European equivalent of http://hgdownload.cse.ucsc.edu/

[Mike Rightmire]

Hello,

I'm having a hard time finding the European equivalent of the http://hgdownload.cse.ucsc.edu/ download site that can function within the browserSetup.sh

I am aware of  http://genome-euro.ucsc.edu, but FTP is not available directly from this address.

Is there a browserSetup.sh / FTP capable site in Europe for downloads?

Many thanks!
Mike

--

Universitäts Klinikum Heidelberg - University Hospital Heidelberg

Section of Bioinformatics and Systems Cardiology
Analysezentrum III - Klaus Tschira Institute

Mike Rightmire 

Bioinformatics and IT

Im Neuenheimer Feld 669

69120 Heidelberg

Tel.: +49 6221 56 - 34213

Fax.: +49 6221 56 - 6868

Cell: +49 176 7131 8758

Michael....@uni-heidelberg.de


http://www.klinikum.uni-heidelberg.de

[Brian Lee]

Dear Mike,

Thank you for using the UCSC Genome Browser and your question about the European equivalent of http://hgdownload.soe.ucsc.edu/.

We have available a European MySQL server, genome-euro-mysql.soe.ucsc.edu (http://genome.ucsc.edu/goldenPath/help/mysql.html), that can be accessed with commands like the following:

mysql --user=genome --host=genome-euro-mysql.soe.ucsc.edu -ANe "show tables;" hg38

When using the browserSetup.sh script, and edit to the $CGIBINDIR/hg.conf configuration file can enable pointing to this server by adjusting this entry: slow-db.host=genome-euro-mysql.soe.ucsc.edu

This slow-db.host= setting is used to define the location of the mysql server that is used if data cannot be found locally (e.g. chromosome annotations, alignment summaries, etc).

We are also working on creating a European version of hgdownload. Once we have it up and running, would you be interested in giving it a test?

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UC Santa Cruz Genomics Institute

Michael.Rightmire@uni-heidelberg.de


http://www.klinikum.uni-heidelberg.de

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