Usage:
abi-load
abi-load [ ] [ ]
input-spec:
( -r | --run-xml ) path # path to run.xml describing input files
spot-descriptor:
( -e | --experiment ) path # path to experiment.xml
# with spot descriptor
output-spec:
# produce output to run
output-mode:
-c | --create # create only new run (fail if exists)
-o | --output # create new or replace existing run
-a | --append # create new or update existing run
run-name:
path # full or working-directory relative
# file-system path to run
options:
( -n | --spotnumber) spots_to_run # tells the loader to stop processing after that many spots
# helpful in testing
( -b | --bad-spot-number ) bad_spot_number # number of spot creation errors to be tolerated
# default = 50
( -p | --bad-spot-percentage ) bad_spot_percentage> # PERCENTAGE of the number of bad spots against
# the number of good spots, default = 5
help:
( -h | --help ) # print usage and option details
verbosity:
( -l | --log-level ) #logging level: fatal|sys|int|err|warn|info default=info
debug:
( -+ | --debug ) #module: APP|KFS|XML|VDB|SRA|REF|LEGREF default=APP