Ask help to build local UCSC Genome Browser

︶oh,a momo

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Jul 22, 2015, 12:37:14 PM7/22/15

to genome-mirror

Dear Sir,

I am a student from the Institute of Biophysics, Chinese Academy of Sciences.Recently, I am updating a database and trying to add a local UCSC genome browser web to display genomic information in bed files. Fortunately, I find a mirror site was built for a brother database of our lab sever years ago. The mirror site and my database data are in the same server. But I wonder if I can use the existing mirror site in my database update and show tracks in my demand, while do not influence the local genome browser web of the brother database. Or do I need to build a mirror site again? If needn't, could you please give me some advice how to do? I am really a fresher of the mirror site of UCSC genome browser and web develop.

Thank you for your attention and your reply will help me a lot!

Best,

Wei

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Wei Wu

Institute of Biophysics, Chinese Academy of Sciences

15 Datun Road, Chaoyang District

Beijing, 100101

P.R.China

Gmail:weiws...@gmail.com

Tel:+86-18600987501

Lachlan Musicman

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Jul 28, 2015, 12:22:51 PM7/28/15

to ︶oh,a momo, genome-mirror

Wei,

You can have them in the same browser.

Each Genome is put into a separate database within the MySQL, and is linked to by the template/cgi-bin.

These are the instructions to follow to build and add a new database.

http://genomewiki.ucsc.edu/index.php?title=Building_a_new_genome_database

cheers

L.

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The most dangerous phrase in the language is, "We've always done it this way."

- Grace Hopper

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Jonathan Casper

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Jul 28, 2015, 4:28:20 PM7/28/15

to Lachlan Musicman, ︶oh,a momo, genome-mirror

Hello Wei,

Thank you for your question about adding a database to an existing mirror site. Lachlan is right. You can add a new assembly to the existing mirror site, and then display your BED files as tracks for the new assembly. This requires that you add a new database to the mirror to hold your data - you cannot use the same database as the old site. For example, if the old mirror site uses the database "abcDef1", then you cannot load your data into the abcDef1 database without influencing the old site. You would need to create a new database (e.g., "abcDef2") to hold your data. If you decide to add to the existing mirror, please be careful when making changes to the hgcentral database. The tables in hgcentral contain configuration information for the entire mirror server, and any errors there can affect both your new browser and the old one.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.