Initial revision of an ERCC spike-in QC command.  This needs to be in a pipeline with software results.
A new version of the ERCC spike-in QC that uses existing RNA-seq alignments to a reference and annotation that includes the ERCC transcripts.
Minimally functional version of show-docs for variant reporting
Put all printing into show-docs

Each component can add its own sections to the documentation
which are all printed in a standard place
Add overview doc section
Add doc to full reporter
Ensure that disk-allocations get cleaned up upon rollback

In the case we:
    1) create transaction
    2) call $process->create_disk_allocation
    3) rollback transaction
We need to be assured that the disk allocation is deleted.  Since disk
allocations are created in separate processes, there is no log in our
transaction about the disk allocation creation, so we have to log it
ourselves.
Avoid using the ghost_class if possible

My hand tests show that this has the same behavior of ensuring that the
disk allocation is cleaned up when the current transaction commits but
not if it gets rolled back.
set status with 'update_status' not 'status'

The way UR automatically creates undo-subroutines inside of transactions
makes it so that when the transaction rolls back an invalid status
transition will occur.  If the status method has logic to disallow such
transitions it will not allow us to roll back UR transactions, which is
bad.
Add 'genome process view' command
Have create_disk_allocation create the log_directory
Processes can now be run

The branch that bsub's and runs the workflow on LSF (with flow) has been
pretty extensively hand-tested.  It wasn't clear how to automate that
testing until we have a test-database service that we can use.
Expose interface for type lookup to use in tests
bugfix: call execute instead of non-existing method
CgHub: add gmt command tree
CgHub: mv gene torrent to cg hub dir
CgHub: update gene torrent class name
Epitope Prediction : New Module Added
Merge branch 'master' of github.com:genome/genome
CgHub: add base class