bisweb/devel repository overview

This container contains both the source code and a build of BioImageSuite Web. It is meant to aid users who are interested in working with the source code of the software. The container can store the source code (and the internal user's home directory) either inside the container (in /home/user) or in an external volume/directory mounted in /hostfiles. If you prefer to store all files inside the container, you can start it using

       docker run  -it  -p 8080:8080 -p 24000:24000 bisweb/devel 

If you prefer to store your data in an external directory on the host, you start the container in full transient mode using a script of the form⁠:

  #!/bin/bash

  # Directory to store persistent data in (the container will create a folder biswebcontainer inside this)
  DIR=${HOME} 

  # User id to match external user to sync permissions
  USERID=`id -u $USER`

  docker run --rm  -it  -p 8080:8080 -p 24000:24000 \
      --mount src=${DIR},target=/hostfiles,type=bind \
       -e LOCAL_USER_ID=${USERID} \
       bisweb/devel 

If you are using Windows: take a look at the script file dockerrun.bat⁠

Here is some additional information:

• The main build script isfullbuild.sh -- this builds bisweb. This is located in ${HOME}/bisweb/src/compiletools.

• Once this is done you can find zip/tar.gz files of the various components in

    ${HOME}/bisweb/src/build/install
  

  Copy

• To run the JS development environment simply type:

    cd ${HOME}/bisweb/src
    gulp
  

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Details as to how the build is performed can be found in the four component scripts (which are also located in ${HOME}/bisweb/src/build on the container disk):

• nativebuild.sh -- builds the C++ code for use from python/matlab
• testbuild.sh -- runs some regression tests
• wasmbuild.sh -- builds the C++ code for use from JS
• webbuild.sh -- builds the web-based tools

For more information on BioImage Suite Web see

• The source repository -- https://github.com/bioimagesuiteweb/bisweb⁠
• The actual web application -- https://bioimagesuiteweb.github.io/webapp/⁠

BioImage Suite Web (bisweb) is a web-based medical image analysis suite primarily geared towards Neuroimaging Analysis. We gratefully acknowledge support from the NIH Brain Initiative under grant R24 MH114805 (Papademetris X. and Scheinost D. PIs).