Add codeml code to Bioruby
Reported by Michael Barton | July 25th, 2008 @ 02:27 PM | in Estimate sitewise evolution rates
Dump the CodeML code in my own BioRuby branch. It's not really practical to have in my own library as I have to copying it around to different servers. Add to my own BioRuby github version, then I can clone it into my own gems repository.
Comments and changes to this ticket
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Michael Barton July 25th, 2008 @ 04:55 PM
- State changed from “new” to “open”
Dumped code. Added testing next.
Then stick into cost in evolution.
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Michael Barton July 28th, 2008 @ 04:47 PM
Put a section of testing into BioRuby code.
Not possible to test CodeML running it self as is platform specific and will require a compiled binary.
Instead will split portion of code into separate parser so the results can be correctly parsed. Therefore configuration loading options can be tested, as well as the result parsing options for the follow up.
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Michael Barton July 31st, 2008 @ 01:50 PM
Created parsers
Majority of CodeML code is in BioRuby now.
Just need to fix few minor things
- Default config for run method is not appropriate
- rate file needs to be an essential parameter
- Finish Documentation
Test CodeML in project, then send pull request.
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Michael Barton July 31st, 2008 @ 01:53 PM
- State changed from “open” to “hold”
Wait till alignment positions can be loaded quickly and in parallel using skynet.
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Michael Barton August 19th, 2008 @ 02:12 PM
- State changed from “hold” to “resolved”
Codeml added to bioruby by managers
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Michael Barton