Re: [Genome] Genome Digest, Vol 93, Issue 10

[Belinda M. Giardine]

***original message***

Hello,
My name is Steve Bullard and I work at the University of Iowa. I am trying
to put up a custom track of our variants on chrom 9. I can get them to
upload but would like to attach data to each snp similar to what you get
when you click on those linked to dBSnp. We have our own sequencing data
and
also would like to include associated P-values and raw #'s of case control
data. Is there a way to link the data to the Snp shown. I have been
working
with Robert Kuhn as my PI Jeff Murray is involved in the Facebase project
and has contact with Bob. However Bob suggested I contact his staff via
this
link. I have attached the file I have been uploading to get the track
basics
to show up.

Thanks,
Steve Bullard

*************************

Hi. What you want is on genome-test, and will be coming to genome as soon
as it has been more thoroughly tested. It is a new format for custom
tracks that I call bedDetail that adds two fields to the normal bed format
to allow added information on the detail page like you requested.

Belinda

[Alex Reynolds]

I am making genome-wide figures using the Genome Graphs tool of the UCSC browser. This looks and works great.

However, as I have a number of these to make, I'd like to try to automate the process.

I downloaded the hgGenome cgi-bin binary via instructions at http://genome.ucsc.edu/admin/jk-install.html, but I'm not sure what arguments it takes, or if I can use it as a command-line tool to automate making figures.

Is anyone familiar with hgGenome or its use on the command line?

Thanks,
Alex

[Galt Barber]

The cgi programs are typically intended to be run inside of apache
and they use additional resources such as databases and the cart
and various binary data formats.

-Galt

[Alex Reynolds]

I understand that. Our lab has a local installation of a UCSC Genome Browser, so I would have access to those database resources.

Is there a way to issue (for example) a "wget" or "curl" command, packaging the requisite POST and GET variables in an HTTP request to hgGenome, so as to automate figure generation?

-Alex

[Maximilian Haussler]

Hi Alex,

If you have your own mirror, you can run all CGI programs from the command
line (see:
http://genomewiki.ucsc.edu/index.php/Browser_Installation#If_it_doesn.27t_work...
):

* Use the arguments from the URL and replace the & with spaces
* Call the CGI from a command line and copy the arguments just after the
CGI, like this "/var/www/cgi-bin/hgc hgsid=337 o=14394787 t=14395353

It should create the images which you can then use in your own cgi scripts.
If you need more details no this, don't hesitate to email the list again.

cheers
Max

> _______________________________________________
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>

[Galt Barber]

Note that cgi run from the command-line will use $HOME/.hg.conf
which must be configured appropriately. You will probably
want to use the settings in your cgi-bin/hg.conf for the most part.

-Galt

> Genome maillist - Gen...@soe.ucsc.edu <mailto:Gen...@soe.ucsc.edu>
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>

[Galt Barber]

In addition to the direct command-line method,
you can use wget, curl, perl or python with web libraries, etc.

Here is an example from one of our mailing list users of driving
hgGenome via URL:

http://hg/cgi-bin/hgGenome?db=hg18&hgGenome_dataSetName=hmYRI_CEU_tdt_TDTgg&hgGenome_dataSetDescription=GalaxyGG_data&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess&hgGenome_columnLabels=first%20row&hgGenome_maxVal=&hgGenome_labelVals=&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http%3A%2F%2Fgalaxy%2Fdisplay_as%3Fid%3D351%26display_app%3Ducsc&hgGenome_doSubmitUpload=submit

In particular, note that the data is made available to hgGenome
via URL. That URL is then itself url-encoded inside the larger URL.

&hgGenome_uploadFile=url-encoded-url-to-actual-data-in-genome-graphs-text-input
-format

You could also use an html form POST and provide the data contents
directly via
hgGenome_uploadFile form variable.

The output will be a graphic file (png) stored in trash.
You will have to parse the output to find the url or path.

When run from the commandline, cgis will make directories and files
under both . and ../trash

-Galt