Merge branch 'mutect_version_check'
Updated exome method comparison script with minimal BAM preparation pipeline. Provide template with FreeBayes min-BAM prep approach
Provide more useful error message if argparse missing when running installer
Use cutadapt with do.run for provenance tracking
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Update docs with network troubleshooting information for clusters.

Hopefully help's others resolve the underlying issue in #138
Merge pull request #145 from porterjamesj/patch-1

Update docs with network troubleshooting information for clusters.
Add James to contributors. Thanks for degugging documentation: #145
Provide easier mechanism to upgrade with third party tools included by using saved installation details. Avoid confusing errors with old bare  upgrade option
Release v0.7.4
Remove intermediate trimmed files during cutadapt.
Documentation on developing with bcbio-nextgen and anaconda directory #147. Bump version to next development
Remove multiprocessing dependency from trimming.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Added read_through change.
Provide better error messages and documentation when  not saved in configuration #148
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Link to contributor information from the start of the README. #147
Begin removing custom QC code in favor of full QC packages + supplement programs as needed. Integrates qualimap and eliminates custom pdflatex PDF generation
Remove pdflatex dependence and creation of custom PDF report file.