How to add file upload function in my webBlat

[Chen Sun]

Hi everyone,

 

I build a webBlat server on my local server. But I don ‘t find the file upload function like UCSC genome browser.

 

So, How can I add this function?

 

Thanks,

 

Chen Sun

[Jonathan Casper]

Hello Chen Sun,

Thank you for your question about running webBlat. webBlat itself does not have any support for file upload. The UCSC Genome Browser uses a different CGI named hgBlat, which does support file upload. hgBlat can be found as part of the kent source repository, which is described on our download server at http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads. Like webBlat, hgBlat is designed to work with the gfServer program. While webBlat depends on the "webBlat.cfg" file for its configuration options, hgBlat depends instead on settings found in a combination of a configuration file named "hg.conf" and settings stored in a database named "hgcentral". More information on installing a browser mirror, and the accompanying hgBlat CGI, can be found at http://genome.ucsc.edu/admin/mirror.html.

One of our engineers comments, however, that only 25 sequences can be submitted to hgBlat at a time. That limit also applies to uploaded files. If you would like to run BLAT on more than 25 sequences, we suggest that you try running standalone BLAT on the command line instead.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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[Chen Sun]

Hi Jonathan,

 

The problem is that my reference is not hg19, so the hgBlat is not suitable with me.

 

I am not familiar with CGI, and how can I modify the webBlat to support file uploading?

 

Best Wishes,

 

Chen Sun

 

发件人: Jonathan Casper [mailto:jca...@soe.ucsc.edu]
发送时间: 2015年8月8日 8:56
收件人: Chen Sun <ver...@sjtu.edu.cn>
抄送: gen...@soe.ucsc.edu
主题: Re: [genome] How to add file upload function in my webBlat

[Luvina Guruvadoo]

Hello Chen Sun,

As my colleague Jonathan mentioned in his previous email, webBlat does not have any support for file upload. This is something you will have to implement into the code. Unfortunately, we do not provide programming advice.

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.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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