Urgent help: Voila View command- portal

[Swethaa NG]

Hey,

Hope you are doing well!

I have recently started using Majiq 2.5.7 for my RNASeq myopathy data (deltapsi 2 groups, 8 controls, 5 patients) and I must say that the software is very well built, easy to understand and the commands are very straightforward for a bioinformatics beginner. Thank you! :)

 I have performed the analysis until the quantifying part and I need help with the voila view command. I have read some of the comments before and I have trouble understanding how to make my external server (which I am working on) accessible to the localhost:5000 that voila mentions the final summary report to be. Currently, I using windows terminal with virtual env venv activated to run majiq commands. I am stuck in the part where voila view results showcase: Serving on localhost:5000"... :/

I have read this: https://blog.trackets.com/2014/05/17/ssh-tunnel-local-and-remote-port-forwarding-explained-with-examples.html but I do not have sudo rights to make changes in sshd config file. Can you please help me with this final step? What else can I do to make my web browser to be accessible with these results?

Since I have been learning about code and RNA-Seq data only recently, I am unable to proceed in viewing the results I obtained. ANY help would be appreciated.

Thank you,

Swethaa

[San Jewell]

Hi Swethaa,

Can you describe the arrangement of machines/networks that you are working with and what exactly you are trying to do? There are a few things that could be going on here.

First, in general, you will only use the "localhost" address, if you are connecting to "localhost" (i.e. the current machine, not a remote one) So if you have two machines, your local laptop, and an ssh/web server with the hostname "sshserver1.something.net" , and you log into sshserver1 and start voila, then when you want to connect to it from your local machine, instead of putting "localhost:5000" in your browser, you would put "sshserver1.something.net:5000". Additionally, for security reasons, by default voila only hosts on localhost, so that other random users cannot connect and see the data. If you want to host for any user to connect to, you would run voila view with the switch "--host 0.0.0.0" (0.0.0.0 for all hosts, or some specific address/cidr to limit to certain viewing clients)

Now, that's assuming you have access to this other machine and there isn't a firewall which might block certain ports, such as 5000, in between your local machine and the server. To bypass the firewalls, is where the "ssh tunnel" comes in. To do this, you can open a second SSH connection with something like $ ssh -N -L 5000:sshserver1.something.net:5000 user...@sshserver1.something.net     ; This will run but not show anything. Is is redirecting the remote:5000 data to localhost:5000 ; so now you can go to localhost:5000 in your browser to see the result.

I hope it makes sense as there are a few different concepts to understand here. Please let me know if you are able to make progress.

Thanks,

-San

[Swethaa NG]

Hi,

Thank you very much for your detailed reply San! I really appreciate it. I ran the code and searched with specific server name as you mentioned: "sshserver1.something.net:5000" and the browser page shows as no connection to this page. I believe I have to check the firewall block possibly to this port or any other port that voila chooses. I am checking this firewall part with our IT team, I will update once I have progressed with this. Thanks again for your help! 

Kind regards,

Swethaa

[Swethaa NG]

So sorry for my delayed response, and I also forgot to elaborate more in my answer above. I am running your pipeline in my local laptop for a set of sample data present in an external ssh server in Linux epouta setting. You are right in your explanation.

I would like to open the voila generated URL in firefox directly, by opening firefox page in another terminal window (and by keeping voila view running of course). But I believe I am facing issues with firefox connection here. It may not have access to the page being directed by my ssh server port. This is why I am trying to get in touch with IT.

What do you suggest?

Thanks

Swethaa

[Swethaa NG]

Hello! The problem is fixed. There was a connection issue from my end. Thanks again for your timely support!

Best regards,

Swethaa

[San Jewell]

Hi Swethaa,

I'm glad you got it resolved! I hope your experience here continues to serve you with other network/ssh annoyances down the line in life, hah.

Thanks,

-San