FredHutch/batch-demo

Name: batch-demo

Owner: Fred Hutchinson Cancer Research Center

Description: null

Created: 2017-12-12 20:26:36.0

Updated: 2017-12-12 21:53:05.0

Pushed: 2017-12-13 00:19:07.0

Homepage: null

Size: 6

Language: Python

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README

Simple Array Job example in AWS Batch

Before trying this example, please read the documentation for using AWS Batch at Fred Hutch. In particular, be sure you understand how to set up your AWS credentials, and make sure you have asked for and received the permissions necessary to run AWS Batch.

Running the example

The following commands should be run on one of the Center's Linux servers (you should either be connected to one of the rhino machines via ssh or to one of the NX servers (manx, sphinx, lynx, etc.) via NoMachine).

Step 1: Clone the repository

Clone this repository:

clone https://github.com/FredHutch/batch-demo.git
atch-demo

Step 2: Edit variables

Edit the file setup.sh. Change the value of BUCKET_NAME to your lab's bucket. If your PI's name is Jane Doe, your lab's bucket name is fh-pi-doe-j.

Change the value of BATCH_USER to your HutchNet ID (your email address without the @fredhutch.org).

These changes are necessary because each user only has permission to write to their own PI's bucket. Within that bucket, your username will make it clear who the files belong to.

Source the setup file

Now source the file setup.sh as follows:

ce setup.sh

This will export the variables BUCKET_NAME and BATCH_USER to your shell and make them available to the commands you are now going to run.

Step 3: Set up the Job Definition