}-htslib.patch
+	"${FILESDIR}"/${P}-catch2.patch
+	"${FILESDIR}"/${P}-gcc11.patch
+)
+
+src_prepare() {
+	cmake_src_prepare
+	# bundled catch2
+	rm -r ext || die
+	# bundled htslib structs
+	rm src/kseq.h || die
+
+	# the test suite is cheesy and relies on a
+	# specific builddir nesting structure.
+	sed -e "s|../test/input/short_reads.fastq|$(readlink -f unit_tests/input/short_reads.fastq)|g" \
+		-i unit_tests/test_kmerhashtable.cpp || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_HDF5=$(usex hdf5)
+		-DBUILD_TESTING=$(usex test)
+		# convenience library only
+		-DBUILD_SHARED_LIBS=OFF
+	)
+	cmake_src_configure
+}