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Merge pull request #131 from yana-safonova/testing
Testing
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,134 @@ | ||
| project(igrec) | ||
| cmake_minimum_required(VERSION 2.8) | ||
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| if(NOT CMAKE_BUILD_TYPE) | ||
| set(CMAKE_BUILD_TYPE "RelWithAsserts" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." FORCE) | ||
| endif(NOT CMAKE_BUILD_TYPE) | ||
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| add_subdirectory(configs) | ||
| add_subdirectory(src) | ||
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| if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) | ||
| set(CMAKE_INSTALL_PREFIX "/usr/local" CACHE PATH "default install path" FORCE) | ||
| endif() | ||
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| # Expand tildas and convert to absolute path | ||
| FILE(TO_CMAKE_PATH "${CMAKE_INSTALL_PREFIX}" CMAKE_INSTALL_PREFIX) | ||
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| set(INSTALL_DIR "share/igrec") | ||
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| install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/VERSION" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/README" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/GPLv2.txt" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/init.py" | ||
| DESTINATION "${INSTALL_DIR}" | ||
| COMPONENT runtime) | ||
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| install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/manual.html" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/diversity_analyzer_manual.html" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/dsf_manual.html" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/barcodedIgReC_manual.html" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/igquast_manual.html" | ||
| DESTINATION "${INSTALL_DIR}" | ||
| COMPONENT manual) | ||
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| install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/docs" | ||
| DESTINATION "${INSTALL_DIR}" | ||
| COMPONENT manual | ||
| PATTERN "*.pdf" EXCLUDE) | ||
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| install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/test_dataset" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/data" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/pipeline_makefiles" | ||
| "${CMAKE_CURRENT_SOURCE_DIR}/configs" | ||
| DESTINATION "${INSTALL_DIR}" | ||
| COMPONENT runtime | ||
| PATTERN "*.template" EXCLUDE | ||
| PATTERN "CMakeLists.txt" EXCLUDE | ||
| PATTERN ".gitignore" EXCLUDE) | ||
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| install(DIRECTORY "${CMAKE_BINARY_DIR}/bin" | ||
| DESTINATION "${INSTALL_DIR}/build/release" | ||
| COMPONENT runtime | ||
| USE_SOURCE_PERMISSIONS | ||
| PATTERN "test_*" EXCLUDE) | ||
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| install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/py" | ||
| DESTINATION "${INSTALL_DIR}" | ||
| COMPONENT runtime | ||
| USE_SOURCE_PERMISSIONS | ||
| PATTERN "*.pyc" EXCLUDE | ||
| PATTERN ".gitignore" EXCLUDE) | ||
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| set(tools "igrec.py;mass_spectra_analyzer.py;dense_subgraph_finder.py;igquast.py;barcoded_igrec.py;diversity_analyzer.py;ig_simulator.py") | ||
| foreach(tool ${tools}) | ||
| install(PROGRAMS ${tool} | ||
| DESTINATION "${INSTALL_DIR}" | ||
| COMPONENT runtime) | ||
| endforeach() | ||
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| foreach(tool ${tools}) | ||
| # Conctruct fake symlinks | ||
| EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E create_symlink "../share/igrec/${tool}" "${CMAKE_BINARY_DIR}/${tool}") | ||
| # ...and add them into the installation | ||
| # I know, I know, I definitely know how much dirty it is | ||
| # Unfortunately, cpack cannot trace symlinks automatically and cmake-install does not support smth like install(SYMLINK) | ||
| install(FILES "${CMAKE_BINARY_DIR}/${tool}" | ||
| DESTINATION "bin" | ||
| COMPONENT runtime) | ||
| endforeach() | ||
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| # Disabled. We have already created symlinks manually above | ||
| # foreach(tool ${tools}) | ||
| # install(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E create_symlink \"${CMAKE_INSTALL_PREFIX}/${INSTALL_DIR}/${tool}\" \"${CMAKE_INSTALL_PREFIX}/bin/${tool}\")") | ||
| # endforeach() | ||
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| set(CPACK_PACKAGE_NAME "igrec") | ||
| set(CPACK_PACKAGING_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") | ||
| set(CPACK_GENERATOR "TGZ;ZIP;DEB;RPM") | ||
| set(CPACK_SOURCE_GENERATOR "") | ||
| set(CPACK_OUTPUT_FILE_PREFIX "${CMAKE_CURRENT_SOURCE_DIR}/packages") # TODO add an arg | ||
| set(CPACK_RESOURCE_FILE_README "${CMAKE_CURRENT_SOURCE_DIR}/README") | ||
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| FILE(READ "${CMAKE_CURRENT_SOURCE_DIR}/VERSION" VERSION) | ||
| STRING(STRIP "${VERSION}" VERSION) | ||
| set(CPACK_PACKAGE_VERSION ${VERSION}) | ||
| # Are they really necessary? | ||
| # SET(CPACK_PACKAGE_VERSION_MAJOR "3") | ||
| # SET(CPACK_PACKAGE_VERSION_MINOR "0") | ||
| # SET(CPACK_PACKAGE_VERSION_PATCH "0") | ||
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| set(CPACK_DEBIAN_PACKAGE_DEPENDS "python") | ||
| # TODO Add seaborn somehow | ||
| # set(CPACK_DEBIAN_PACKAGE_SUGGESTS "python-matplotlib, python-biopython, python-numpy, python-scipy, python-pandas") | ||
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| set(CPACK_PACKAGE_CONTACT "Alexander Shlemov <shlemovalex@gmail.com>") | ||
| set(CPACK_DEBIAN_PACKAGE_HOMEPAGE "http://yana-safonova.github.io/ig_repertoire_constructor/") | ||
| set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Y-tools: tools for construction of full-length adaptive immune repertoires and immunoinformatics analysis") | ||
| # TODO: Add full description | ||
| set(CPACK_PACKAGE_DESCRIPTION "Y-tools: tools for construction of full-length adaptive immune repertoires and immunoinformatics analysis") | ||
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| set(CPACK_PACKAGE_VENDOR "Center for Algorithmic Biotechnology, Saint Petersburg University, Russia") | ||
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| # trace debug information during CPackDeb run | ||
| set(CPACK_DEBIAN_PACKAGE_DEBUG TRUE) | ||
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| # RPM | ||
| # trace debug information during CPackRPM run | ||
| set(CPACK_RPM_PACKAGE_LICENSE "GPLv2") | ||
| set(CPACK_RPM_PACKAGE_DEBUG TRUE) | ||
| set(CPACK_RPM_PACKAGE_DESCRIPTION ${CPACK_PACKAGE_DESCRIPTION}) | ||
| set(CPACK_RPM_PACKAGE_REQUIRES ${CPACK_DEBIAN_PACKAGE_DEPENDS}) # TODO check | ||
| # set(CPACK_RPM_PACKAGE_SUGGESTS ${CPACK_DEBIAN_PACKAGE_SUGGESTS}) | ||
| set(CPACK_RPM_PACKAGE_URL ${CPACK_DEBIAN_PACKAGE_HOMEPAGE}) | ||
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| set(CPACK_STRIP_FILES TRUE) | ||
| set(CPACK_PACKAGE_EXECUTABLES $tools) | ||
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| set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE") | ||
| set(CPACK_MONOLITHIC_INSTALL TRUE) | ||
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| # Package parameters should be set BEFORE include(CPack) | ||
| include(CPack) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,67 @@ | ||
| all: | ||
| # Default build type | ||
| build_type?="RelWithAsserts" | ||
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| # Default install prefix | ||
| prefix?="/usr/local" | ||
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| .PHONY: clean clean_tests cmake all pack | ||
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| all: igrec | ||
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| cpcfg: | ||
| mkdir -p build/tmp | ||
| cd build/tmp && cmake ../../configs -DCMAKE_OVERWRITE_CONFIGS=true | ||
| rm -r build/tmp | ||
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| cmake: | ||
| mkdir -p build/release | ||
| cd build/release && cmake ../.. -DCMAKE_BUILD_TYPE="${build_type}" -DCMAKE_INSTALL_PREFIX=${prefix} -Wno-dev | ||
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| igrec: cmake | ||
| $(MAKE) -C build/release all | ||
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| rig: | ||
| $(MAKE) -C build/release/ig_repertoire_constructor ig_repertoire_constructor | ||
| rpm: igrec | ||
| cd build/release && cpack -G RPM | ||
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| dig: | ||
| $(MAKE) -C build/debug/ig_repertoire_constructor ig_repertoire_constructor | ||
| deb: igrec | ||
| cd build/release && cpack -G DEB | ||
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| dsf: | ||
| $(MAKE) -C build/release/dense_sgraph_finder dense_sgraph_finder | ||
| tgz: igrec | ||
| cd build/release && cpack -G TGZ | ||
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| metis: | ||
| $(MAKE) -C build/release/ext_tools/metis-5.1.0/ metis | ||
| install: igrec | ||
| cd build/release && cmake -P cmake_install.cmake | ||
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| check: all | ||
| dsf: cmake | ||
| $(MAKE) -C build/release dense_sgraph_finder | ||
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| check: cmake | ||
| $(MAKE) -C build/release check | ||
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| check_essential: all | ||
| $(MAKE) -C build/release check_essential | ||
| memcheck: cmake | ||
| $(MAKE) -C build/release memcheck | ||
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| rnd: cmake | ||
| $(MAKE) -C build/release rnd | ||
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| vjf: cmake | ||
| $(MAKE) -C build/release vj_finder | ||
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| cdr: cmake | ||
| $(MAKE) -C build/release cdr_labeler | ||
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| umi: cmake | ||
| $(MAKE) -C build/release umi_correction_stats umi_graph umi_naive umi_to_fastq | ||
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| vjf: | ||
| $(MAKE) -C build/release/vj_finder | ||
| igs: cmake | ||
| $(MAKE) -C build/release ig_simulator | ||
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| cdr: | ||
| $(MAKE) -C build/release/cdr_labeler | ||
| clean: | ||
| -rm -r build | ||
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| umi: | ||
| $(MAKE) -C build/release/umi_experiments | ||
| clean_tests: | ||
| -rm *.pyc | ||
| -rm -r igrec_test | ||
| -rm -r ms_analyzer_test | ||
| -rm -r ig_simulator_test | ||
| -rm *~ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| 3.0.0 | ||
| 3.1.0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| project(configs) | ||
| cmake_minimum_required(VERSION 2.8) | ||
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| function(cpcfg overwrite) | ||
| if (${overwrite}) | ||
| MESSAGE("Configs will be overwritten") | ||
| endif() | ||
| file(GLOB config_templates "*/*.template") | ||
| foreach(config_template ${config_templates}) | ||
| # Remove extention | ||
| STRING(REGEX REPLACE "\\.template$" "" config ${config_template}) | ||
| if(NOT EXISTS "${config}" OR ${overwrite}) | ||
| configure_file("${config_template}" | ||
| "${config}" | ||
| @ONLY) | ||
| endif() | ||
| endforeach() | ||
| endfunction(cpcfg) | ||
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| if (NOT CMAKE_OVERWRITE_CONFIGS) | ||
| SET(CMAKE_OVERWRITE_CONFIGS "FALSE") | ||
| endif() | ||
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| cpcfg(${CMAKE_OVERWRITE_CONFIGS}) |
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