Windows installation of Voila

[Delong Zhou]

Hello,

I remember there used to be a Win version of voila to browse the events. I can't seem to find it for the latest version.

Is git the only way now?

Thank you!

[Delong Zhou]

Bump!

[Delong Zhou]

To give a bit of context, I'm doing majiq on a HPC cluster with command only interface, then I would like to use my desktop (windows) to visualize the events. In addition it would be nice if there is an easy way to install voila for my wet lab collegues so they can browse the events on their own.

I also notice the MAJIQ-SPEL webtool, but it seems that its doc is not updated for MAJIQ v2?

Thank you!

[San Jewell]

Hello,

I think the most efficient way to accomplish both of these goals is to run voila view on your HPC and then view it on your local laptops with your web browsers. It is possible to open an SSH tunnel to view the web interface from your laptop in the case that your HPC administrator doesn't have any provision for hosting your own web apps on specific ports. (i.e. if they block this with a firewall)

What do you think?

-San

[Delong Zhou]

Hi Sam

Yes it was indeed my intention to run voila view on the server then browse the output from my laptop. Currently my majiq folder contains only .majiq, .voila, .sql etc and there is no .html or similar file for browsing the events.

I remember there used to be a packed version that you can install and launch locally, then interactively browse the events. I also remembered reading that the interactive mode has to be launched via a server instead of pre-generated web pages.

Is that still the case?

Thank you,

Delong

San Jewell <sje...@biociphers.org> 于2025年2月17日周一 13:46写道：

--
You received this message because you are subscribed to a topic in the Google Groups "Biociphers" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/majiq_voila/9ubn9ZfySr0/unsubscribe.
To unsubscribe from this group and all its topics, send an email to majiq_voila...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/majiq_voila/467b804d-2153-4b35-b02c-225c71ee09f1n%40googlegroups.com.

[San Jewell]

Hi Delong,

A few things of note:

There was some requests from users of the voila 1.x versions to have the ability to generate html files for easily distributing to collaborators. This went back and forth for a while : the main issue is that there are a number of useful features on each voila page which are interactive, and communicate with the server process to render. Eventually, we have a compromise solution added, which has put a "floppy disk icon" near the top right of the screen, which allows saving an html version of the page with still useful but limited features. However, this is a one-at-a-time solution, in that you would need to find a gene of interest and click the save button in your browser. This is because each page is generated using some javascript for plots which goes beyond some of the raw html versions we had in earlier versions of voila. From a technical perspective, in order to generate html files for _all_ genes, it would basically be running a browser emulator, such as selenium headless, to go through each gene page and "save" it, as the browser renders it. This is not impossible but it has more requirements to set up, and would be slow and probably overkill for most use cases. I would be interested to hear your feedback on these decisions and the future direction of the software.

Now as for running a "server" , what I mean is, a server on some system you have access to host on. For example, we run a slightly modified version of voila to host the "majiqlopedia" tool at https://tools.biociphers.org/majiqlopedia_normal/ ; This is just a voila view, running on a server on the default web port. This has the advantage that you do not need to send any majiq/voila files around or install anything, you can just pass the user a link (and optionally a passphrase, which can be enabled on voila command line). The biggest issue with this method is that usually hpc nodes are behind a firewall, so the viewer would need a VPN account if that's the case.

Alternatively, installing voila from python on windows is also not daunting, and can be done with just a few steps. I'd be happy to guide you through it.

Thanks,

-San

[Delong Zhou]

Hi San,

(Sorry about misspelling your name in my last message)

I think setting up a server on my machine would be the best way to go.

Could you outline a best practice to set up this on a windows machine? Like which version / distribution of python to use, any other requirements etc.
Thank you!

Best,

Delong

San Jewell <sje...@biociphers.org> 于2025年2月26日周三 14:11写道：

To view this discussion visit https://groups.google.com/d/msgid/majiq_voila/cc7e36bd-c090-4166-bd4e-72eb2e935186n%40googlegroups.com.

[San Jewell]

Hi Delong,

I've gotten ahold of a recent version of windows to try this on so there should be no issue, please let me know if you run into any problems:

download python 3.10 64 bit installer here and install it: download python 3.10 here: https://www.python.org/downloads/release/python-3100/

then open cmd.exe and run the following:

cd C:\Users\<USER NAME>\AppData\Local\Programs\Python\Python310

python.exe -m pip install git+https://bitbucket.org/biociphers/majiq_academic.git#subdirectory=voila

You will need to replace <USER NAME> with your user name. Alternatively you can find this folder by searching on the windows start menu for python3.10 and right click and "open file location". (However by default for me it went to another shortcut so again I had to right click on the shortcut and click open file location.)

This should install voila.

Then, as the warning says, voila.exe is not on your path. You can add it to your path in system settings or just run

C:\Users\<USER NAME>\AppData\Local\Programs\Python\Python310\Scripts\voila.exe [your arguments to voila]

Let me know if it works for you.

Thanks,

-San

[Madison Reeves]

Hi!

I have a very similar issue, in which my institution does not allow for ssh tunneling or hosted web view of .voila files. I tried your steps above in my local machine (I first navigated to a local directory containing copies of .voila files and the splicegraph.sql file), then executed voila, but I was immediately blocked with an "Access Denied" error when trying to run .voila view.

Here is a rough pipeline of the Windows approach:

cd C:/User/Documents/voila_files

C:\Users\USER\AppData\Local\Programs\Python\Python310\Scripts\voila.exe

voila view sample_name.psi.voila

Apologies, perhaps I am misunderstanding this approach? Is there no other way to very simply view and share the .voila files if we don't have the ability to host the web server?

Thank you in advance!

-Madison

[San Jewell]

Hi Madison,

As voila itself is a web server (process), it is generally required to run it in order to get the full functionality of displaying the results. As mentioned previously, it is possible to save specific gene pages as html, but this does still require running the server process at least one time somewhere.

As far as your "access denied" error, I've not heard of this happening before. Would you be able to send a screenshot of what you are seeing? I should be able to help you work through it.

Thanks!

-San

[Madison Reeves]

Hi San,

Wow, thank you so much for your speedy reply! 

voila_files is a local directory with all .voila files and splicegraph.sql. 

C:\Users\M> cd Documents
C:\Users\M\Documents> cd voila_files

C:\Users\M\Documents\voila_files>C:\Users\M\AppData\Local\Programs\Python\Python310\Scripts\voila.exe
usage: voila.exe [-h] [-v] [--license LICENSE] {tsv,view,modulize,filter,split,recombine,lr} ...

VOILA is a visualization package for Alternative Local Splicing Events.

positional arguments:
  {tsv,view,modulize,filter,split,recombine,lr}
    tsv                 Generate tsv output for the supplied files.
    view                Start service to view the visualization for the supplied files.
    modulize            Modulize splicing events and generate a breakdown of the modulization in multiple TSV files.
    filter              Make truncated versions of the input files of a more manageable file size for easier collaboration.
    split               Split classifier input dataset (splicegraph and voila files) into <N> equal parts, for the purpose of running on a compute cluster
    recombine           Used to combine output from a `voila split` run, after all initial runs are complete
    lr                  Preprocess long read data from a variety of tools to append to the voila view visualization

options:
  -h, --help            show this help message and exit
  -v                    show program's version number and exit
  --license LICENSE

C:\Users\M\Documents\voila_files>voila view splicegraph.sql Ctrl-Disease.deltapsi.voila
Access is denied.

Apologies, this may be a very simple issue! I really struggle with Windows but I saw this thread and was hoping this might circumvent my issues with the firewalls.

Thank you!

-Madison

[San Jewell]

Hi Madison, no worries! Can you report back if you run something like:

C:\Users\M\AppData\Local\Programs\Python\Python310\Scripts\voila.exe view splicegraph.sql Ctrl-Disease.deltapsi.voila

If that makes any difference?

Thanks,

-San

[Madison Reeves]

Hi San,

I did try that, but it did not seem to work! I got a "The system cannot find the path specified." error when I tried running that command as-is. Is there perhaps a local way to launch Jupyter notebooks that I am not aware of?

Thank you!

-Madison

[San Jewell]

Hi Madison,

So I am confused a little bit through some inconsistency. You have in a few posts ago, this:

C:\Users\M> cd Documents
C:\Users\M\Documents> cd voila_files

C:\Users\M\Documents\voila_files>C:\Users\M\AppData\Local\Programs\Python\Python310\Scripts\voila.exe
usage: voila.exe [-h] [-v] [--license LICENSE] {tsv,view,modulize,filter,split,recombine,lr} ...

VOILA is a visualization package for Alternative Local Splicing Events.

positional arguments:
  {tsv,view,modulize,filter,split,recombine,lr}
    tsv                 Generate tsv output for the supplied files.
    view                Start service to view the visualization for the supplied files.
    modulize            Modulize splicing events and generate a breakdown of the modulization in multiple TSV files.
    filter              Make truncated versions of the input files of a more manageable file size for easier collaboration.
    split               Split classifier input dataset (splicegraph and voila files) into <N> equal parts, for the purpose of running on a compute cluster
    recombine           Used to combine output from a `voila split` run, after all initial runs are complete
    lr                  Preprocess long read data from a variety of tools to append to the voila view visualization

options:
  -h, --help            show this help message and exit
  -v                    show program's version number and exit
  --license LICENSE

This indicates that voila is actually ran successfully, it's just printing out the help screen because no arguments were given. You should be able to run the same thing but just add in "view" and your voila file paths:

C:\Users\M> cd Documents
C:\Users\M\Documents> cd voila_files

C:\Users\M\Documents\voila_files>C:\Users\M\AppData\Local\Programs\Python\Python310\Scripts\voila.exe view splicegraph.sql Ctrl-Disease.deltapsi.voila

If truly the first command shows the usage instructions but the second command says it cannot find the file specified, can you take a screenshot? I believe it should work.

Thanks!

-San

[Madison Reeves]

Hi San,

Thank you so much for your help!

I tried that example-

C:\Users\M\Documents\voila_files> C:\Users\M\AppData\Local\Programs\Python\Python310\Scripts\voila.exe view splicegraph.sql Ctrl-Disease.deltapsi.voila

Access is denied.

With the same windows popup that I encountered before. Do I need Jupyter Notebooks installed locally as well? Perhaps that is the issue?

Thank you again for your quick responses!

-Madison

[San Jewell]

Hi Madison,

Huh, thank you for confirming. I've never seen that particular message, and web searches tell me that the causes of this problem are rather diverse, so, I'd rather you not try them all. I will try again with a fresh install of windows on my test machine to see if I can reproduce this issue. Which version of windows is it? 10 or 11 or something else?

Thanks!

-San

[Madison Reeves]

San,

Thank you so very much! I am still on Windows 10. I tend not to do very much work within Windows CMD, so the issue may be with the packages? I'm not sure. 

Thank you again for your help,

Madison

[San Jewell]

Hi Madison, I had a chance to load up a new windows 10 virtual box today to check out this situation. In the end, it didn't take me too long to launch the process and view the app:

I did leave out a few minor things I had to do to make this work apart from my instructions earlier:

1) download git for windows and install it

2) direct the command to the majiq license file or put it in your home directory

3) add the -j 1 option to the command to avoid a multithreading bug on windows.

However, I don't think any of these three things are related to the error you are seeing. Indeed, "access denied" sounds almost like there is some kind of institution firewall / virus blocker / etc which is blocking voila from running. Is that possible? Is it your machine or provided by someone?

In the meantime, I can attest that the biggest issue I had with the old .exe file approach was actually more related to mac OSX users, so I can see if I can make available a newer version just for this case, but it might take me a little time.

Thanks,

-San