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https://github.com/refgenie/seqcolapi
https://github.com/refgenie/seqcolapi
Last synced: about 2 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/refgenie/seqcolapi
- Owner: refgenie
- License: bsd-2-clause
- Created: 2021-01-28T15:41:33.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2024-07-06T01:42:08.000Z (7 months ago)
- Last Synced: 2024-07-06T04:31:05.424Z (7 months ago)
- Language: Python
- Size: 199 KB
- Stars: 0
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
# seqcolapi
This repository contains:
1. Sequence collections API software (the `seqcolapi` package). This package is based on the `refget` package. It simply provides an wrapper to implement the Sequence Collections API.
2. Configuration and GitHub Actions for demo server instance ([servers subfolder](/servers)).
## Instructions
### Run locally for development
To run a local server with a **local database**:
```
source servers/localhost/dev_local.env
uvicorn seqcolapi.main:app --reload --port 8100
```
To run a local server with **the production database**:
```
source servers/seqcolapi.databio.org/production.env
uvicorn seqcolapi.main:app --reload --port 8100
```
### Running with docker
To build the docker file:
```
docker build --no-cache -t scim .
```
To run in a container:
```
export POSTGRES_PASSWORD=`pass aws/rds_postgres`
docker run --rm -p 8000:8000 --name sccon \
--env "POSTGRES_PASSWORD" \
--volume $CODE/seqcolapi.databio.org/config/seqcolapi.yaml:/config.yaml \
scim seqcolapi serve -c /config.yaml -p 8000
```
To deploy container to dockerhub:
Use github action in this repo which deploys on release, or through manual dispatch.
Left to do:
- [x] it already retrieves from a refget server.
- [x] let me insert stuff using only checksums.
- [ ] make it take 2 refget servers correctly.
## To load new data into seqcolapi.databio.org
```
cd analysis
source ../servers/localhost/dev_local.env
ipython3
```
Now run `load_fasta.py`
## Deploy to AWS ECS
### Testing locally first
Build the seqcolapi image
```
cd
docker build -t docker.io/databio/seqcolapi:latest .
```
```
docker pull docker.io/databio/seqcolapi:latest
cd servers/seqcolapi.databio.org
docker build -t scim .
docker run \
-e POSTGRES_HOST=$POSTGRES_HOST \
-e POSTGRES_PASSWORD=$POSTGRES_PASSWORD \
--network=host \
scim
```
### Deploying
To upgrade the software:
Use config file located in `/servers/seqcolapi.databio.org`. This will use the image in docker.io://databio/seqcolapi, github repo: [refgenie/seqcolapi](https://github.com/refgenie/seqcolapi) as base, bundle it with the above config, and deploy to the shefflab ECS.
1. Ensure the [refget](https://github.com/refgenie/refget/) package master branch is as you want it.
2. Deploy the updated [secqolapi](https://github.com/refgenie/seqcolapi/) app to dockerhub (using manual dispatch, or deploy on github release).
3. Finally, deploy the instance with manual dispatch using the included GitHub action.