This is the GeneTrail 3 C++ library, a collection of algorithms and statistics for processing gene expression data. It provides the compute kernels for the GeneTrail 3 web service.
If you use this code in your publication, please consider citing the following publication:
Gerstner N., Kehl T., Lenhof K., M{"u}ller A., Mayer C., Eckhart L., Grammes N. L., Diener C., Hart M., Hahn O., Walter J., Wyss-Coray T., Meese E., Keller A., Lenhof H.-P. GeneTrail 3: advanced high-throughput enrichment analysis, Nucleic acids research 2020, doi: https://doi.org/10.1093/nar/gkaa306
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
Currently we only support building GeneTrail 3 under Linux. Windows and MacOS X are not supported. For compiling GeneTrail 3 you need the following software:
- GCC >= 4.9 or clang >= 3.5
- CMake >= 2.8.12.2
- Boost >= 1.55
- Eigen >= 3.2.3
- RapidJSON >= 1.0.2
- GMP >= 5.0.0 (optional)
- Google Test Framework >= 1.7.0 (optional)
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
The code of the GeneTrail 3 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.