Could it be an issue of port opening? I do everything as super user, thus I assumed that biomart would open the port by itself. Should I, and can I, open the port beforehand?
To put things in context, all I did from the start was checkout the repository, run ant, and then follow the quickstart example as presented in the manual. I wouldn't be surprised if I skipped a basic local setting, not worth mentioning in a user manual. I assume that there must be some IT issue, rather than anything related to biomart itself. Do you have any suggestion of key points I should check separately to the BioMart set up? Based on my experience in installing software, issues generally arise from very basic considerations, such as access right and network security. I think the key point here is the "time out" error message. If anyone got that before, I'd be grateful to know how they fixed it. I am pretty sure that the server is starting (the button turns to "Stop Server", after the error message pops up), but the communication is probably blocked at the port level. I don't have experience in network security, I don't really dare to change anything without advice. Thanks for for your answer though! Kevin On 4 October 2012 14:55, Arek Kasprzyk <[email protected]> wrote: > Hi Kevin, > I regularly install BioMart on various versions of Mac OS X (recently > 10.7.5) and never encountered the type of problems that you are > experiencing. > > a > > > On Wed, Oct 3, 2012 at 9:50 PM, Kevin Rue <[email protected]> wrote: > >> Hello everyone, >> >> I am an early PhD students in bioninformatics, and wish to integrate gene >> expression microarray data that my group has generated into the BioMart >> context. (We've mapped the probes to the Entrez & EnsEMBL genes IDs) >> >> As per a previous email yesterday, I tried installing BioMart on the >> current small server of the lab. The installation was successful, but I get >> a timeout error every time try to start the quick start example in the >> manual. (which is missing some details about troubleshooting, to my taste). >> The server runs on Debian 5.0.9, quite outdated since even the apt-get >> command isn't able to read headers... >> >> I got an blank PC to try and set up a new server, and now I'm turning to >> you, dear community, to advise me with a configuration proven to be >> compatible, and run smoothly a BioMart instance. >> Could anyone suggest such a configuration (OS)? >> >> Thanks in advance, >> Kévin >> >> -- >> Kévin RUE-ALBRECHT >> Computational Infection Biology PhD Programme >> University College Dublin >> Ireland >> http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en >> >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> >> > -- Kévin RUE-ALBRECHT Computational Infection Biology PhD Programme University College Dublin Ireland http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en
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