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docker-ucsc-blat's Introduction

Docker containers for UCSC BLAT servers with reference genomes, human hg19, hg38 and mouse mm10

Running containers

$ sudo docker run -it -p 55519:55519 misshie/ucsc-blat-hg19
$ sudo docker run -it -p 55538:55538 misshie/ucsc-blat-hg38
$ sudo docker run -it -p 55510:55510 misshie/ucsc-blat-mm10

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) 2015 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)

License: The MIT license

docker-ucsc-blat's People

Contributors

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Forkers

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docker-ucsc-blat's Issues

Deploy to cloud server

A question: is it possible to deploy these containers to a cloud server Ubuntu VM, eg: Google or Amazon?

access to running container

Hi,

docker build -t docker-blast .
...
Successfully built 6601f7b70760
Successfully tagged docker-blast:latest
docker run docker-blast

It failed to open http://localhost:55538/ in the browser.

What did I miss?
Thank you in advance,

Michal

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