Merge branch 'hotfix/cython' into develop

Conflicts:
	nextgen/bcbio/solexa/samplesheet.py
Merge branch 'hotfix/cython' into develop
Merge pull request #230 from SciLifeLab/develop

Develop - merge into master
Merge branch 'hotfix/skip_default_phix_filtering' of github.com:b97pla/bcbb
Merge conflict
Merge pull request #231 from b97pla/master

HOTFIX: Skip default phix-filtering of samples
Merge pull request #233 from b97pla/develop

updated pattern for catching miseq runs
Merge pull request #234 from SciLifeLab/develop

Develop
Merge branch 'develop' of https://github.com/SciLifeLab/bcbb into develop
Added specific version to download picard-tools. Solves conflict with Debian-med repository
Merge branch 'hotfix/picard-tools'
Merge branch 'hotfix/picard-tools' into develop
Since fabric is a dependency in setup.py, removed the try statement in transfer.py
Formatting
Refactored a try block to a dict.get() call
Added a funciton for simple rsync uploading in illumina_finished_msg.py
Added libsam-java to be compatible with our picard-tools
Merge branch 'hotfix/libsam-java'
Merge branch 'hotfix/libsam-java' into develop
Merge pull request #235 from guillermo-carrasco/master

Picard issues with the pipeline