semvec/pypi-packages huggingface dataset:
miniwdl-aws-studio 0.0.2
AWS CDK app to add miniwdl+GWFCore to existing SageMaker Studio
Requires Python: >=3.6


# miniwdl + GWFCore + SageMaker Studio

This repository is a recipe for deploying **[miniwdl-aws](https://github.com/miniwdl-ext/miniwdl-aws)** and [GWFCore](https://github.com/aws-samples/aws-genomics-workflows) to use within [Amazon SageMaker Studio](https://aws.amazon.com/sagemaker/studio/), a web IDE with a terminal and filesystem browser. You can use the terminal to operate `miniwdl run` against GWFCore's AWS Batch stack, the filesystem browser to manage the inputs and outputs on EFS, and the Jupyter notebooks to further analyze the outputs.

## CDK boilerplate

The `cdk.json` file tells the CDK Toolkit how to execute your app.

This project is set up like a standard Python project.  The initialization
process also creates a virtualenv within this project, stored under the `.venv`
directory.  To create the virtualenv it assumes that there is a `python3`
(or `python` for Windows) executable in your path with access to the `venv`
package. If for any reason the automatic creation of the virtualenv fails,
you can create the virtualenv manually.

To manually create a virtualenv on MacOS and Linux:

```
$ python3 -m venv .venv
```

After the init process completes and the virtualenv is created, you can use the following
step to activate your virtualenv.

```
$ source .venv/bin/activate
```

If you are a Windows platform, you would activate the virtualenv like this:

```
% .venv\Scripts\activate.bat
```

Once the virtualenv is activated, you can install the required dependencies.

```
$ pip install -r requirements.txt
```

At this point you can now synthesize the CloudFormation template for this code.

```
$ cdk synth
```

To add additional dependencies, for example other CDK libraries, just add
them to your `setup.py` file and rerun the `pip install -r requirements.txt`
command.

## Useful commands

 * `cdk ls`          list all stacks in the app
 * `cdk synth`       emits the synthesized CloudFormation template
 * `cdk deploy`      deploy this stack to your default AWS account/region
 * `cdk diff`        compare deployed stack with current state
 * `cdk docs`        open CDK documentation

Enjoy!
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