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Question: Toolshed tools for Blastn output for galaxy
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gravatar for rlee03
3.4 years ago by
rlee03 • 50
United States
rlee03 • 50 wrote:

I cowrote a wrapper to run blast off the command line and now it can be executed off my galaxy instance. However I want to know if there are any tools in the toolshed that can run blast output in a graphic html (not TXT). I tried using -html as an output parameter, but I am only getting the tagged html, not the html view.    Other outputs I would be interested in include, but not limited to, phylogeny trees, and anything the ncbi can use. Thanks!

I am familiar already with the outfmt parameter in galaxy. 
output outfmt galaxy blastn blast • 898 views
ADD COMMENT • link •
modified 3.4 years ago by Bjoern Gruening ♦ 5.1k • written 3.4 years ago by rlee03 • 50
0
gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

have a look at the following publication:

NCBI BLAST+ integrated into Galaxy. P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo bioRxiv DOI: http://dx.doi.org/10.1101/014043

Ciao,

Bjoern
ADD COMMENT • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern,

Thank you for your response. I have the blast suite installed but all of the output is text. Is it possible to have html output on a webpage? currently, the only way I can view the html file w/o the tags is if I open up the browser independently?

Thanks.

ADD REPLY • link written 3.4 years ago by rlee03 • 50

Ah, now I got the problem, sorry for being so slow. Have a look at you config/galaxy.ini file and change the following line to True and remove the hashtag.

#sanitize_all_html = False

Cheers,

Bjoern

ADD REPLY • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k
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