GEM-Tools

GEM-Tools is a C API and a Python module to support and simplify usage of the GEM Mapper.

The C API curtly supports fast and exhaustive support for parsing GEM .map files and other mapping formats.

The Python gem module allows to integrate the GEM Mapper in python scripts and simplifies development of mapping pipelines.

The Python modules also distributes current GEM binaries that are compatible with the library code. Note that the GEM binaries are distributed under the GEM Non commercial binary license while the GEM-Tools is licensed under GPL.

Note that the python module is also distributed through pypi and can easily be installed with either pip or easy_install:

pip install gemtools
easy_install gemtools

Examples

We host [https://github.com/gemtools/gemtools-examples](another GIT reposirory) with pipeline examples that are self contained and can be run immediately to explore the basic functionallity of the library.

Bugs and feature requests

Please feel free to use the Github bug tracker to report issues and feature requests that you find in the GEM-Tools library. If you run into problems with GEM and the included GEM binaries, please use the GEM bugtracker.

Deveopment

In order to develop on the GEM-Tools library, node that the repository contains a Vagrant files to be able to quickly setup a virtual machine to test and run GEM on you local non-linux-64bit machine.