README

BisQue:

An application for the management and analysis of complex multi-dimensional data including bio-imaging and other scientific data.

How do I get set up?

• Original full instruction [http://biodev.ece.ucsb.edu/projects/bisque]

Quick setup using docker

1. Getting a running bisque server locally on your development machine
2. Using host mounted modules to make it easier to edit
3. Registering a module to your local server
4. Use an external data directory and database so you don't lose data when service stops
5. This script [https://bitbucket.org/CBIucsb/bisque-stable/downloads/build_bisque_docker_modules.sh] run the following commands for you.

Full instructions

0. Ensure you have the latest stable locally

     docker pull cbiucsb/bisque05:stable
   

1. Run a bisque server on the host port 9898:

```
docker run --name bisque --rm -p 9898:8080 cbiucsb/bisque05:stable
```
and point your browser at `http://<hostname>:9898`

2. Using host mounted modules to make it easier to edit.

   1. Copy the module directory out of the container

      docker cp bisque:/source/modules container-modules
   

   2. restart the container with host mounted module

      docker stop bisque
      docker run --name bisque --rm -p 9898:8080 -v $(pwd)/container-modules:/source/modules  cbiucsb/bisque05:stable
      

3. Registering a module to your local server

   • Login to your bisque server using admin:admin
   • Find the module manager under Admin button
   • put http://localhost:8080/engine_service in the right panel and hit load
     • use localhost:8080 here because it's internal to the container.
   • Drag and Drop "MetaData" to the left panel

4. Use an external data directory so you don't lose data when service stops

   • Uploaded image and workdirs are store in /source/data. You can change this to be a host mounted directory with

    docker run --name bisque --rm -p 9898:8080 -v $(pwd)/container-data:/source/data  cbiucsb/bisque05:stable
   

   • The default sqlite database is stored inside the container at /source/data/bisque.db
   • The uploaded images are stored inside the container at /source/data/imagedir

5. (Optional) Use an external database server for performance and durability

```
   docker run --name bisque --rm -p 9898:8080 -e BISQUE_DBURL=postgresql://dbhost:5432/bisque  cbiucsb/bisque05:stable
```

6. (Optional) All together:

```
    docker run --name bisque --rm -p 9898:8080 \
         -v $(pwd)/container-data:/source/data \
         -v $(pwd)/container-modules:/source/modules \
         -e BISQUE_DBURL=postgresql://dbhost:5432/bisque \
         cbiucsb/bisque05:stable

```

Contribution guidelines

• Writing tests
• Code review
• Other guidelines