Package: mccloud-cli
Intromccloud_cliis a command line interface to the McCloud service. McCloud provides
a simple means to run aShastagenome assembly
in the cloud.mccloud_clican generate presigned URLs for use with the
McCloud web UI, and submit McCloud jobs directly from the command line.To usemccloud_cli, you must have theAWS command lineset up and working
correctly with your AWS account. Please refer to theAWS CLI User Guidefor more information on this prerequisite.Quick startEnsure you have the AWS CLI installed and working correctly with your account.
A good test is the ability to successfully move data in and out of your own
S3 bucket (e.g.,aws --profile your-aws-profile-name s3 ls s3://your-bucket-name/)[optional] We highly reccommend that you run all python programs in avirtual environment. Set up
and activate a virtual environment.pip install mccloud-climccloud_cli --helpPresigned URLs examplemccloud_clican generate AWS presigned URLs. This is useful when you want to store your
data inyour ownAWS S3 bucket (i.e., privately), but temporarily grant McCloud
access to read input data, and write results back to your bucket.IMPORTANT: AWS S3 presigned URLs are a standard way to share data, but make the assumption
that you won't share the URL with anyone. For more information on presigned URLs, please read theAWS S3 User Guide.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.
  --expires-in INTEGER       Number of seconds until the pre-signed URLs expire.  [default: 172800]
  --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 172800 seconds [2 days] from now.

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

Do you wish to proceed? [y/N]: y

Your presigned URLs will expire in 24 hours.

Please launch the McCloud job with these URLs.

Presigned INPUT URLs:
---------------------
https://s3.amazonaws.com/my-bucket/reads.fasta.gz?AWSAccessKeyId=...Job submission examplemccloud_cliwill also submit jobs directly from the command line. Input and output URLs must
behttpsURLs ors3URLs in a bucket you have access to.Usage:$ mccloud_cli submit-job --help
Usage: mccloud_cli submit-job [OPTIONS]

Options:
  --mcat TEXT                     McCloud Access Token, ie, MCAT-****.  [required]
  --email EMAIL ADDRESS           Email address for job notifications.  [required]
  -i, --input-url TEXT            S3 URL which will be presigned to allow READ (input) access.  [required]
  -o, --output-url TEXT           A single S3 URL which McCloud has write access to.  [required]
  --shasta-version TEXT           [required]
  --shasta-config TEXT            [required]
  --shasta-cli-opts TEXT
  --I-have-read-and-agree-to-McCloud-terms-of-use
                                  Confirm that you have read, and agree to, the McCloud terms of use, available at
                                  https://mccloud.czi.technology/terms-of-use
  --tail-job-log                  After job is submitted, print out job log messages.
  --profile TEXT                  Use a specific profile from your AWS credential file.
  --help                          Show this message and exit.For example:$ mccloud_cli submit-job --mcat 'MCAT-XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX' --email my@email.com --profile my-aws-profile -i s3://my-bucket/reads.fasta.gz -o s3://my-bucket/output-folder --shasta-version 0.7.0 --shasta-config Nanopore-Sep2020
I have read and agree to mccloud terms of use [y/N]: Y
Starting McCloud job, id = ec39baa4-ea68-4c1e-8040-40277b2a48a0
You can view logs at https://mccloud.czi.technology/jobs/ec39baa4-ea68-4c1e-8040-40277b2a48a0/monitor