add better error messages if program not found. see #13
Merge pull request #14 from brentp/error-msg

add better error messages if program not found. see #13
Documentation: graphical overviews of variant calling and parallelization
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Ensure selection of cores for multicore jobs respects configured algorithm choices. Avoids problems where cores are set differently for bwa/novoalign and only a single aligner is used
Update requirements to use latest ipython with large cluster fix and ipython-cluster-helper. Remove celery as required dependency
Improve documentation for getting started and update example configurations. Thanks to Zhengqiu Cai and @brentp for useful feedback
Add formal list of contributors and license information
Add formal list of contributors and license information
Provide piped GATK recalibration as part of post-alignment processing. Allows a fully piped process with recalibration, de-duplication and realignment
Provide useful error message when non-supported samtools deduplication used with full-GATK pipeline
Tweak HaplotypeCaller workarounds for GATK 2.5-2
Update setup.py requirement versions to match requirements.txt. Fixes pysam 0.7 problem. Thanks to @brentp
Add graphics for region selection strategy for parallel processing
Added a namespace for collecting file format tools.

These types of functions are sprinkled around, making them
hard to find/reuse, maybe collecting them in one spot is good.

Also included a decorator to check for file types to remove
some of the is-this-file-of-the-right-format-if-not-bail
boilerplate.
Added a bam -> chromosome sizes converter.
Changed output extension for bam -> sizes conversion.
Added converter from bam -> chromosome length sizes for freec.
Fixed bam2sam import.
Provide ability to customize program resources for specific samples. Use customization to pass array of specific options to novoalign