Question: Newbler And Ubuntu?
0
gravatar for Prohan
8.7 years ago by
Prohan350
United States
Prohan350 wrote:

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

installation assembly linux • 4.0k views
ADD COMMENTlink modified 8.3 years ago by Leonor Palmeira3.7k • written 8.7 years ago by Prohan350
7

Consider posting some specific(s) of the issues you are encountering - perhaps people unfamiliar with Newbler might then be able to offer insights.

ADD REPLYlink written 8.7 years ago by Bio_X2Y3.7k
7

"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?

ADD REPLYlink written 8.7 years ago by Neilfws48k
2

Also give versions of Newbler and version of Ubuntu you tried. That way others may learn what potentially be a problem.

ADD REPLYlink written 8.7 years ago by Darked894.2k
2

PROhan, you can simlpy edit your question and add the requested details.

ADD REPLYlink written 8.7 years ago by Egon Willighagen5.2k
3
gravatar for Pawel Szczesny
8.7 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

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.

ADD COMMENTlink written 8.7 years ago by Pawel Szczesny3.2k
2

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.

ADD REPLYlink written 8.7 years ago by Daniel Swan13k
1

@Daniel: good to know. It would be great to somehow have some accessible database of what works on which platform, or maybe just what does not work on i.e. current stable Debian distro.

ADD REPLYlink written 8.7 years ago by Darked894.2k
1

Using it with Ubuntu and Debian here with success.

ADD REPLYlink written 8.3 years ago by Eric Normandeau10k

Ubuntu 11.04/Newbler 2.5.3. Have 2 problems : 1- GUI: syntax error (" unexpected, 2- CLI: cannot execute binary files. And I don't know how to solve them.

ADD REPLYlink written 8.0 years ago by Mariam Rizkallah20

It worked ;) "extract newbler_CLI_2.5.3.i686" instead of newbler_CLI_2.5.3.x86

ADD REPLYlink written 8.0 years ago by Mariam Rizkallah20
2
gravatar for Leonor Palmeira
8.3 years ago by
Leonor Palmeira3.7k
Li├Ęge, Belgium
Leonor Palmeira3.7k wrote:

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.

ADD COMMENTlink written 8.3 years ago by Leonor Palmeira3.7k
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