Deploying sequenceserver on our LAN

sequenceserver
#1

I am running into trouble configuring the apache server “httpd.conf”. I would like to allow multiple users on our LAN to connect to the server to run their BLAST searches on our local sequence databases. Everything seems to be installed and running properly. Invoking sequenceserver from the command line is successful and serves on the localhost at http://0.0.0.0:4567. As for apache, I am able to connect to the machine over the network and get the “It works” page, but not much more than that.

I’m sure this is a very simple thing to do, but I have no experience setting up webservers. Should I even be bothering with apache for this? If so, what is the simplest way to modify httpd.conf to allow users on our network to run their BLAST searches?

The instructions on the website were great, but when I got to the section on Deploying Sequence Server, I got lost. I’ve figured out how to restart the server and the location of httpd.conf (these things are different on Mac OS X, it turns out) but I am at an impasse in modifying the config file properly. Please help! If you can give directions about setting up the Root URI or Sub URI that are as explicit as the rest of the setup instructions, I’m sure I’ll have no trouble making things work!

With best regards,

John

#2

Hi John,

Thanks for your interest in seqserv. From what I’m reading I’m wondering if you really require apache.

Can other people access you seqserv just using your IP address (or computer name?). For instance if your IP is 192.168.1.56, then does http://192.168.1.56:4567 work, for instance?

ben

#3

Hi Ben,

Thanks for your prompt response. I tried to connect using the server’s IP on our network and port 4567, but it timed out. If I open a browser on the machine itself I am able to go to localhost:4567 with no problems, so the server is definitely working and running. As for the network connection, I’m sure that’s not the problem, as I can ssh between the two with no trouble.

I agree that apache is far more webserver than I need for this task, but the question then just becomes, how do I configure Thin for this task? Sorry to be such a n00b. Please advise.

Best,

John

#4

Hi John,

No worries. If you cannot log into the server, then I would suggest that potentially there is a networking problem. Some networks selectively block ports, so that port 22 (ssh) is unblocked, but port 4567 is blocked. You might have to check with whoever is administering the network?

Neither thin nor apache is required for seqserv, though to “configure” thin just means installing it, like this:

$ gem install thin

ben

#5

Thanks for the info. I’ll look into that.

#6

I’ve had this sort of problem on my local machines too, with their own internal firewall. Are you certain that the machine hosting SequenceServer has the firewall set to allow traffic to port 4567?

#7

Wolfgang,

Yes, in fact, that was the problem in the end. The server on which sequenceserver was installed was running the internal MacOS firewall which, at least on my MacBook Pro, is inactive by default, which is why I didn’t realize that might be the issue. So I had to allow an exception for the Ruby process that corresponds to sequenceserver. Now all is Kool and The Gang. Thanks for the heads up, though.

#8

Yup. You described a typical diagnostic result for that problem - works on the machine itself but can’t be accessed from another machine on the same network…glad I could help!