Initial implementations for MuTect tests.

Needs review and adjustment, it's marked as expected failure because the
data set is not yet present (or chosen)
Add the changes to the test program
Merge remote-tracking branch 'upstream/master' into mutect-tests
Support arbitrary configuration option as inputs to snpEff from bcbio_system and bcbio_sample. Partial work towards supporting better control over snpEff #52
Merge pull request #59 from lbeltrame/mutect-tests

Initial implementation of MuTect tests
Finalize integration test suite for tumor/normal cancer calling with MuTect. Provide a small test set to work with from TCGA datasets. #59
Allow pyzmq from conda for installation to avoid issues on non-standard systems with building zeromq
Additional cleanup of installation packages and versions. Avoid forced upgrade of dependency packages when upgrading bcbio_nextgen to development version
Ensure upgrade of bcbio-nextgen library from GitHub for development updates but avoid forced dependency upgrade
Update introduction.rst

I am adding my support to this pipeline. Please feel free to polish my language.
Provide  configuration hook to change snpEff output options and add cancer specific reporting on snpEff when tumor/normal calling in progress. Turn off snpEff logging by default. Fixes #52
Merge pull request #70 from tanglingfung/patch-1

Update introduction.rst
Merge bcbio-nextgen usage from Luca
Merge slurm and SciLifeLab introduction from Roman. Fixes #64
Small cleanups in users section for formatting
New release v0.7.0. Move new installer in place. Update documentation. Bump versions for requirements
Remove travis link until automated CI tests work cleanly
Update version in documentation
Add more verbose RNA-seq section to 0.7.0 changelog.
Merge pull request #72 from lbeltrame/doc-version-fix

Update version in documentation