voila view errors

[Lauren Malsick]

Hello! This might just be because I am a newbie to all of this, but I have an academic license of majic and voila (majiq 3.0.15.dev1+g720c9976, voila 3.0.15.dev1+g720c99768) and have successfully created .tsv files with voila modulize. 

I get all my .tsv files and everything seems to be going well. I then want to use voila view and I'm having some challenges:

I run this:

voila view --lazy-load-zarr -j 20 /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/splicegraph.zarr /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/deltapsi_results/744_12hr_vs_Mock_12hr/744_12hr_vs_Mock_12hr.deltapsi.voila /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ01.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ02.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ03.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ13.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ14.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ15.sgc

OUTPUT:
2025-11-08 14:26:37,859 (PID:3934520) - INFO - Command: software/anaconda/envs/majiq/bin/voila view --lazy-load-zarr -j 20 /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/splicegraph.zarr /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/deltapsi_results/744_12hr_vs_Mock_12hr/744_12hr_vs_Mock_12hr.deltapsi.voila /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ01.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ02.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ03.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ13.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ14.sgc /scratch/alpine/email/Genewiz_sequencing/03_output/majiq_output/sgc_files/AJ15.sgc
2025-11-08 14:26:37,859 (PID:3934520) - INFO - Voila v3.0.15.dev1+g720c99768
2025-11-08 14:26:37,875 (PID:3934520) - INFO - ╔═══════════════════════════════════════════════════════════════╗
2025-11-08 14:26:37,875 (PID:3934520) - INFO - ╠╡ ACADEMIC License applied                                     ║
2025-11-08 14:26:37,875 (PID:3934520) - INFO - ║  Name: Official Majiq Academic-only License                   ║
2025-11-08 14:26:37,875 (PID:3934520) - INFO - ║  File: majiq_license_academic_official.lic                    ║
2025-11-08 14:26:37,875 (PID:3934520) - INFO - ║  Expiration Date: Never                                       ║
2025-11-08 14:26:37,875 (PID:3934520) - INFO - ║                                                               ║
2025-11-08 14:26:37,875 (PID:3934520) - INFO - ╠╡ The academic license is for non-commercial purposes by       ║
2025-11-08 14:26:37,875 (PID:3934520) - INFO - ╠╡ individuals at an academic or not for profit institution.    ║
2025-11-08 14:26:37,875 (PID:3934520) - INFO - ╚═══════════════════════════════════════════════════════════════╝
2025-11-08 14:26:37,875 (PID:3934520) - INFO - config file: /tmp/voila-config-b82033191201a132e5dfcb1b985dac8d
2025-11-08 14:26:39,687 (PID:3934520) - INFO - Generating Caches...
  0%|                                                                                                                                                                                                                                                                                    | 0/29413 [00:15<?, ?it/s

Then the process just gets killed... I am using a HPC so I may just be misunderstanding how to set this up? I was trying to follow the documentation (https://biociphers.bitbucket.io/majiq/VOILA_view.html) but I think that's for version 2 as I don't have .sql files....

If there is a documentation I am missing or another piece of the puzzle, I'd appreciate any advice and thank you again for your time!

[Miriam Martínez]

Hello Lauren,

I also use the MAJIQ toolkit in a HPC and I had the same issue. What I did is to create the index beforehand using the --only-index option when using voila view, which just builds the index and then exits voila. After, when it finishes the job, I run the voila view command and in my case it didin't kill the process. I hope this helps.

Best,

Miriam

[San Jewell]

Thank you Miriam, the --only-index step is helpful to make sure everything is prepared for view to work if you run steps in a pipeline. 

For the original question, looking at documentation again it is indeed not very clear how to find the view information. At the moment the best instructions are part of the heterogen sample walkthrough: https://biociphers.bitbucket.io/majiq-docs/gallery/heterogen-vignette.html#Interactively-visualizing-results-with-voila-view  ; I will put it on my list to make a better section or link to this one in the documentation. 

For your question in general though, as Miriam says it can be helpful (though not necessary) to run view with --index-only in a HPC batch run pipeline. For actually running the viewing server itself though, you should not use an HPC batch job and should instead use an HPC interactive job. View is meant to be used as an interactive interface. You run it, then use a web browser to load pages you are interested in, and close it when you are finished. Depending on how your HPC is configured it might not be seamless to host a web server on a compute node and then view it from the head (submit) node. I would be willing to try to give some tips here if ports are blocked, or you could reach out to your own IT folks about how to access a web server running on a compute node. 

For example usually if you have a web browser running on one machine 'subhost' (submit host) and then run voila on port 5000 on a compute node 'compnode1', you should be able to access the interface by opening the URL "http://compnode1:5000" on the browser on subhost. But the system may be configured to block things. You can also try running voila view on the same machine as the browser, if it has enough resources, and in this case there should be no network block and you should be able to go to "http://localhost:5000" in the browser and see voila that way. 

Let me know if you have success!

Thanks, 

-San