1.1.14 (2013-02-08)
===================

- For Bam files that are paired do not do all the checks

- Integer arguments are validated properly now

1.1.13 (2012-12-21)
===================

- Add MAXINTRONLENGTH option

- Update documentation section, and document accession parameters

1.1.12 (2012-11-09)
===================

- Fix Quick runs. Soft links were not made correctly, and some accession
  parameters are now filled in correctly as well.

- Pep8 for prepare.py

1.1.11 (2012-11-08)
===================

- add FLUXMEM parameter to control the maximum number of GB of memory
  that the Flux can use

- add MIN_RECURSIVE_MAPPING_TRIM_LENGTH parameter that allows tuning the
  minimum length to which a read will be trimmed during the recursive
  mapping.

- Add Makefile generated by tooth.paste

1.1.10 (2012-09-13)
===================

- check read labels for consistency

1.1.9 (2012-08-23)
==================

- Integrate the new version of Grape, installed by grape.recipe.pipeline

Documentation
-------------

- Add Sphinx documentation, and make it available at 
  http://graperecipepipeline.readthedocs.org/

Internal
--------

- Integrate with Travis-CI

- Use tempfile for testing instead of writing to a sandbox folder

1.1.8 (2012-07-20)
==================

- Remove labeling through RestrictedPython, promoting explicit labels

1.1.7 (2012-07-05)
==================

Features
--------

- Install FastQC

1.1.6 (2012-06-26)
==================

Features
-------- 

- Install Cufflinks binaries

Documentation
-------------

- Description and long description added to setup.py

Internal
--------

- Refactoring and increase unit test coverage

1.1.5 (2012-05-18)
==================

Internal
--------

- Fix unit tests now that flux.sh is flux

- Remove import of call from subprocess because the installation of the flux
  does not need it any more

1.1.4 (2012-05-18)
==================

Features
--------

- New installation routine for the new Flux version now using the flux binary
  instead of a flux.sh

1.1.3 (2012-04-20)
==================

Documentation
-------------

- Add a README.txt detailing the motivation, installation and configuration

Bug Fixes
---------

- Fastq files need to be gzipped, but for bam files this does not make sense.
  Removing the error that was raised when encountering a bam file that was
  not gzipped.

1.1.2 (2012-04-12)
==================

Bug Fixes
---------

- Raise an error when files and label/mate_id/pair_id don't have the 
  same length

1.1.1 (2012-04-11)
==================

Bug Fixes
---------

- Raise an error when the pair_id, mate_id, and label attributes of accessions
  are not specified

- Raise an error when a fastq file given in an accession file is not gzipped

1.1 (2012-03-29)
================

Features
--------

- Quick run mode for running one set of reads for predefined species.

1.0 (2012-03-22)
================

- First release
