Downloading UCSC complete database

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Downloading UCSC complete database

Perez, Ricardo
Dear all,

I am currently working on downloading the genome data from the UCSC database.
I have figured out how to obtain the genome of one species at a time, however this would take a bit of time if I have to type every command by hand.
Is there any command that would download the all the data from the UCSC databases?
If not, how would I go to start in writing a script that would do so.

Thank you for your time.
-Ricardo
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Re: Downloading UCSC complete database

Sean Davis
On Sun, Oct 7, 2012 at 10:38 AM, Perez, Ricardo <[hidden email]> wrote:
> Dear all,
>
> I am currently working on downloading the genome data from the UCSC database.
> I have figured out how to obtain the genome of one species at a time, however this would take a bit of time if I have to type every command by hand.
> Is there any command that would download the all the data from the UCSC databases?
> If not, how would I go to start in writing a script that would do so.

We mirror directly out of the mysql data directory.  In this script,
the /var/local/mysql directory is where the actual server files are
kept.

https://gist.github.com/3848717

Note, this does not download the .txt and .sql files.  Instead, it is
reading and writing the mysql files directly and may break if the
server versions are too dissimilar.  Also, be sure that you test this
a bit before trying it on your production database to make sure that
it is working as expected.

Sean
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