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
Documentation improvements: add more information on motivation, add user page, rework README to be more concise
Documentation improvements: add more information on motivation, add user page, rework README to be more concise
Provide documentation on JVM memory settings. Thanks to @brentp
Work towards increased Galaxy support for configuring reference file locations: allow custom indices for novoalign and bowtie2, falling back to old remapping path approach. Read galaxy INI file for configuration options. #63
Handle update of bcbio-nextgen when symlinked from local virtualenv directories
Improvements to new in development installer: correctly update to development version of code, match dependencies to conda packages
Support reading column information and tool *.loc locations from galaxy tool_data_table_conf.xml if it exists. Supports full flexibility of Galaxy configuration and fixes #63
Package and symlink fixes for new bcbio-nextgen installer
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
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