Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[IBCDPE-386] Update README.md #93

Merged
merged 1 commit into from
Oct 11, 2023
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 6 additions & 6 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -60,9 +60,9 @@ The instructions to trigger the workflow can be found at [Sage-Bionetworks-Workf
Your configured Synapse credentials can be used to run this package both locally and using Docker, as outlined below.

### Locally
Perform the following one-time steps to set up your local environment and to obtain the required Synapse permissions:
Perform the following one-time steps to set up your local environment and obtain the required Synapse permissions:

1. This package uses Python, if you have not already, please install [pyenv](https://github.com/pyenv/pyenv#installation) to manage your Python versions. Versions supported by this package are all versions >=3.7 and <3.11. If you do not install pyenv make sure that Python and `pip` are installed correctly and have been added to your PATH by running `python3 --version` and `pip3 --version`. If your installation was successful, your terminal will return the versions of Python and `pip` that you installed. **Note**: If you have `pyenv` it will install a specific version of Python for you.
1. This package uses Python, if you have not already, please install [pyenv](https://github.com/pyenv/pyenv#installation) to manage your Python versions. Versions supported by this package are all versions >=3.7 and <3.11. If you do not install `pyenv` make sure that Python and `pip` are installed correctly and have been added to your PATH by running `python3 --version` and `pip3 --version`. If your installation was successful, your terminal will return the versions of Python and `pip` that you installed. **Note**: If you have `pyenv` it will install a specific version of Python for you.

2. Install `pipenv` by running `pip install pipenv`.

Expand All @@ -88,22 +88,22 @@ Perform the following one-time steps to set up your local environment and to obt

### Docker

There is a publicly available [DockerHub repository](https://hub.docker.com/r/sagebionetworks/agora-data-tools) automatically built via DockerHub. That said, you may want to develop using Docker locally on a feature branch.
There is a publicly available [GHCR repository]([https://hub.docker.com/r/sagebionetworks/agora-data-tools](https://github.com/Sage-Bionetworks/agora-data-tools/pkgs/container/agora-data-tools)) automatically built via GitHub Actions. That said, you may want to develop using Docker locally on a feature branch.

If you don't want to deal with Python paths and dependencies, you can use Docker to run the pipeline. Perform the following one-time step to set up your docker environment and to obtain the required Synapse permissions:
If you don't want to deal with Python paths and dependencies, you can use Docker to run the pipeline. Perform the following one-time step to set up your Docker environment and obtain the required Synapse permissions:
1. Install [Docker](https://docs.docker.com/get-docker/).

Once you have completed the one-time setup step outlined above, execute the pipeline by running the following command and providing your PAT and the desired [config file](#config) as an argument. The following example command will execute the pipeline in Docker using ```test_config.yaml```:

```
# This creates a local docker image
# This creates a local Docker image
docker build -t agora-data-tools .
docker run -e SYNAPSE_AUTH_TOKEN=<your PAT> agora-data-tools adt test_config.yaml
```

## Testing Github Workflow
In order to test the GitHub Actions workflow locally:
- install [act](https://github.com/nektos/act) and [docker](https://github.com/docker/docker-install)
- install [act](https://github.com/nektos/act) and [Docker](https://github.com/docker/docker-install)
- create a .secrets file in the root directory of the folder with a SYNAPSE_USER and a SYNAPSE_PASS value*

Then run:
Expand Down
Loading