Problem related to the pre-installed software and packages

[katerinaoleynikova]

Good day!

Is it possible to take into account a case when prerequisites (for example, htslib library) are already installed on my own? A "rigid" installation of these packages there leads to a problem of incompatibility of the versions.

Best wishes. p.s. the same issue was created in the REViewer repo: https://github.com/Illumina/REViewer/issues/12

[serge2016]

Nice suggestion! It would be nice!

[Stikus]

Hello, any news about it?

Moreover - for some reason in last release not only support for external htslib wasn't added but even existing support for external boost was removed: https://github.com/Illumina/ExpansionHunter/blob/v4.0.2/CMakeLists.txt#L67 v0.4.2:

find_package(Boost 1.4 REQUIRED COMPONENTS program_options filesystem regex date_time system)

https://github.com/Illumina/ExpansionHunter/blob/v5.0.0/CMakeLists.txt#L42 v0.5.0:

ExternalProject_Add(Boost
	BUILD_IN_SOURCE YES
	URL https://boostorg.jfrog.io/artifactory/main/release/1.73.0/source/boost_1_73_0.tar.bz2
	UPDATE_COMMAND ""
	PATCH_COMMAND ${BOOST_PATCH_COMMAND}
	CONFIGURE_COMMAND ./bootstrap.sh --prefix=${installDir}/lib
	BUILD_COMMAND ./b2 install -j8   --prefix=${installDir} --with-filesystem --with-system --with-program_options link=static ${B2_OPTIONS}
	INSTALL_COMMAND ""
)

[egor-dolzhenko]

Hi Konstantin, Katerina, Sergey,

I am sorry this fell through the cracks.

The latest changes to the build script are aimed at decoupling external dependencies from ExpansionHunter itself:

• The top-level CMakeLists.txt file builds htslib, Boost, spdlog, googletest, and abseil libraries and then builds ExpansionHunter (passing the location of all installed libraries using CMAKE_INSTALL_PREFIX CMake variable).

• It should now be possible to build ExpansionHunter without building dependencies by running cmake from "ehunter" subdirectory. The CMakeLists.txt file inside this subdirectory assumes that the above dependencies are already installed.

Best wishes, Egor