Merge pull request #68 from roryk/master

Made memory lookup more platform independent
Increase timeouts for contacting controller from enginges to avoid ipcluster failure on networked filesystems
Merge branch 'master' of github.com:chapmanb/bcbb
Add psutil to pip requirements
Provide automated upgrade from latest release, handling localized automated install
Install local software inside tool directory as part of automated install process
Improve defaults for system configuration and handle certificate errors on downloads from GitHub
Ensure isolated virtualenv for packages and installed with latest distribute
Use sam_fa_indeces as default Galaxy location file to remove dependence on bowtie. Clean up main script with upgrade support
Improvements for ipython parallelization: use sys.execuctable python to launch cluster, fix checkpointing with multiple functions using same name, keep sort output file in transaction
Correctly merge item and base configuration when deciding if fastq is necessary for the pipeline. Thanks to Warren Emmett
Fixed the sam->bam conversion step.