Off line installation of UCSC Genome Browser with only 3 organisms

[Minard-Smith, Angela (US)]

Hello,

I am working on installing the UCSC Genome Browser on a workstation that will be taken offline once all programs are installed. I am using GBiB installation.  I want to minimize storage space for the installation and I want only Human, Rat and Sheep available in my installation. How do I set things up this way? 

Thank you,

 

Angela Minard-Smith, MS Bioinformatics

Bioinformatics Data Scienist II

Health Outcomes and Biotechnology Solutions

Office: 614.424.4755 |

minard...@battelle.org

 

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[Matthew Speir]

Hello, Angela.

Thank you for your question about setting up a UCSC Genome Browser mirror.

Our GBiC help page contains instructions on using the script to set up your mirror: https://genome.ucsc.edu/goldenPath/help/gbic.html. It also contains several useful example commands for downloading data. 

After the initial install using browserSetup.sh, you can use the "mirror" command to download specific databases using their UCSC database names (e.g. hg38). Use the "-t" option with "mirror" to download specific subsets of data tracks, see the GBiC page or the browserSetup.sh help message for a list of these subsets.

Once you've downloaded all the organisms and data tracks needed, you can put your mirror offline using the "-o" option for browserSetup.sh.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Genome Browser, User Support

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