index.md

site	documentclass	bibliography	biblio-style	link-citations	description	output
bookdown::bookdown_site	bookdown	book.bib packages.bib	apalike	true	Bisque (Bio-Image Semantic Query User Environment) : Store, visualize, organize and analyze images in the cloud.	bookdown::gitbook highlight pygments

Getting Started {-}

Our modules currently span research areas that include Material Science, Biological Science, Biomedical Imaging, and Marine Science.

Users can develop and deploy custom state of the art modules by simply containerizing their module with Docker.

BisQue Docker Installation {-}

If you would like to have your own version of BisQue with minimal effort, use the Docker version of BisQue. The source code installation can be found here.

1. Ensure you have the latest stable locally

     docker pull cbiucsb/bisque05:stable
   

2. Run a bisque server on the host port 8080:

     docker run --name bisque --rm -p 8080:8080 cbiucsb/bisque05:stable
   

and point your browser at http://<hostname>:8080

3. 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 8080:8080 -v $(pwd)/container-modules:/source/modules  cbiucsb/bisque05:stable
      

4. 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

5. 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 8080:8080 -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