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README.md

inbix

In Silico Bioinformatics

** This is a pre-release version. **

Description

inbix is a free, open-source bioinformatics tool, designed to perform a range of large-scale analyses in a computationally efficient manner. The inbix program integrates many different analyses developed by the McKinney In Silico Lab for Bioinformatics and Computational Biology at the University of Tulsa.

inbix is built upon the PLINK project developed by Shaun Purcell at the Center for Human Genetic Research (CHGR), Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT, with the support of others.

For more details, visit the inbix website

Dependencies

  • cmake is required to build the executable from source.

  • The libz/zlib compression library is required, but this is installed by default on most Unix systems. In MinGW libz is installed via mingw-get.

  • LAPACK is a soft dependency: not explicitly required, but highly encouraged to take advantage of linear algebra routines that have decades of optimization.

  • Boost Mostly header extensions to the standard C++ libraries.

  • Armadillo Linear algebra header library.

  • GNU Scientific Library Deprecated- to be replaced by standard c++11 and boost and removed.

  • Doxygen to generate documentation from source code annotations.

  • Finally, OpenMP is required to take advantage of the parallelized epistasis analysis code. This is another library typically installed alongside the compiler toolchain.

Compilation Environment and Instructions

GNU g++ 6.3.0 successfully compiles the code using the cmake 3.7.2 build system.

We have successfully built and run inbix on:

  • Linux (64-bit) Debian 9.2, Ubuntu 14.04

To build inbix, change to the build directory. run 'cmake ..' to indicate the cmake configuration file is in the parent directory, the top level project directory. cmake builds a standard 'Makefile'. Finally, run 'make'. 'make install" will install the build files into the base '/usr/local/'.

The following commands if successful produce an executable file named 'inbix':

$ cd build
$ cmake ..
$ make
$ ./inbix --help

To build with documentation:

$ cd build
$ cmake .. -DBUILD_DOC=ON
$ make
$ sudo make install
$ ./inbix --help

Contributors

See AUTHORS file.

References

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.

In Silico Lab Publications document the algorithms added to PLINK to make inbix.