Removing hg19 and mm9 from menu selection

[Mike Rightmire]

Good Morning,

My boss has tasked me with removing the selections "hg19" and "mm9" from the "Genomes" drop down in the local copy of the UCSC home page.

I have removed the corresponding database from MySQL, and the related files from "/gbdb"...however, the selections still appear.

I do not that all the selections (including the ones we want to keep - usch as hg38 and mm10) require the ../mysql/hgcentral directory.

Is it possible to remove those additional selections from the web page? DOes the cgi or html docs need to be edited?

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 work to establish a mirror for your group.

For your mirror, if you enter the MySQL hgcentral database and edit the databases table called "dbDb" you can edit the "active" field from 1 to 0 for hg19 and mm9.

UPDATE dbDb SET active=0 WHERE name like "mm9";
UPDATE dbDb SET active=0 WHERE name like "hg19";

You may also be interested to learn about an existing line in the configuration file in /usr/local/apache/cgi-bin/hg.conf that enables a GBiB to point to our remote MySQL server:

slow-db.host=genome-mysql.cse.ucsc.edu

The "slow-db" settings allows a GBiB to source MySQL files outside of the local site. If your mirror had no use of our databases (like hg38, mm10), you could even comment these lines out.

Any advice on this new section, this seems to be a way to edit the bar, but is it best?
For the drop down menus you can edit a menubar file in /usr/local/apache/htdocs/inc/globalNavBar.inc and remove these two lines:

        <li><a href="../cgi-bin/hgTracks?db=mm9&amp;position=lastDbPos">Mouse NCBI37/mm9</a></li>
        <li><a href="../cgi-bin/hgTracks?db=hg19&amp;position=lastDbPos">Human GRCh37/hg19</a></li>

The globalNavBar.inc file is used to define what link options display in the top blue menu bar.

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further questions and reply to gen...@soe.ucsc.edu messages will be 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

Training videos & resources: http://genome.ucsc.edu/training/index.html
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

Michael.Rightmire@uni-heidelberg.de


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

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