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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
113 stars 25 forks source link

Write a server #16

Closed noporpoise closed 9 years ago

noporpoise commented 9 years ago

Write a server command to respond to queries about kmers and links. Requests would be HTTP and responses in JSON. At first the server would hold the graph and links in memory and the data would be read only. Javascript apps could then be written to visualise and interact with the graph.

iqbal-lab commented 9 years ago

This stimulated by GA4GH? Is a good idea.

noporpoise commented 9 years ago

Brought about through debugging and Kiran's visualisation. I got something working quickly that just takes interative input from the user at the terminal:

mccortex31 server -m 1G -p links.ctp.gz graph.ctx

You type in a kmer and it tells you everything it knows about it. Adding HTTP/other requests would allow anyone to write third-party programs to visualise the graph, use it for genotyping etc.

iqbal-lab commented 9 years ago

V cool.

noporpoise commented 9 years ago

Addressed by e458358d. Start webserver with scripts/mccortex-server.py.