Using Nipype with Amazon Web Services (AWS)

Several groups have been successfully using Nipype on AWS. This procedure involves setting a temporary cluster using StarCluster and potentially transferring files to/from S3. The latter is supported by Nipype through DataSink and S3DataGrabber.

Using DataSink with S3

The DataSink class now supports sending output data directly to an AWS S3 bucket. It does this through the introduction of several input attributes to the DataSink interface and by parsing the base_directory attribute. This class uses the boto3 and botocore Python packages to interact with AWS. To configure the DataSink to write data to S3, the user must set the base_directory property to an S3-style filepath.

For example:

In [ ]:
from import DataSink
ds = DataSink()
ds.inputs.base_directory = 's3://mybucket/path/to/output/dir'

With the "s3://" prefix in the path, the DataSink knows that the output directory to send files is on S3 in the bucket "mybucket". "path/to/output/dir" is the relative directory path within the bucket "mybucket" where output data will be uploaded to (Note: if the relative path specified contains folders that don’t exist in the bucket, the DataSink will create them). The DataSink treats the S3 base directory exactly as it would a local directory, maintaining support for containers, substitutions, subfolders, "." notation, etc. to route output data appropriately.

There are four new attributes introduced with S3-compatibility: creds_path, encrypt_bucket_keys, local_copy, and bucket.

In [ ]:
ds.inputs.creds_path = '/home/neuro/aws_creds/credentials.csv'
ds.inputs.encrypt_bucket_keys = True
ds.local_copy = '/home/neuro/workflow_outputs/local_backup'

creds_path is a file path where the user's AWS credentials file (typically a csv) is stored. This credentials file should contain the AWS access key id and secret access key and should be formatted as one of the following (these formats are how Amazon provides the credentials file by default when first downloaded).

Root-account user:



User Name,Access Key Id,Secret Access Key

The creds_path is necessary when writing files to a bucket that has restricted access (almost no buckets are publicly writable). If creds_path is not specified, the DataSink will check the AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY environment variables and use those values for bucket access.

encrypt_bucket_keys is a boolean flag that indicates whether to encrypt the output data on S3, using server-side AES-256 encryption. This is useful if the data being output is sensitive and one desires an extra layer of security on the data. By default, this is turned off.

local_copy is a string of the filepath where local copies of the output data are stored in addition to those sent to S3. This is useful if one wants to keep a backup version of the data stored on their local computer. By default, this is turned off.

bucket is a boto3 Bucket object that the user can use to overwrite the bucket specified in their base_directory. This can be useful if one has to manually create a bucket instance on their own using special credentials (or using a mock server like fakes3). This is typically used for developers unit-testing the DataSink class. Most users do not need to use this attribute for actual workflows. This is an optional argument.

Finally, the user needs only to specify the input attributes for any incoming data to the node, and the outputs will be written to their S3 bucket.

workflow.connect(inputnode, 'subject_id', ds, 'container')
workflow.connect(realigner, 'realigned_files', ds, 'motion')

So, for example, outputs for sub001’s realigned_file1.nii.gz will be in:


Using S3DataGrabber

Coming soon...

Home | github | Nipype