GenBank/RefSeq Update Goals

• Incremental update of mRNAs and ESTs for multiple species and assemblies based on daily updates from NCBI.
• Automatically run from cron, possibly every night.
• Only require manual intervention on non-recoverable errors or when a large cluster run is required to do a large alignment.
• Incremental across GenBank releases; don't force a full realignment every quarter.
• Allow removal of older genbank full releases (and still not force a full realignment).
• Avoid corruption of disk files and databases.
• Recover from failures state, automatically when possible, making manual recover easy.
• Allow restarting failed steps without restarting the entire process.
• Don't require the process to be run at defined intervals. When a run is done, data files will be updated to reflect the current state of the NCBI repository.
• Include HTS files in automated download process.