Data base question

[Ziyue Chen]

Dear Genome Browser team,

We are trying to set up a mirror for research use and are currently downloading the mm9 data base. It is 2.7 Tb and I wonder if I download only the full data set of mm9, which is much smaller, how can we set it up as the data base?

Thank you 

Ziyue Chen

[Cath Tyner]

Hello Ziyue,

Thank you for your question regarding your UCSC Genome Browser installation and the mm9 size concerns. One of our engineers has shared the following information:

It is the /gbdb/mm9/bbi/wgEncode* data that consumes the most space:

[qateam@hgdownload1 /mirrordata] du --apparent-size -hsc gbdb/mm9 mysql/mm9 goldenPath/mm9/database

 2.1T    gbdb/mm9

82G     mysql/mm9

19G     goldenPath/mm9/database

2.2T    total

The only size oddity is that the text database dumps in goldenPath/mm9/database

is smaller than the loaded database because the indexes in the database tables

take up a lot of space.

If possible, you might consider skipping the wgEncode files in gbdb/mm9/bbi/wgEncode*

By doing this, you can save most of the space:

du --apparent-size -hsc gbdb/mm9/bbi/wgEncode*

2.0T total

As a side

​ ​

note, I thought I would point out a new installation script that was recently released. This installation script provides quick automation for the setup of a UCSC Genome Mirror, thus essentially replacing the manual procedures. While the script's name is "Genome Browser in the Cloud (GBiC)," the GBiC script automates an installation equally well on a dedicated server or a cloud server.

Via GBiC, there is an easy option to install mm9 without encode, with examples noted on the User Guide.

For more information see:
The Genome Browser in the Cloud User Guide

If this response still does not provide you with the help that you need, please feel free to respond to this forum with follow-up questions so that our support team can help you further!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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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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