FredHutch/batch-wrapper-client-golang

Name: batch-wrapper-client-golang

Owner: Fred Hutchinson Cancer Research Center

Description: golang wrapper client is easier to deploy

Created: 2018-03-05 03:23:46.0

Updated: 2018-03-05 03:24:09.0

Pushed: 2018-03-05 20:08:05.0

Homepage: null

Size: 1938

Language: Go

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README

Command-line wrapper for AWS Batch

As described in the AWS Batch At Fred Hutch documentation, Fred Hutch users must use a wrapper for some aspects of interacting with AWS Batch (submitting, terminating, and canceling jobs).

This wrapper is meant for command-line use only. The Python wrapper is in a separate repository.

Installation

Note that this wrapper is already installed on the rhino and gizmo systems. The command batchwrapper is already in your PATH.

For other systems, follow the instructions on the releases page.

Prerequisites

You must have previously obtained your AWS credentials and requested access to AWS Batch.

Usage

Usage is similar to that of the AWS CLI for Batch.

In fact, you should continue to use the CLI for everything except submitting jobs (submit-job), terminating jobs (terminate-job), and canceling jobs (cancel-job).

Running the batchwrapper command without any arguments gives brief help:

e: batchwrapper [<flags>] <command> [<args> ...]

el, terminate, and submit AWS Batch jobs. Full docs at
s;//bit.ly/HutchBatchDocs

s:
help  Show context-sensitive help (also try --help-long and --help-man).

ands:
lp [<command>...]
Show help.

ncel --job-id=JOB-ID --reason=REASON
Cancel a job you submitted

rminate --job-id=JOB-ID --reason=REASON
Terminate a job you submitted

bmit --cli-input-json=JSON_FILE
Submit a job

Submitting a job

You can get some help with batchwrapper submit --help:

e: batchwrapper submit --cli-input-json=JSON_FILE

it a job

s:
help                      Show context-sensitive help (also try --help-long
                          and --help-man).
cli-input-json=JSON_FILE  JSON file containing job info

To submit a job, you need to put the pertinent information in a JSON file. Unlike with the AWS CLI, you don't put the file:// prefix in front of the JSON file.

You can prepare a JSON file by following the example in the Fred Hutch batch documentation.

Assuming your JSON file is called job.json, you can submit it as follows:

hwrapper submit --cli-input-json job.json

The batch wrapper will return the Job ID and name.

Terminating a job

Brief help is available with batchwrapper terminate --help:

e: batchwrapper terminate --job-id=JOB-ID --reason=REASON

inate a job you submitted

s:
help           Show context-sensitive help (also try --help-long and
               --help-man).
job-id=JOB-ID  Job ID
reason=REASON  reason for termination

So, for example, you can terminate a job you own with the following command (replace the job ID with your own):

hwrapper terminate --job-id 13732097-3f5d-42bc-b60f-2cd166486074 \
-reason "there is a problem"

Canceling a job

Brief help is available with batchwrapper cancel --help:

e: batchwrapper cancel --job-id=JOB-ID --reason=REASON

el a job you submitted

s:
help           Show context-sensitive help (also try --help-long and
               --help-man).
job-id=JOB-ID  Job ID
reason=REASON  reason for termination

So, for example, you can cancel a job you own with the following command (replace the job ID with your own):

hwrapper cancel --job-id 13732097-3f5d-42bc-b60f-2cd166486074 \
-reason "there is a problem"