Skip to content

Commit

Permalink
Update example usage, suggest to open labeled issues for support
Browse files Browse the repository at this point in the history
  • Loading branch information
matthewwiese committed Aug 22, 2023
1 parent 533240c commit 3dc0ff3
Show file tree
Hide file tree
Showing 3 changed files with 27 additions and 1 deletion.
7 changes: 7 additions & 0 deletions docs/_config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,3 +3,10 @@ description: "The Breeder Genomics Hub is a batteries-included JupyterHub distri
remote_theme: just-the-docs/just-the-docs
plugins:
- jekyll-remote-theme

color_scheme: nil
callouts_level: quiet
callouts:
note:
title: Note
color: blue
17 changes: 16 additions & 1 deletion docs/example.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,14 @@ This page of the documentation will walk you through how to set up the Breeder G

## Set Up
### Load Public Maize 2.1 Database Dump

{: .note }
> You will need to add a line to `prod.env` for the Postgres read-only user's password:
>
> ```
> PGPASSWORD=<Password for read_only_user>
> ```
Before running the Compose script, you must load the public maize data into Postgres. To do so, follow the steps below:
1. Ensure the most recent public maize release is stored on the mounted `/mnt/volume_nyc3_01/20230717_public_maize_2_1` volume.
2. Execute the [`load_maize.sh`](https://github.com/maize-genetics/breeder-genomics-hub/blob/main/example/load_maize.sh) script from within the `example/` directory.
Expand All @@ -25,4 +33,11 @@ Source: [Lynn's instructions](https://bucklerlab.slack.com/archives/CCJ65QR0U/p1
From the root of this repository:
```console
docker compose -f hub.yml -f example/example.yml up -d
```
```

The second `-f` will apply [`example.yml`](https://github.com/maize-genetics/breeder-genomics-hub/blob/main/example/example.yml) as a [Compose merge](https://docs.docker.com/compose/multiple-compose-files/merge/) on top of `hub.yml`. This is a powerful feature of Docker Compose, enabling you to extend the Breeder Genomics Hub without having to modify `hub.yml` itself, providing for easy `git pull` updates.

### Extending / Developing
Chances are that the Breeder Genomics Hub doesn't satisfy all your lab's requirements. Given this reality, the project is [distributed under the MIT license](https://github.com/maize-genetics/breeder-genomics-hub/blob/main/LICENSE) and users are encouraged to modify or extend the various configuration files in order to best meet their research objectives.

If you encounter problems while doing so, or otherwise have questions, please [open an issue with the "support" label](https://github.com/maize-genetics/breeder-genomics-hub/issues/new?labels=support) and we will do our best to help you out!
4 changes: 4 additions & 0 deletions docs/getting-started.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,10 @@ permalink: /getting-started
---

# Getting Started

{: .note }
> If you have questions about using or deploying your own Breeder Genomics Hub, [create a GitHub issue with the "support" label](https://github.com/maize-genetics/breeder-genomics-hub/issues/new?labels=support)!
## Quick Start
Clone the repository:
```bash
Expand Down

0 comments on commit 3dc0ff3

Please sign in to comment.