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Docker containers for UCSC BLAT servers with reference genomes, hg19 and hg38

Running containers

$ sudo docker run -it -p 55519:55519 misshie/ucsc-blat-hg19
$ sudo docker run -it -p 55538:55538 misshie/ucsc-blat-hg38

Note that it takes servers for several minuites to prepare k-mer indices.

Query

You have to install gfServer locally

$ wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer

And try command for queries. See http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/

For example, you can see the server status by the following command: gfServer status localhost 55519.

Copyright

Copyright: (c) 2014 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)

License: The MIT license

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