/ 
Bio-CIPRES-0.005
River stage zero No dependents
/ run_cipres

NAME

run_cipres - run a CIPRES tool via the REST API and fetch all outputs

SYNOPSIS

run_cipres --tool_id SOME_TOOL --dir_out /path/to/outputs --input key=file --param key=value [...]

DESCRIPTION

This tool takes a tool ID and set of input files, submits a job to CIPRES, and fetches the results upon completion. The command line syntax is described further below.

PREREQUISITES

Requires the following non-core Perl libraries to be installed:

Bio::CIPRES

OPTIONS

--tool_id string

(Required) The tool ID as expected by CIPRES (e.g. 'BWA_XSEDE')

--dir_out path

(Required) The directory to which output files are written. Will be created if it doesn't already exist.

--runtime path

The time (in hours) requested for the run. Setting this too low will result in the job timing out before completion. Setting it too high may increase the time that the job waits in the queue to be run. If in doubt, err on the long size. Default: 0.5

--input key=filename

Specifies an input file to be submitted with the job. The value of this option is itself a key/value pair separated by a '='. The first part must correspond exactly to an input ID as expected by CIPRES. To find this you will probably need to read through the PISE XML file. The second part is the path to the file on disk. This option may (and often will) be specified multiple times, but the key must be unique each time or it will be silently overwritten.

--param key=value

Specifies an extra parameter to be submitted with the job. The value of this option is itself a key/value pair separated by a '='. The first part must correspond exactly to a parameter ID as expected by CIPRES. To find this you will probably need to read through the PISE XML file. The second part is the value of the parameter to be sent. This option may (and often will) be specified multiple times, but the key must be unique each time or it will be silently overwritten.

CAVEATS AND BUGS

Please submit bug reports to the issue tracker in the distribution repository.

AUTHOR

Jeremy Volkening (jdv@base2bio.com)

LICENSE AND COPYRIGHT

Copyright 2014-19 Jeremy Volkening

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.