简介

mccloud_cli是McCloud服务的一个命令行界面。McCloud提供了一个简单的手段，在云中运行Shasta基因组组装。 mccloud_cli可以生成预签名URL，用于McCloud Web UI，并可以直接从命令行提交McCloud作业。

要使用mccloud_cli，您必须安装并正确设置AWS命令行，使其与您的AWS账户协同工作。有关此先决条件的更多信息，请参阅AWS CLI用户指南。

快速入门

1. 确保您已安装AWS CLI并正确设置，使其与您的账户协同工作。一个好的测试是能够成功将数据移动到您的自己的S3桶中（例如，aws --profile your-aws-profile-name s3 ls s3://your-bucket-name/）
2. [可选] 我们强烈建议您在虚拟环境中运行所有Python程序。设置并激活虚拟环境。
3. pip install mccloud-cli
4. mccloud_cli --help

预签名URL示例

mccloud_cli 可以生成 AWS 预签名 URL。这在你想要将数据存储在你自己的 AWS S3 桶中（即私有的）时很有用，但暂时授予 McCloud 读取输入数据的访问权限，并将结果写回到你的桶中。

重要提示：AWS S3 预签名 URL 是一种标准的数据共享方式，但假设你不会将 URL 分享给任何人。有关预签名 URL 的更多信息，请阅读 AWS S3 用户指南。

使用方法

$ 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.

例如

$ 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=...

作业提交示例

mccloud_cli 也可以从命令行直接提交作业。输入和输出 URL 必须是你有权访问的桶中的 https URL 或 s3 URL。

使用方法

$ 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.

例如

$ 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