mBARq app

Streamlit application to run a versatile and user-friendly framework for the analysis and interpretation of RB-TnSeq and other barcoded sequencing data.

Changes for deploy:

• Versions relaxed in the requirements file:

  • altair == 4.2
  • streamlit == 1.23.1
  • biopython == 1.79

• The old requirements file is preserved in requirements_bu20240115.txt

How to run in docker

docker build -t mbarq_app:0.1 .
docker run -p 8501:8501 mbarq_app:0.1
# check if the app is healthy
curl -i http://localhost:8501
HTTP/1.1 200 OK
Server: TornadoServer/6.4
Content-Type: text/html
Date: Fri, 22 Mar 2024 11:03:55 GMT
Accept-Ranges: bytes
Etag: "85c873604085732a292417b9cda592560938848813798b7e98d66d9233d2cb072ae85d199d602a71e2e1f49164da4f0d8d2fafb374dc2a2314fa439bdc4b76bd"
Last-Modified: Fri, 22 Mar 2024 10:41:59 GMT
Cache-Control: no-cache
Content-Length: 891
Vary: Accept-Encoding

Instructions to deploy in the server

Prerequisite

• Docker !!! Ensure you can do docker without sudo in your local env
• Access the micro-flask server micro-flask-dev.ethz.ch

By Script

1. run the script

chmod +x buildDockerToServer.sh
./buildDockerToServer.sh

2. login the server and run the bash script to redeploy docker

cd /docker-run
./clean_docker_and_restart-mbarq.sh

3. check if https://mbarq.microbiomics.io/ is running