Local installation of UCSC Genome Browser
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Entering edit mode
14 months ago
dahun73 ▴ 10

Hi.I have some questions for local installation of UCSC genome browser.

I know that there are 5 methods of installation(https://genome.ucsc.edu/goldenPath/help/mirror.html ).

But I'm poor at computer managing. So I have chosen 4th pathway(GBIC installation).

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

It was simplest method that i could . but during installation, I had to change my directory because of storage capacity.

It needs at least 2TB minimal version, but my main hard storage is just 1TB. So I need to change directory.

But there was no options for changing directory of installation guide.

Does anyone can change directory for installation UCSC genome browsers?

If so, help me. Thank you.

genome ucsc browser • 505 views
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Entering edit mode
14 months ago
Luis Nassar ▴ 420

Hello,

As you have said, we have a few different options if you want a mirror installation. We recommend GBiB (https://genome.ucsc.edu/goldenPath/help/gbib.html) as the simplest method, it's a self-contained virtual machine containing a functional Genome Browser.

GBiC is another solution, when you would like to install a mirror on your own machine, or cloud instance.

The GBiC installation (as well as the GBiB) can be quite large. Both of these can be installed with a minimal amount of data, and then they will query the Genome Browser servers live on demand as more data is explored. This minimal installation, depending on settings and assemblies, can be up to 1-2TB, though often less.

In our help docs we do cover the scenario when your partition is too small, see Root file system too small for all data.

If you need to move data to another partition because the root file system is too small for all of the assembly's data, the following steps will help complete the installation. First, create the following directories and then make symlinks to the directory that will contain the data:

mkdir /home/xxx/storage1/gbdb
mkdir /home/xxx/storage1/mysql
ln -s /home/xxx/storage1/mysql /var/lib/mysql
ln -s /home/xxx/storage1/gbdb /gbdb


If you have any follow up questions, our help desk can always be reached at genome@soe.ucsc.edu. You may also send questions to genome-www@soe.ucsc.edu if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.