local UCSC Genome Browser

[Zhang, Suiyuan (NIH/NHGRI) [C]]

Dear UCSC Genome Browser support:

 

I am working with a group that is sequencing a new genome. They’d want to display the genome and annotation tracks in the UCSC Genome Browser framework. We are considering setting up a local Genome Browser that would be password-protected to allow access only by collaborators. What is the best way to do that? Is it possible to set up the GBiB to serve the new genome through an Assembly Hub?  Or do we need to set up a full genome browser? Would we do that with GBiC or a manual installation?  We will be running this on a linux server.

 

Thanks,

 

Suiyuan

 

 

Suiyuan Zhang [C]

Bioinformatics Scientist

Columbus Technologies & Services, Inc.

NHGRI/NIH

Email: zha...@mail.nih.gov

Office: 301-496-7925 |  Fax: 301-480-1109

50 South Drive,  Bethesda, MD  20892

 

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[Cath Tyner]

Hello Suiyuan,

Here are some "getting started" resources for your installation:

About installations:

http://genome.ucsc.edu/admin/mirror.html

Considerations before installing a Genome Browser

https://genome.ucsc.edu/goldenpath/help/mirror.html#considerations-before-installing-a-genome-browser

Here's where to get the script "GBiC" (Genome Browser in the Cloud), which automates the old manual process for setting up a mirror (on a cloud instance, a dedicated server, etc). The GBiC script is a quick and easy way to set up a fully-functioning mirror.

https://genome-store.ucsc.edu/

Here's is the User Guide for the GBiC script:

https://genome.ucsc.edu/goldenpath/help/gbic.html

How to add a single UCSC genome to a mirror:

http://genome.ucsc.edu/admin/mirrorManual.html#adding-a-custom-genome-to-the-browser

Without installing a mirror (GBiC/GBiB), you can always display your novel genome via an assembly hub in the UCSC Genome Browser. The level of security may or may not not be sufficient for you; only others with the hub url will have access.

Regarding password protection for mirrors:

Protecting your mirror depends on setting up Apache correctly, and is separate from the UCSC Genome Browser installation. One way to accomplish this is through Apache Basic Authentication. 

Apache Basic Authentication will essentially cause a dialog box pop-up in your internet browser, which will prompt for an username and password (set by you/admin). 

Here are some previously answered mailing list questions regarding password protection:

https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome-mirror/password/genome-mirror/4vhTyZ4Ea68/BbjvbpOLtA0J

https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome-mirror/password$20protected/genome-mirror/azPz87kJgKQ/pnbmO3sJVJsJ

Once you have set up either a GBiB or an installation through GBiC, you will have a full working mirror. You can then either display your novel genome either through an assembly hub or you can add your assembly as though it was a native assembly in the browser. For your installation, you will have the choice of whether or not to download other native genomes such as human or mouse, etc. 

For example, using GBiC:

See the examples in the "GBiC commands" section from https://genome.ucsc.edu/goldenPath/help/gbic.html. If you want to partially mirror the browser (minimal tables),  and only download hg38, you can run the install command like this:

>sudo bash browserSetup.sh minimal hg38

For an installation demonstration, see the Genome Browser in the Cloud (GBiC) Introduction video:

https://www.youtube.com/watch?v=dcJERBVnjio

Please respond to this list if you have further questions!

Thank you for contacting the UCSC Genome Browser support team. 

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private help: Email

 genom...@soe.ucsc.edu

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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