3. The RAST batch interface

With the servers, we have supplied a set of RAST batch scripts. Each of these RAST scripts (except for the submission script, which has much more complex arguments) takes as the first two arguments the username and password of a valid account on the RAST server.  
A single job may be submitted using svr__submit_RAST_job. This script takes a number of arguments which define the parameters for the submission:
--user usernameRAST login for the submitting user
--passwd passwordRAST password for the submitting user
--genbank filenameIf submitting a genbank file, the file of input data.
--fasta filenameIf submitting a FASTA file of contigs, the file of input data.
--domain Bacteria or
--domain ArchaeaDomain of the submitted genome.
--taxon_id taxonomy-idThe NCBI taxonomy id of the submitted genome
--bioname "genus species str."Biological name of the submitted genome
--genetic_code ( 11 | 4 )Genetic code for the submitted genome, either 11 or 4.
--gene_callerGene caller to use (FigFam-base RAST gene caller or straight Glimmer-3)
--reannotate_onlyPreserve the original gene calls and use RAST

A set of jobs may be submitted using svr_run_RAST_jobs. This script takes a file of Genbank contig ids on the standard input, and will determine all Genbank contigs that are part of the same Genbank project, and submit them as a single RAST job.

svr_run_RAST_jobs username password < contig-ids

The script will return information and statistics about the job submission, as well as a job number. 

The status of one or more jobs may be checked using svr_status_of_RAST_job:

svr_status_of_RAST_job username password jobnumber jobnumber ...

When it returns a status of "completed", the job is ready for retrieval.

The results of a job may be retrieved using svr_retrieve_RAST_job. The supported formats are as follows.

• genbank(Genbank format)
• genbank_stripped(Genbank with EC numbers removed)
• embl(EMBL format)
• embl_stripped(EMBL with EC numbers stripped)
• gff3(GFF3 format)
• gff3_stripped(GFF3 with EC numbers stripped)
• rast_tarball(gzipped tar file of the entire job)

svr_retrieve_RAST_job username password jobnumber format > output-file

If necessary, an executing job may be killed:

svr_kill_RAST_job username password jobnumber

And deleted from the system entirely (careful, this may not be undone):

svr_delete_RAST_job username password jobnumber