I am trying to build a UCSC track hub (a private one).

I have all my hub files on a university server in a simple folder called /hub. I am using Ubuntu 16.04 and the server is also Ubuntu (16.04.3 LTS (GNU/Linux 4.4.0-98-generic x86_64).

I have tried using hubCheck and also simply upload the hub as instructed in the UCSC instructions.

The URL I have used to indicate the location of my hub is:

http://pcxxx.xx.xx.ac.uk/home/username/projects/project-name/hub/hub.txt

However, in both cases, I get the following error:

Couldn't open http://webserver-id/home/username/projects/project-name/hub/hub.txt
TCP non-blocking connect() to webserver timed-out in select() after 10000    milliseconds - Cancelling!

I am not very knowledgeable in servers and protocols (http, ftp etc). But am I right to think that this error means that my hub is somehow not internet accessible? I'm struggling to understand what this error means. When I log onto the server, I automatically arrive in my home folder: /home/username. My hub is in /projects/project-name/hub.

Is there a way I can check if my folder location is indeed internet accessible?

  • Please edit your question and explain how you've set up your server in more detail. What operating system are you using? What server software? When do you get this error? What instructions did you follow (your link doesn't show any instructions; tell us what you did). The more details you give us, the likelier it is we'll be able to help you. – terdon Sep 4 at 14:05
  • Apologies. I have just added more details. – m93 Sep 4 at 14:09
  • Thanks, now we know the operating system, but the other questions are also relevant. Please edit and clarify. Also tell us whether you actually use http://webserver-id/home/username/projects/project-name/hub/hub.txt as the URL. I assume you use an actual URL, right? We need to know what kind of web server you are using (apache?), how you've configured it and all the other things I asked in my previous comment. – terdon Sep 4 at 14:16
  • So what is webserver-id? Are you using the actual string webserver-id? not the ID of your web server? If so, you need to take a step back and learn about how to set up a webserver. I suggest you read help.ubuntu.com/community/ApacheMySQLPHP or other tutorials (search for LAMP). If I misunderstand, please edit and clarify what works, how you set it up and what should work but doesn't. – terdon Sep 4 at 14:19
  • Just added the URL I actually used. As I said, I have no real idea if this is how you contruct a URL. As far as I know, the server is using Canonical landscape. – m93 Sep 4 at 14:19
up vote 2 down vote accepted

Check your webserver functions from the top down. You can do this from any WEB browser, even one that is on the webserver system itself. For example, does this link function: http://webserver-id/ and provide you with a home page for that WEB service ? If not, then there is not apache WEB server on that system, or is mis-configured.

Next, depending upon how that Apache is configured, try this URL http://webserver-id/~username/ which would be a normal way to get to user directories via Apache. This would actually be looking for a special directory in your HOME directory, perhaps something like $HOME/public_html/ You would need to place something in public_html/ to access, for example a tiny WEB page:

<html><head><title>my home directory</title></head>
<body><h1>hello world</h1></body></html>

If that works, then you need to place your hub files in this public_html/ directory.

Your Answer

 

By clicking "Post Your Answer", you acknowledge that you have read our updated terms of service, privacy policy and cookie policy, and that your continued use of the website is subject to these policies.

Not the answer you're looking for? Browse other questions tagged or ask your own question.