The C++ library powering the GeneTrail2 (https://genetrail2.bioinf.uni-sb.de) webservice
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README.md

README.md

GeneTrail2

This is the GeneTrail2 C++ library, a collection of algorithms and statistics for processing gene expression data. It provides the compute kernels for the GeneTrail2 web service.

Citing

If you use this code in your publication, please consider citing the following publication:

Stöckel D., Kehl T., Trampert P., Schneider L., Backes C., Ludwig N., Gerasch A., Kaufmann M., Gessler M., Graf N., Meese E., Keller A., Lenhof H.-P., Multi-omics Enrichment Analysis using the GeneTrail2 Web Service, Bioinformatics 2016, doi: 10.1093/bioinformatics/btv770

Installation

Currently we only support building GeneTrail2 under Linux. Windows and MacOS X are not supported. For compiling GeneTrail2 you need the following software:

Create a directory named build in the source directory. Inside the build directory type:

cmake -DEIGEN3_INCLUDE_DIR=/path/to/eigen3/ -DGTEST_SRC_DIR=/path/to/gtest/ -DCMAKE_BUILD_TYPE=Release ..

If all goes well you can now compile a version of GeneTrail2 by typing:

make

For installing GeneTrail2 specify the installation path using -DCMAKE_INSTALL_PATH= and type:

make install

If you built with support for the Google Test Framework, you can run the unit tests by typing

make test

A suite of more expensive integration tests can be started by typing

make integration_test

License

The code of the GeneTrail2 C++ library is licensed under the GNU Lesser General Public License 3 (LGPL v3). This means you are allowed to use the library in your code with little restrictions. Especially you do not need to make your source code available as long as you are just using the library. However, you are required to open source all your changes to the library itself under the conditions of the LGPLv3.

The GNU project hosts an extensive FAQ covering possible licensing questions.