eukaryotic gene annotation plugin

Michael Thon

• March 08, 2013 04:32

I'm woking on a plugin for ab initio gene annotation using Augustus.  I have a development version working on Mac OS and I'd like to get it running on the other platforms before I ask for testers.  I don't have a windows box set up for compiling C sources, nor do I know how to set it up.  Can someone who is set up for windows development download augustus 2.7 from here:

http://bioinf.uni-greifswald.de/augustus/binaries/

and compile static binaries for me?

Thanks!

0

• 

  Michael Thon

  • March 10, 2013 09:27

  Actually, I may have been able to cross compile them - but I haven't tested my executables yet.

  On Windows, do the paths that I pass to the com.biomatters.geneious.publicapi.utilities.Execution instance need to be windows-like strings (with forward slashes) or are they converted automatically? I'm trying to get this plugin running on Windows without installing a full dev environment on windows.  so far, no joy...

  0
• 

  Hilary Miller

  • March 11, 2013 03:01

  That sounds like a great plugin to develop.

  Forward and back slashes generally interchangeable in code on Windows although in case it gets displayed to the user, it is best to make them look correct by using File.pathSeparator.

  0
• 

  Michael Thon

  • March 12, 2013 05:13

  I had to hack the augustus sources a wee bit but I got it running on windows as well as mac and linux.  Here's a very preliminary version if anyone wants to try it.  Its missing a lot of features, there is no documentation, and it will probably crash and present error messages.  If that concerns you, its probably best to wait for a future version. (its working fine for me though...)  

  https://dl.dropbox.com/u/320712/Augustus-0.1rc1.gplugin

  0
• 

  Michael Thon

  • March 12, 2013 05:15

  P.S. If it does work for you, please met me know! (and include your operating system and Geneious version please)  Any and all feedback is welcome.

  0
• 

  Hilary Miller

  • March 12, 2013 07:24

  It works fine for me on Windows 7 using Geneious 6.1.2. It took longer than I cared to wait (several minutes) on human chromosome 22 and the progress bar gives no indication how long it might take, but running it on a small subsequence of it worked well and it correctly found the genes I already knew existed.

  Excellent plugin thanks Michael. I look forward to seeing the finished version.

  0

Please sign in to leave a comment.