This site is a beta test.
Question: How to get raw Github URL for a large file
0
Entering edit mode
13 months ago
m93 • 150

I am trying to host a UCSC hub from GitHub. I followed all the instructions at the link pasted below.

From what I can see, they ask that for the bigDataUrl in the trackDb.txt file, you provide a raw.githubusercontent.com URL. I can obtain this easily for text file in my repository but how do I get it for large files (around 40-50MB) that cannot be visualized in GitHub?

In the following link, it shows you where to click (the "Raw" button) to get the URL but you don't have that option for large binary files.. (they are bigwig files). How can I get the raw URL for these files?

https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting

Thanks

ADD COMMENTlink 13 months ago m93 • 150 • updated 13 months ago jared.andrews07 ♦ 2.4k
4
Entering edit mode
13 months ago
jared.andrews07 ♦ 2.4k
St. Louis, MO

You can just type the name of the file at the end of the path. Get the URL for your text file and replace the filename/path with the path to your datafile.

raw.githubusercontent.com/username/myhub/master/myhub.txt

Can be changed to:

raw.githubusercontent.com/username/myhub/master/pathto/mybigwig.bw
ADD COMMENTlink 13 months ago jared.andrews07 ♦ 2.4k
Entering edit mode
1

Yes this is correct. Also note that if your file is too large to be stored on Github, you can use the CyVerse Discovery Environment to host the file:
https://www.cyverse.org/

Cyverse might be a little easier since you should be able to upload a single directory of your hub data (including hub.txt and trackDb.txt, etc) and then with one click get a link you can paste into the Genome Browser.

ADD REPLYlink 13 months ago
genecats.ucsc
• 560
Entering edit mode
0

Ah right! I was just confused cause when you click on Raw for the .txt file, you end up on a new page and the URL is longer than what you say. It has lots of random letter, something like:

raw.githubusercontent.com/username/myhub/master/myhub.txt?token=hddaixuxbzdcguadada6%3%D etc

So I thought that was the whole URL

ADD REPLYlink 13 months ago
m93
• 150

Login before adding your answer.

Powered by the version 1.5.2