mccloud-cli 0.0.3

A command line to assist McCloud users.

Intro

mccloud_cli is a command line interface to the McCloud service. McCloud provides a simple means to start a Shasta assembly in the cloud.

mccloud_cli currently provides an easy means to generate presigned URLs to use with the McCloud. Eventually it will also provide a means to submit jobs directly from the command line.

Quick start

1. [optional] we highly suggest you run all python programs in a virtual environment.
2. pip install mccloud-cli
3. mccloud_cli --help

Presigned URLs example

mccloud_cli will generate AWS presigned URLs. This is useful when you want to store your data in your own AWS S3 bucket (ie, privately), but want to temporarily grant McCloud access to read input data, and write results back to your bucket.

Usage:

$ mccloud_cli generate-s3-presigned-url --help
Usage: mccloud_cli generate-s3-presigned-url [OPTIONS]

Options:
  --profile TEXT             Use a specific profile from your AWS credential file.
  --no-confirmation BOOLEAN  Perform requested actions without user confirmation.
  -i, --input-url TEXT       S3 URL which will be presigned to allow READ (input) access.
  -o, --output-url TEXT      S3 URL which will be presigned to allow WRITE (output) access.
  --expires-in INTEGER       Number of seconds until the pre-signed URLs expire.  [default: 28800]
  --help                     Show this message and exit.

For example:

$ mccloud_cli generate-s3-presigned-url --profile my-aws-profile -i s3://my-bucket/reads.fasta.gz -o s3://my-bucket/results.tar.gz

This action will generate AWS S3 presigned URLs for the input and output URLs you have specified, with an expiration time 28800 seconds [8 hours] from now.

Read (input) URLs:
------------------
s3://my-bucket/reads.fasta.gz

Write (output) URLs:
--------------------
s3://my-bucket/results.tar.gz
        
Do you wish to proceed? [y/N]: Y

Your presigned URLs will expire in 8 hours.

Please launch the McCloud job with these URLs.

Presigned INPUT URLs:
---------------------
https://s3.amazonaws.com/my-bucket/reads.fasta.gz?AWSAccessKeyId=...

Presigned OUTPUT URLs:
----------------------
https://s3.amazonaws.com/my-bucket/results.tar.gz?AWSAccessKeyId=...