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Script for deploying CompuCell3D simulations as tools in nanoHUB

This script was made to make the generation of GitHub repositories to deploy CompuCell3D tools an easier task.

Note:

The current version of CompuCell3D in nanoHUB is 4.2.5

Requirements:

  • Python 3
  • Be able to run python from the command line. You can 1) edit your PATH system variable, 2) provide the full path command, or 3) create an alias.
  • GitHub account
  • NanoHub account
Posible requirement:
  • Run git from the command line

How to use:

  1. Dowload / Clone this repository to your machine.
  2. Create a GitHub repository where you're going to have your nanoHub tool ("tool repo"). Have it cloned to your computer.
  3. On a command line from the cc3d-nanoHub-settuper directory on your machine call the script tool_maker.py. If successfull it'll copy all the necessary files for the nanoHub tool. You will provide three arguments to the script:
python tool_maker.py <short tool name> <full-path-to-new-tool-directory> <full-path-to-your-cc3d-project>

The <short tool name> needs to be between 3 and 15 lowercase alphanumeric characters without spaces. The <full-path-to-your-cc3d-project> is where the .cc3d of your CompuCell3D simulation is. <full-path-to-new-tool-directory> is the tool repo.

Some files might have lost run permissions. You need to check two files in your tool repo:

  1. invoke file in the middleware subdirectory,
  2. And the .sh file in the bin subdirectory.

To check if they still have the executable permission you should go into the tool repo in the GitHub website:

.sh executable

invoke executable

If any of them is not executable you should, from a command line, go to the relevant directory and issue the following commands:

$ git update-index --chmod=+x invoke
$ git commit -m "Changing file permissions"
$ git push

Changing the first command accordinly if you're dealing with the .sh file.

nanoHub deployement:

Go to https://nanohub.org/tools/create and follow the instructions there. The one thing you must be carefull about is that the <short tool name> you gave before is the same as the one you input on the first box (Tool Name) on nanoHub's tool creation page.