gentoo resync : 12.03.2021

2 files changed, 62 insertions, 0 deletions

diff --git a/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
new file mode 100644
index 000000000000..7617d9f9a665
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
@@ -0,0 +1,38 @@
+From 1877d143ad9f42d80692073538e3f32b37e15967 Mon Sep 17 00:00:00 2001
+From: Andreas Sturmlechner <asturm@gentoo.org>
+Date: Sun, 7 Mar 2021 19:35:44 +0100
+Subject: [PATCH] Fix linking with BUILD_SHARED_LIBS=ON default in EAPI-7
+
+Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>
+---
+ apps/mason2/CMakeLists.txt         | 2 +-
+ apps/pair_align/lib/CMakeLists.txt | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/apps/mason2/CMakeLists.txt b/apps/mason2/CMakeLists.txt
+index 2218187..c042ea7 100644
+--- a/apps/mason2/CMakeLists.txt
++++ b/apps/mason2/CMakeLists.txt
+@@ -52,7 +52,7 @@ add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}")
+ add_definitions (-DSEQAN_DATE="${SEQAN_DATE}")
+ 
+ # We define a library for the reusable parts of Mason.
+-add_library (mason_sim
++add_library (mason_sim STATIC
+              external_split_merge.h
+              external_split_merge.cpp
+              fragment_generation.h
+diff --git a/apps/pair_align/lib/CMakeLists.txt b/apps/pair_align/lib/CMakeLists.txt
+index 75faef7..3b9576e 100644
+--- a/apps/pair_align/lib/CMakeLists.txt
++++ b/apps/pair_align/lib/CMakeLists.txt
+@@ -53,5 +53,5 @@ endforeach(GAPS_T)
+ 
+ # This part can be used instead for cmake version greater or equal to 2.8.8. 
+ # This requires to update the script above as well.
+-add_library(pair_align_lib pair_align_lib.cpp pair_align_lib.h ${LIB_TARGETS})
++add_library(pair_align_lib STATIC pair_align_lib.cpp pair_align_lib.h ${LIB_TARGETS})
+ target_link_libraries(pair_align_lib ${SEQAN_LIBRARIES})
+-- 
+2.30.1
+
diff --git a/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
new file mode 100644
index 000000000000..35f0718f9d8d
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
@@ -0,0 +1,24 @@
+--- a/util/cmake/SeqAnBuildSystem.cmake	2018-01-11 12:32:45.591134000 +0100
++++ b/util/cmake/SeqAnBuildSystem.cmake	2018-01-11 12:51:55.193282581 +0100
+@@ -399,10 +399,10 @@
+         # Install pkg-config file, except on Windows.
+         if (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
+             configure_file("util/pkgconfig/seqan.pc.in" "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" @ONLY)
+-            install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig)
++            install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+         endif (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
+         # Install FindSeqAn TODO(h-2) rename seqan-config.cmake to seqan-config${SEQAN_VERSION_MAJOR}.cmake after 2.x cycle
+-        install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/cmake/seqan/)
++        install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/seqan2/)
+ 
+         # Install headers
+         file (GLOB HEADERS
+@@ -473,7 +473,7 @@
+             set (CMAKE_INSTALL_DOCDIR "${CMAKE_INSTALL_DATAROOTDIR}/doc" CACHE STRING "Documentation root (DATAROOTDIR/doc)" FORCE)
+         endif ()
+         set (SEQAN_PREFIX_SHARE "${CMAKE_INSTALL_DATADIR}/${APP_NAME}")
+-        set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/${APP_NAME}")
++        set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/examples/")
+     endif ()
+ endmacro (seqan_setup_install_vars)
+