Merge pull request #9 from pepkit/deployment_update

Update deployment Dockerfile

Dockerfile

@@ -1,6 +1,2 @@
-FROM databio/pephub:latest
-COPY peps/ /app/peps/
-COPY config.yaml /app
-COPY schemas.yaml /app
-RUN mkdir /app/uploads
-ENTRYPOINT [ "pephub", "serve", "--port", "80" ]
+FROM pephub
+# pass - nothing else is needed

README.md

@@ -1,59 +1,15 @@
-# data.pephub
-Data stores for the [pephub](https://github.com/pepkit/pephub) server. All PEPs hosted with pephub can be located here. New PEP's are added via pull requests to this repository.
-
-## Repository Structure
-PEPs are stored in this reopsitory under a hierarchical folder structure, `{namespace}/{project}/`. Namespace folders represent teams/organizations/labs. Inside each namespace folder, individual folders correspond to each PEP. For example:
-
-```
-├── ChangLab
-│   ├── PEP_1
-│   │   ├── 180113_mergeTable.csv
-│   │   ├── README.md
-│   │   ├── TCGA_AllSamples_FinalBamList_annotation.csv
-│   │   └── TCGA_AllSamples_FinalBamList_config.yaml
-│   └── PEP_2
-│       ├── 180113_mergeTable.csv
-│       ├── README.md
-│       ├── TCGA_AllSamples_FinalBamList_annotation.csv
-│       └── TCGA_AllSamples_FinalBamList_config.yaml
-└── demo
-    ├── BiocProject
-    │   ├── data
-    │   │   ├── laminB1Lads.bed
-    │   │   └── vistaEnhancers.bed
-    │   ├── project_config.yaml
-    │   ├── project_config_resize.yaml
-    │   ├── readBedFiles.R
-    │   ├── readBedFiles_resize.R
-    │   └── sample_table.csv
-    ├── BiocProject_exceptions
-    │   ├── project_config.yaml
-    │   ├── readBedFilesExceptions.R
-    │   └── sample_table.csv
-```
-
-## The `.pep.yaml` file
-By default, pephub assumes the project config will be named `project_config.yaml` (`<namespace>/<project>/project_config.yaml`). Optionally, users may use their own file naming conventions by including a `.pep.yaml` file inside the PEP folder. The `.pep.yaml` file should specify location of the project config like this:
-
-```yaml
-config_file: path/to/file.yaml
-```
+# pephub.databio.org
+This is the publically available instance of [PEPhub](https://github.com/pepkit/pephub) provided by the Sheffield lab. You can view the deployed instance at https://pephub.databio.org
 
 ## Development
-To test/develop the server locally, **build and run** the docker containers:
-
-### Build:
-```
-docker build -t pephub .
+### Build the container
 ```
-
-### Run
-```
-docker run -p 80:80 --name pephub pephub
+docker build -t pephub.databio.org .
 ```
 
-Visit http://localhost:80 to view the server.
-
-## Contributing a PEP
+### Launch
+PEPhub requires many parameters to run. You can read more about those [here](https://github.com/pepkit/pephub/blob/master/docs/server-settings.md). These must be injected as environment variables. You can manually do this and inject one-by-one. There is an example script in this repo called [launch_docker.sh](launch_docker.sh).
 
-If you would like to contribute a PEP, please do so by forking this repository and creating a pull-request where the PEP will be verified and merged.
+ ```
+ launch_docker.sh
+ ```

launch_docker.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+docker run -p 80:80 \
+    --env POSTGRES_HOST=$POSTGRES_HOST \
+    --env POSTGRES_DB=$POSTGRES_DB \
+    --env POSTGRES_USER=$POSTGRES_USER \
+    --env POSTGRES_PASSWORD=$POSTGRES_PASSWORD \
+    --env QDRANT_HOST=$QDRANT_HOST \
+    --env QDRANT_PORT=$QDRANT_PORT \
+    --env QDRANT_ENABLED=$QDRANT_ENABLED \
+    --env QDRANT_API_KEY=$QDRANT_API_KEY \
+    --env HF_MODEL=$HF_MODEL \
+    --env GH_CLIENT_ID=$GH_CLIENT_ID \
+    --env GH_CLIENT_SECRET=$GH_CLIENT_SECRET \
+    --env BASE_URI=$BASE_URI \
+    databio.pephub.org