Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Default points to /usr/local/share instead of /usr/share.
Added Tophat2 as a _tool.
Point to bowtie2 genome locations.
Bump to next development version
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Template generator fixed.
Illumina RNA-seq template file added.
Improvements for processing large samples through coverage calculations: scale memory with cores and avoid X connection errors on shared ssh connections
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Use samtools for sorting merged files: handles larger files better than bamtools at the expense of extra temporary disk space. #86
Add pointer to whole genome scaling documentation and more information about expected runtimes. #85
Save file list to process to persistent file to help with debugging #86
Save file list to process to persistent file to help with debugging #86
Added upload option to configuration file.
Break uploaded sections into their own functions.

Makes it easier to add new upload scripts.
Added RNA-seq-specific upload files.
Add command line option to get version; bug fix for saving bam file list for debugging
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
More verbose documentation about the upload field.