error: Couldn't open trackDb.txt in hubCheck
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16 days ago
LDT ▴ 210

I am trying to check my hub via

hubCheck hub.txt


and no matter what I try and do, I am getting the following error

Couldn't open arath/trackDb.txt


Does anyone have any idea or thing on how to solve the error? Here is a link to my data

UCSC hubCheck • 295 views
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Just two comments: (1) normally you would put the groups.txt file in the genome directory (arath/) in your case. And (2) wouldn't you normally call hubCheck using the URL for your hub file? If you run it with -verbose=2 is that the only output you get?

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I see. Well, if you want to make your data generally available regardless of computer, you need to know how to serve files to the internet, which it seems you can do with ftp. However, the documentation states: "please note that hosting hub files on HTTP tends to work even better than FTP"...and this is my experience as well. So learning how to serve a file via http is recommended, though admittedly, it's essentially the same as knowing how to serve a website, which seems less and less common these days (though still very doable, and may or may not be easy depending on your situation).

Nonetheless, if you have access to an ftp server, you should be able to figure out how to access a file via ftp. You'll have to put your hub at that location, and use the URL. So if I were you I would focus on trying to find out how you would place a file on your computer, and then use a URL to access it from a second computer. If you can do that, then you should be able to build you hub there. (as an aside, have you considered Genome Browser in a Box? This would allow you to do everything locally without requiring http or ftp servers).

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Thank you Seidel. It’s so amazing to talk with a pro about it. Thanks a lots, I have learnt a lot

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Dear Seidel, Thank you so much for your reply! (1) I agree
(2) Good point. But I do not know how to do it. Forgive my ignorance. Now I have all my files in the terminal, and I want through the FTP server to mount them to UCSC. Shall I create a URL from the FTP server? Sorry for my naive questions

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Dear Seidel You are awesome. All your suggestions worked well, and now my genomes are uploaded to the browser. Thank you

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Thank you! I'm glad you were able to get it to work :)