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Update README.md
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jbygdell committed Nov 16, 2023
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Expand Up @@ -9,6 +9,7 @@ cp ./config/config.yaml.example ./config/config.yaml
cp ./config/iss.json.example ./config/iss.json
cp ./.env.example ./.env
```

no further editing to the above files is required for running the stack locally.

## Starting the full stack with LS-AAI-mock
Expand All @@ -18,15 +19,15 @@ the file `docker-compose.yml`. Note that this requires a running [`LS-AAI-mock`]

Add the following line to `/etc/hosts` file:

```
```conf
127.0.0.1 aai-mock
```

First clone the [startet-kit-lsaai-mock](https://github.com/GenomicDataInfrastructure/starter-kit-lsaai-mock) repo.

Under its root folder, change the first two lines of the file `configuration/aai-mock/application.properties` to:

```
```conf
main.oidc.issuer.url=http://aai-mock:8080/oidc/
web.baseURL=https://aai-mock:8080/oidc
```
Expand Down Expand Up @@ -62,7 +63,7 @@ Note that the above two commands need to be run in that specific order because t

The file `docker-compose-demo.yml` is used to start the `storage-and-interfaces` services in *demo* mode with an example dataset preloaded and ingested to the sensitive data archive when the deployment is done. This comes with its own python implementation of a mock-oidc in place of LS-AAI and can be run as standalone for demonstration purposes.

The files imported by the data loading script come from here: https://github.com/ga4gh/htsget-refserver/tree/main/data/gcp/gatk-test-data/wgs_bam
The files imported by the data loading script comes from [here:](https://github.com/ga4gh/htsget-refserver/tree/main/data/gcp/gatk-test-data/wgs_bam)

To deploy use the following command:

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