Additional error checking of input YAML configuration file: identify incorrect algorithm arguments, aligner and variantcaller inputs
Update installation script to recognize Mac OSX systems
Remove calling htseq via the command line.

Added the count script from Simon to the
count script instead to prevent being able to not find
the htseq-count command.
Test for failed anaconda installs and recover with reinstallation
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Detect core and memory availability on multicore and ipython parallel runs. First step in providing general resource planning for memory intensive jobs
Pass predicted job memory requirements to cluster schedulers. Use available cores and memory to ensure submitted jobs fall within available resources and scale core requres to work with memory intensive jobs
Enable scaling of GATK HaplotypeCaller runs with increased memory usage using adjustments in resources. Scale jobs for single-core submissions to avoid overscheduling due to memory
Added OSX-specific Vagrant install instructions.
Make OSX title smaller.
Remove comments added during testing.
Fixed paths to raw files.
Actually fixed the raw paths.
Update bootstrap path.
Avoid scaling cores or jobs when system information not found. Allows initial bootstrapping on ipython systems. Thanks to @brentp
Avoid bare calls to samtools when checking version, instead pulling paths from resources. Fixes #91
Let picard determine quality format, removing hack code that guesses from platform. Generalize naming to FastqToSam to use new data structures. Fixes #92
Improve logic for removing data directory from install options before calling upgrade. Thanks to David McWilliams
Provide explicit minimal/standard pipeline that does alignment and QC
Drop looking for the deprecated "info" field.