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Light1992

Chat Supporto / BLAST in JBrowse

Light1992
May 22nd, 2019
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  1. I'd need some help with the paragraph "How can I link BLAST results to JBrowse" from JBrowse FAQ on GMOD Wiki => http://gmod.org/wiki/JBrowse_FAQ
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  3. I also have SequenceServer on my future website, and it would come in handy to make the outputs of the search appear as a track on JBrowse!
  4. I don't know if I got it right, because the instructions aren't really clear.
  5. 1) I created an empty file called links.rb in the same folder where SequenceServer loads the databases from.
  6. 2) I ran this code:
  7. sequenceserver -D database_dir -r links.rb
  8. changing -D with the path of the folder where they are stored.
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  10. Then, I don't think I got what I have to do later well...
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  12. 3) Possibly, I added the code which appears in the first grey block, only changing my website URL, to jbrowse.conf in the JBrowse directory (I'm not sure at all this was the right place).
  13. 4) I wrote the code shown in the second block in the links.rb file in the SequenceServer databases directory and made the same change.
  14. 5) I ran a BLAST search with my SequenceServer... against a genome... for the same organism for which I had set the reference sequence in my browser, but nothing happened, no tracks appeared.
  15. 6) It mentions a links.rb Ruby config file I can't find.
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  17. I'm sure I missed a lot, and maybe I didn't change some needed parameters in both the jbrowse.conf and links.rb files ... (I just changed the URL) ... Can you help me here? And was what I did correct?
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  27. the way that works
  28. is that it creates a special link in the sequenceserver output
  29. that allows you to view the blast hit in jbrowse, e.g. that link goes to jbrowse with a special track
  30. the links.rb file is the code that is listed in the FAQ entry
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  40. Yes, I figured that out, but I don't get where to add the first block of code when it says...
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  42. We use the addFeatures URL parameter of JBrowse to make the features appear. [...]
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  44. And if it needs or not other changes in the code, besides the URL of my website.
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  51. the addFeatures thing is just in that code block
  52. I think it only needs to put your website inside that codeblock and not much else
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  60. Hmmm. I don't think I got it well because it does nothing :) As I said, I added the first codeblock in jbrowse.conf and the second is the content of the links.rb file.
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  69. which version of sequenceserver?
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  77. SequenceServer 1.0.11
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  87. I got this while trying to let SequenceServer acquire my links.rb file.
  88. I get the same error running as a sudo user.
  89.  
  90. https://pastebin.com/0Kmk9pfF
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