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[misc] remove dispatcher; clean-up cmake #221

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Jul 25, 2023
Merged

[misc] remove dispatcher; clean-up cmake #221

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51 changes: 0 additions & 51 deletions bin/lambda3.in
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44 changes: 19 additions & 25 deletions src/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -58,11 +58,6 @@ message( " LAMBDA_WITH_BIFM ${LAMBDA_WITH_BIFM}")
message(STATUS "Run 'cmake -LH' to get a comment on each option.")
message(STATUS "Remove CMakeCache.txt and re-run cmake with -DOPTIONNAME=ON|OFF to change an option.")

# deactivate the version check on broken seqan releases
if (SEQAN_VERSION_STRING VERSION_LESS "2.3.2")
add_definitions (-DSEQAN_DISABLE_VERSION_CHECK="YES")
endif ()

# ----------------------------------------------------------------------------
# Dependencies (continued)
# ----------------------------------------------------------------------------
Expand Down Expand Up @@ -130,7 +125,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "GNU")
ProcessorCount(LAMBDA_COMPILE_THREADS)
endif ()

# This triggers an ICE for some reason
# TODO: this should be fixed; currently triggers an ICE for some reason
# if (LAMBDA_COMPILE_THREADS GREATER 1)
# set (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -flto=${LAMBDA_COMPILE_THREADS}")
# endif()
Expand All @@ -139,11 +134,6 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "GNU")
set (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -s")
endif ()

if (NOT CMAKE_CXX_COMPILER_ID MATCHES "Intel")
# -Wextra not met by current SeqAn on intel
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} -Wextra")
endif ()

# ----------------------------------------------------------------------------
# Build Setup
# ----------------------------------------------------------------------------
Expand Down Expand Up @@ -187,6 +177,12 @@ add_custom_command (OUTPUT lambda3-searchn.1
add_custom_command (OUTPUT lambda3-searchp.1
COMMAND lambda3 searchp --export-help man > lambda3-searchp.1
DEPENDS lambda3)

# searchbs subcommand
add_custom_command (OUTPUT lambda3-searchbs.1
COMMAND lambda3 searchbs --export-help man > lambda3-searchbs.1
DEPENDS lambda3)

# mkindexn subcommand
add_custom_command (OUTPUT lambda3-mkindexn.1
COMMAND lambda3 mkindexn --export-help man > lambda3-mkindexn.1
Expand All @@ -196,9 +192,14 @@ add_custom_command (OUTPUT lambda3-mkindexp.1
COMMAND lambda3 mkindexp --export-help man > lambda3-mkindexp.1
DEPENDS lambda3)

add_custom_target (manual
ALL
DEPENDS lambda3.1 lambda3-searchn.1 lambda3-searchp.1 lambda3-mkindexn.1 lambda3-mkindexp.1)
# mkindexbs subcommand
add_custom_command (OUTPUT lambda3-mkindexbs.1
COMMAND lambda3 mkindexbs --export-help man > lambda3-mkindexbs.1
DEPENDS lambda3)

add_custom_target (manual ALL DEPENDS lambda3.1
lambda3-searchn.1 lambda3-searchp.1 lambda3-searchbs.1
lambda3-mkindexn.1 lambda3-mkindexp.1 lambda3-mkindexbs.1)

# ----------------------------------------------------------------------------
# Installation
Expand All @@ -209,16 +210,7 @@ include (GNUInstallDirs)

# Install lambda binaries into LIBEXECDIR
install (TARGETS lambda3
DESTINATION ${CMAKE_INSTALL_LIBEXECDIR})

# Install dispatcher script into BINDIR
configure_file(../bin/lambda3.in
${CMAKE_CURRENT_BINARY_DIR}/lambda3-dispatch
@ONLY)
install (FILES ${CMAKE_CURRENT_BINARY_DIR}/lambda3-dispatch
DESTINATION ${CMAKE_INSTALL_BINDIR}
RENAME lambda3
PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
DESTINATION ${CMAKE_INSTALL_BINDIR})

# Install non-binary files for the package to DOCDIR, usually ${PREFIX}/share/doc/lambda3
install (FILES ../LICENSE.rst
Expand All @@ -231,8 +223,10 @@ install (FILES ../LICENSE.rst
install (FILES ${CMAKE_CURRENT_BINARY_DIR}/lambda3.1
${CMAKE_CURRENT_BINARY_DIR}/lambda3-searchn.1
${CMAKE_CURRENT_BINARY_DIR}/lambda3-searchp.1
${CMAKE_CURRENT_BINARY_DIR}/lambda3-searchbs.1
${CMAKE_CURRENT_BINARY_DIR}/lambda3-mkindexn.1
${CMAKE_CURRENT_BINARY_DIR}/lambda3-mkindexp.1
${CMAKE_CURRENT_BINARY_DIR}/lambda3-mkindexbs.1
DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)

# ----------------------------------------------------------------------------
Expand All @@ -244,7 +238,7 @@ set (CPACK_PACKAGE_NAME "lambda3")
set (CPACK_PACKAGE_DESCRIPTION_SUMMARY "lambda -- the local aligner for massive bioligical data")
set (CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/../README.rst")
set (CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/../LICENSE.rst")
set (CPACK_PACKAGE_VENDOR "Hannes Hauswedell <[email protected]>")
set (CPACK_PACKAGE_VENDOR "Hannes Hauswedell <[email protected]>")
set (CPACK_PACKAGE_CONTACT "${CPACK_PACKAGE_VENDOR}")
set (CPACK_PACKAGE_VERSION_MAJOR "${SEQAN_APP_VERSION_MAJOR}")
set (CPACK_PACKAGE_VERSION_MINOR "${SEQAN_APP_VERSION_MINOR}")
Expand Down
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