Hi, I'm looking to run Newbler on Ubuntu and can't seem to get it going. Anyone have any luck? If so - do you have the GUI going and on which version of Ubuntu.
Thanks
I did made some progress in running Newbler (couple of versions ago) under both Debian and Ubuntu. I needed to fix some of the paths inside launching scripts and GUI was working fine (it's Java based after all and you have it embedded in the package).
However on the long run Debian/Ubuntu might not be the best OS of choice. We had issues with Newbler hanging on Roche's test data (looked like issues with system-specific paralelization, but I might be wrong). If you don't have RedHat, the whole package runs fine under CentOS.
You can also look into SeqAnswers forum what is the current status on Roche's software.
It also works swimmingly under Fedora. I agree with Pawel though, despite what you might be running in house in general, the chances are that commercial Linux software will be build against a RedHat derivative. We run CentOS and Scientific Linux machines alongside our normal core Debian/Ubuntu machines to alleviate such problems.
In order to run Newbler's GUI under Debian/Ubuntu, you just have to change the paths for a couple of scripts as described here (http://seqanswers.com/forums/showthread.php?t=1048). I have never had any problem running it under Ubuntu.
The command line, however, works directly out of the box, with no fixes needed.
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version 2.3.6
Consider posting some specific(s) of the issues you are encountering - perhaps people unfamiliar with Newbler might then be able to offer insights.
"Can't seem to get it going" is insufficient information. What steps have you tried? Did you follow an online guide? Are there specific error messages?
Also give versions of Newbler and version of Ubuntu you tried. That way others may learn what potentially be a problem.
PROhan, you can simlpy edit your question and add the requested details.