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Documentation Updates #34

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6 changes: 4 additions & 2 deletions README.md
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Expand Up @@ -15,7 +15,7 @@ This Python package provides the components to connect various third-party servi

This repository includes a demonstration script called [`demo.py`](demo.py), which showcases how you can use `py-orca` to launch and monitor your workflows on Nextflow Tower. Specifically, it illustrates how to process an RNA-seq dataset using a series of workflow runs, namely `nf-synstage`, `nf-core/rnaseq`, and `nf-synindex`. `py-orca` can be used with any Python-compatible workflow management system to orchestrate each step (_e.g._ Airflow, Prefect, Dagster). The demonstration script uses [Metaflow](https://metaflow.org/) because it's easy to run locally and has an intuitive syntax.

The script assumes that the following environment variables are set.
The script assumes that the following environment variables are set. Before setting up these environment variables, ensure that you have an AWS profile configured for a role that has access to the dev/ops tower workspace you plan to launch your workflows from.
Refer to [`.env.example`](.env.example) for the format of their values as well as examples. You can set these environment variables using whatever method you prefer (_e.g._ using an `.env` file, sourcing a shell script).

- `NEXTFLOWTOWER_CONNECTION_URI`
Expand All @@ -24,7 +24,9 @@ Refer to [`.env.example`](.env.example) for the format of their values as well a

Once your environment is set, you can create a virtual environment, install the Python dependencies, and run the demonstration script (after downloading it) as follows. Note that you will need to update the `s3_prefix` parameter so that it points to an S3 bucket that is accessible to your Tower workspace.

### Manually creating a virtual environment
### Creating and setting up your py-`orca` virtual environment and executing `demo.py`

Below are the instructions for creating and setting up your virtual environment and executing the `demo.py` If you would like to set up a developer environment with the relevant dependencies, you can execute the shell script [dev_setup](https://github.com/Sage-Bionetworks-Workflows/py-orca/blob/main/dev_setup.sh).
```bash
# Create and activate a Python virtual environment (tested with Python 3.10)
python3 -m venv venv/
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