FW: UCSC

[Uriel Rosen]

Hi , how are you ?

 

We have an issue where  a user gets an sql error,steps taken before the error occurs are in the attached screenshots,

Please advice.

Also do you suggest using a file that is stored on our local network?

 

Thanks,

Uriel.

 

 

From: Ori Roethler <ori.ro...@weizmann.ac.il>
Sent: Sunday, August 1, 2021 10:46 AM
To: Uriel Rosen <uriel...@weizmann.ac.il>
Subject: UCSC

 

Hi Uriel,

 

I enter the mirror site from: http://ibaucscbwv01.wexac.weizmann.ac.il:1234

 

On the home page: My data —> Custom tracks (screenshot 1)

On the manage custom track page: Add custom tracks (screen shot 2)

Under edit configuration I put for example (screenshot 3): 

track type=bigWig name="My Big Wig" description="A Graph of Data from My Lab" color=0,0,0 visibility=2 bigDataUrl=https://de.cyverse.org/dl/d/9EF09B38-AC8C-42E0-8A82-C01A07F890AA/out.bw

Here i just give my track name/descritpion/color etc. and a bigDataURL to the file (out.bw) on the website to which i uploaded my data (CyVerse).

This server gives me a link that can “Accept byte-ranges” for visualization purposes on the UCSC. (a static link won’t work).

Ideally I would like to use the wexac in the same way since all my data is on the server anyway. 

 

 

Besides this, the server appears to be offline, i can only enter the homepage and custom track pages but not the actual genome browser.

It gives me the following error:

 

 

Let me know if something is wrong with the website or perhaps the link to the mirror changed? 

 

Thank you,

 

 

O. Roethler, MSc
PhD Student
Weizmann Institute of Science
Department of Neurobiology
Spiegel Lab

Tel: +972 54 474 5244

 

 

 

[Dan Schmelter]

Hello Uriel,

Thanks for contacting UCSC Genome Browser support about that SQL error.

The Public MySQL server is working as expected. One of our engineers thinks that your issue may be caused by a firewall on your mirror server and that allowing access to its port might help.

The institutional firewall may be blocking their mirror site when it tries to connect to our public MySQL server genome-mysql.soe.ucsc.edu, so if they allow that (default port 3306), it might work.

I hope this was helpful. If you have any more questions, please reply-all to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

[Uriel Rosen]

Hi Bechor,

 

Can you please check if we have a rule allowing access for ibaucscbwv01.wexac.weizmann.ac.il to genome-mysql.soe.ucsc.edu  port 3306?  

if not allowed please add this rule.

 

 

Thanks,

Uriel.

[Uriel Rosen]

Hi Ori ,

 

Please test if this operation works for you and update us.

 

 

Thanks,

Uriel.

 

[Ori Roethler]

Hi Uriel,

Yes, the SQL issue is resolved.

Now I just need to know what path/link the mirror site expect to direct it to files on the wexac to upload custom data to it.

It needs to be able to accept byte-ranges to visualize only part of the data at a time.

Thanks,

Ori

[Uriel Rosen]

If the files you work with are on wexac storage you can use the browse button to select them, assuming you mapped the Wexac storage to your pc as a network drive.