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Installation Instructions for Ragout ==================================== Availability ------------ Ragout is available for Mac OS and Linux. Build Requirements ------------------ * C++ compiler with C++0x support (GCC 4.6+ / Clang 3.2+ / Apple Clang 4.2+) * GNU make / Cmake (for building Sibelia) Runtime Depenencies ------------------- * Python 2.7 * Sibelia [http://github.com/bioinf/Sibelia] or HAL Tools [https://github.com/glennhickey/hal] Binary Distribution ------------------- Pre-compiled binaries are available for Linux and Mac OS from the releases page [https://github.com/fenderglass/Ragout/releases]. In this case you will not need the installation procedures below. Building -------- To build Ragout native modules, type: make You will also need either *Sibelia* or *HAL tools* installed (see below) Sibelia ------- To build and install Sibelia, use: python scripts/install-sibelia.py If you already have Sieblia installed into your system, it will be picked up automatically by Ragout. HAL Tools --------- HAL alignment produced by *Progressive Cactus* could be used for synteny blocks decomposition instead of *Sibelia* (recommended for large genomes). If you want to use HAL alignment as input, you need to install *HAL Tools* package [https://github.com/glennhickey/hal] as it is described in the manual. Do not forget to properly set PATH and PYTHONPATH environment variables. Troubleshooting --------------- Q: Many compilation errors, possibly with "unrecognized command line option '-std=c++0x'" message: A: Probably your compiler is too old and does not support C++0x. Minimum required versions of GCC and Clang are given in the beginning of this document. Q: "libstdc++.so.6: version `CXXABI_1.3.5' not found" or similar error when running A: Ensure that the version of libc++ that was used to compile Ragout is similar to one the you currently using. You can specify an extra search path to a specific library by setting "LD_LIBRARY_PATH" variable.