Please instead use https://github.com/nf-core/eager as EAGERv1 won't be developed any further.
This is the main project for the EAGER project, with links to some tutorials, subsequent tools and HowTos and a FAQ which will be updated once we get feedback from end users. Please use the different bug trackers for other tools than the actual pipeline, e.g. the Clip&Merge issue tracking if you encounter issues with the Clip&Merge application.
There is a successor project on this: https://github.com/nf-core/EAGER2 Check it out - not feature complete (yet!), but soon to be!
Documentation: http://eager.readthedocs.org
FAQ: http://eager.readthedocs.org/en/latest/contents/faq.html#faq
Installation: http://eager.readthedocs.org/en/latest/contents/installation.html
Issues: https://github.com/apeltzer/EAGER-GUI/issues
Tools that we contributed ourselves are all (same as the EAGER Pipeline) available under a GPLv3 license on GitHub:
- EAGER-CLI
- EAGER-GUI
- EAGER-lib
- ClipAndMerge
- CircularMapper
- DeDup
- VCF2Genome
- ReportTable
- MTNucRatioCalculator
- MergedReadExtractor
- AdapterRemovalFixPrefix
- EAGERVersions
Contact me via GitHub or via e-Mail alexander.peltzer@uni-tuebingen.de for questions.
Releases: The releases for this project can be found on Bintray or direct download from there respectively.
The GATK is licensed by the Broad Institute and is made available to academic users of the EAGER pipeline described at http://it.inf.uni-tuebingen.de/?page_id=161 for non-commercial research use only. The full text of the GATK license is available at https://www.broadinstitute.org/gatk/about/license.html. For more information about GATK, please visit the GATK website at https://www.broadinstitute.org.
General GATK documentation can be found at on the GATK website at http://www.broadinstitute.org/gatk/guide/. Users of this pipeline are welcome to ask GATK-related questions and report problems that are not specific to this pipeline in the GATK forum at http://gatkforums.broadinstitute.org/gatk.