Prerequisites for running the pipeline

1) In //uwbc.drive.wisc.edu/gec/Visium there needs to be a JSON file outlining the samples that the pipeline will run. The wrapper script will automatically detect the one with the newest date.

• That JSON is generated via the json_generator.html application.
• The file names must contain .tif when being entered.

2) The images you want to run the pipeline on need to be stored in //uwbc.drive.wisc.edu/Visium/images

• These images will be selected by the newest JSON so you don't have to worry about cleaning that directory out.

Instructions for running the pipeline

1) SSH into visium.biotech.wisc.edu

• Command: ssh netid@visium.biotech.wisc.edu
  • Must be on Biotech network/VPN

2) Run the command below

• runanalysis
  • (This is an alias for a much longer command, but this runs a wrapper script that handles JSON gathering and output storage)

This will run the pipeline assuming the prerequisites are met. 

After the pipeline is ran

Your HTML report will be located in //uwbc.drive.wisc.edu/gec/Visium/reports

• The report directory will be labeled with a dated directory containing the HTML report along with the files generated.

Email or teams kickbush@wisc.edu with any questions / errors.