p3-submit-genome-annotation

Submit a BV-BRC Genome Annotation Job

p3-submit-genome-annotation [options] output-path output-name

Submit a genome to the BV-BRC genome annotation service.

Usage synopsis

p3-submit-genome-annotation [-dfghnPpt] [long options…] output-path output-name

Submit an annotation job with output written to output-path and named output-name. The output-path parameter is a BV-BRC workspace path. The output-name parameter is a name that will describe this annotation in the workspace. It may not contain slash (/) characters.

The following options describe the inputs to the annotation.

-p STR --workspace-path-prefix STR    Prefix for workspace pathnames
                                      as given to input parameters.
-P STR --workspace-upload-path STR    If local pathnames are given as
                                      genbank or contigs file
                                      parameters, upload the files to
                                      this directory in the
                                      workspace. Defaults to the
                                      output path.
-f --overwrite                        If a file to be uploaded
                                      already exists in the
                                      workspace, overwrite it on
                                      upload. Otherwise we will not
                                      continue the service submission.
--genbank-file STR                    A genbank file to be annotated.
--contigs-file STR                    A file of DNA contigs to be
                                      annotated.
--phage                               Set defaults for phage
                                      annotation.
--recipe STR                          Use the given non-default
                                      recipe for this annotation
--reference-genome STR                The BV-BRC identifier of a
                                      reference genome whose
                                      annotations will be propagated
                                      as part of this annotation.
--reference-virus STR                 The name of a virus from the
                                      VIGOR_DB collection to use as
                                      the reference for a vigor4
                                      viral annotation.

The following options describe the genome to be annotated.
In each case where the value for the specified option may be drawn
from a submitted genbank file it is optional to supply the value.
If a value is supplied, it will override the value in the genbank file.

-n STR --scientific-name STR          Scientific name for this genome.
-t INT --taxonomy-id INT              Numeric NCBI taxonomy ID for
                                      this genome. If not specified
                                      an estimate will be computed,
                                      and if that is not possible the
                                      catchall taxonomy ID 6666666
                                      will be used.
-g INT --genetic-code INT             Genetic code for this genome;
                                      either 11 or 4. If not
                                      specified defaults to 11 unless
                                      it can be determined from the
                                      declared or computed taxonomy
                                      ID.
-d STR --domain STR                   Domain for this genome
                                      (Bacteria or Archaea)

Advanced options:

--workflow-file STR                   Use the given workflow document
                                      to process annotate this genome.
--import-only                         Import this genome as is - do
                                      not reannotate gene calls or
                                      gene function. Only valid for
                                      genbank file input.
--raw-import-only                     Perform a raw import on this
                                      this genome - do not reannotate
                                      gene calls or gene function and
                                      perform a bare minimum of
                                      postprocessing. Only valid for
                                      genbank file input
--skip-contigs                        Do not load contigs data. Only
                                      valid for genbank file input.
--index-nowait                        Do not wait for indexing to
                                      complete before the job is
                                      marked as complete.
--no-index                            Do not index this genome. If
                                      this option is selected the
                                      genome will not be visible on
                                      the BV-BRC website.
--no-workspace-output                 Do not write any workspace
                                      output.
--dry-run                             Dry run. Upload files and
                                      validate input but do not
                                      submit annotation

-h --help                             Show this help message