INSTALL.md

Installation Instructions for Ragout

Availability

Ragout is available for Mac OS and Linux.

Bioconda distribitions

Ragout binary releases are available through Bioconda:

conda install -c bioconda ragout

Build Requirements

• C++ compiler with C++0x support (GCC 4.6+ / Clang 3.2+ / Apple Clang 4.2+)
• GNU make
• Cmake

Runtime Depenencies

• Python (2.7 or 3.5+)
• Sibelia [http://github.com/bioinf/Sibelia]
• python-networkx == 2.2
• HAL Tools (optionally) [https://github.com/ComparativeGenomicsToolkit/hal]

Local installation

If you don't want to use bioconda release, you can build Ragout repository clone and run it locally without installing into system. To do this, perform:

git clone https://github.com/fenderglass/Ragout.git
cd Ragout
python setup.py build
pip install -r requirements.txt --user
python scripts/install-sibelia.py

This will also build and install Sibelia and all Python dependencies. See below for HAL installation instructions.

Once installed, you can invoke Ragout from the cloned directory by using:

bin/ragout

System installation

To integrate Ragout into your system, run:

git clone https://github.com/fenderglass/Ragout.git
cd Ragout
python setup.py build
python setup.py install

This assumes that you already have python-networkx package installed into your system (using the respective package manager). Sibelia / HAL tools should also be installed / integrated separately.

HAL Tools

HAL alignment produced by 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/ComparativeGenomicsToolkit/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. Make sure you have at least GCC 4.6+ / Clang 3.2+

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.