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Covidnet_on_WSL.asciidoc

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Running the covidnet workflow on a local ChRIS instance using WSL

  1. Instantiate a local ChRIS instance on WSL by following the steps in the ChRIS_on_WSL guide

  2. cd to the home directory and clone the CHRIS_docs repo

        git clone https://github.com/FNNDSC/CHRIS_docs.git

  3. For the next step, you can either -

    • cd to the workflows directory in CHRIS_docs

          cd CHRIS_docs/workflows

    • Copy covidplugins_upload.sh and paste it into your ChRIS_ultron_backEnd directory

      OR

    • cd to ChRIS_ultron_backEnd

    • create a new bash file titled - covidplugins_upload.sh and paste the following lines of code in that file:

              ./plugin_add.sh  "\
		        	            fnndsc/pl-lungct,		\
			                    fnndsc/pl-med2img,		\
			                    fnndsc/pl-covidnet,		\
        	            		fnndsc/pl-pdfgeneration
        "

  4. Now, doing either of the things in step 3, you should be in the ChRIS_ultron_backEnd directory and have covidplugins_upload.sh in it

  5. Run that script while you have a running ChRIS instance to add your plugins for the covidnet workflow

        ./covidplugins_upload.sh

  6. Run the following command to grep the ip of your localhost

        ip route | grep -v docker

    • This command should print something that resembles this on your terminal:

          default via 111.22.333.1 dev eth0
    111.22.333.0/20 dev eth0 proto kernel scope link src 111.22.126.43

  7. Replace <ip> with the ip address printed after src in the following command and run it:

        export HOST_IP=<ip>

  8. Run the following command to run the covidnet workflow on your local ChRIS instance:

        ./covidnet.sh -a $HOST_IP