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.

Installation

Installing the gemtools python module can be done in different ways. The easiest way is to install using pip. If you do not have pip installed or you do not want to use it, clone the githup repository and insall from source.

Install the latest release

Gemtools is distributed through pypi and you can install the lates released vesion using pip or easy install

As root:

pip install gemtools

As non-root user:

pip install gemtools --user

Install from github

You can use pip to install directly from github:

As root:

pip install git+http://github.com/gemtools/gemtools

As non-root user:

pip install git+http://github.com/gemtools/gemtools --user

If you do not have pip or you cloned the github repository already, you can simply run:

As root:

python setup.py install

As non-root user:

python setup.py install --user

Install as non-root user

There are a couple of different ways to install the gemtools module as non root user, but the simplest is to append the --user option to the installtion method of choice. This will install gemtools (and all other python modules you install that way) into the $HOME/.local folder. This folder is already in your default python paath and you do not have to modify any environment variables.

Verify the installation

To quickly check if gemtools is installed, run:

python -m gem.__main__

If gemtools is installed properly, it will print the paths to the bundled binaries.

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.

Development

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.

Changelog

1.5
- Fixed issues with gem-rna-mapper output and validation
- Moved validation to be a default step after split-mapping
- Added stats filter
- Fixed issue with gem-2-sam binary