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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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Problem related to the pre-installed software and packages #122

Open katerinaoleynikova opened 3 years ago

katerinaoleynikova commented 3 years ago

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 commented 3 years ago

Nice suggestion! It would be nice!

Stikus commented 3 years ago

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 commented 3 years ago

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:

Best wishes, Egor