<aside> 🔬

wrmXpress is a software suite that analyzes worm imaging data generated on an ImageXpress high-content imager. It combines bespoke modules with pipelines developed within other frameworks, and can be deployed locally or distributed on a high-throughput computing network. See the wrmXpress GitHub repository for details.

</aside>

The protocol below is specific to Zamanian lab pipelines deployed at the CHTC. Prerequisites: generating and exporting imaging data to ResearchDrive, transferring it to input/ in staging/ on the CHTC, and uploading experimental metadata to metadata/ in staging/.

Useful links:

Preparing to submit jobs

  1. For each plate, fill out a YAML file that dictates the job's parameters. Use the template in the GitHub repo. A thorough explanation of each parameter is at the repo's homepage. Edit the YAML with a text editor.
  2. Save the file(s) to your computer. Name each parameters file with the plate name (e.g., 20211013-p04-NJW_932.yml). Each plate must have its own YAML file, even if parameters are identical across the batch.
  3. Upload the YAML file(s) to your home directory on the submit server. An SFTP client (Transmit, FileZilla, CyberDuck) is easiest, but Globus or scp also work.
  4. Create a file called plate_list.txt with the plate name of each plate in the batch on a separate line. Upload this to your home directory too.

<aside> 💡

If you already have a plate_list.txt in your home directory, you can edit it in place with vim or nano.

</aside>

Submitting jobs

  1. SSH into the submit server and verify that your home directory has a YAML file for each plate and an updated plate_list.txt.
  2. Clone or pull the chtc-submit repo: git clone <https://github.com/zamanianlab/chtc-submit.git>
  3. Edit chtc-submit/imgproc/wrmXpress.sub to request the correct number of CPUs and amount of RAM and disk space. Do not push these changes back to the remote chtc-submit repo.
  4. Submit the jobs:
condor_submit chtc-submit/imgproc/wrmXpress.sub script=chtc-submit/imgproc/wrmXpress.sh

If everything went correctly, you should see a notice that the jobs have been submitted. The number of jobs corresponds to the number of plates in plate_list.txt.

Errors