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Building

Note: All required executables are included with the release tarball. Rebuilding should only be needed in very specialized cases.

Third-party dependencies

All third-party executables are included in the release, within the subdirectory internals/thirdparty. Deleting this folder and running internals/install/build_thirdparty.sh will regenerate these files (requires an active Internet connection). Most packages will be downloaded in executable form using conda or from the package author's preferred release URL, and a few components will be built from source.

  • Bowtie2>=2.3.0 (2.3.4.3 included)
  • STAR>=2.5.2a
  • Python>=3.5 (3.5.3 included)
  • matplotlib>=1.5.1
  • numpy
  • BBmerge>=37.78 (requires java)
  • Pipe Viewer>=1.6.0
  • Graphviz (optional: for debugging use with --render-flowchart)
  • Ghostscript (optional: for debugging use with --render-mutations)
  • scikit-learn>=0.18.1 (optional: for area under ROC curve tests)

In the rare case that the provided third-party executables are not compatible with your platform (for example, if you get strange "GLIBC-2.XX" or "ABI incompatible" errors), you're on your own. Delete the internals/thirdparty folder entirely, and then install the listed packages at the system level through your package manager or by building from source.

Source code documentation

  • C++ documentation at internals/cpp-src/doc/html/index.html
  • Python documentation in source code comments (folder internals/python)

C++ build requirements

  • recent cmake (>=3.3)
  • gcc compiler with C++11 support
  • git with https support
  • build-essential (should include dpkg-dev, g++, libc-dev, libstdc++)
  • libboost-dev (>=1.60.0)
  • libboost-filesystem-dev
  • libboost-iostreams-dev
  • libboost-program-options-dev
  • doxygen (optional)

Building C++ modules

To rebuild ShapeMapper executables

  • Delete the folders build and build_deps if present
  • Run internals/install/build_binaries.sh --use-system-libs
  • This assumes the tools and libraries listed above are already present at the system level.

Alternatively, run internals/install/build_all.sh

  • This will take substantial disk space and time
  • Compiler and library dependencies listed above (with the exception of Doxygen) will be downloaded and built locally within the internals/build_deps folder

    

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