Tag Archives: ubuntu

MrBayes and Ubuntu

A quick tutorial on how to install MrBayes on an Ubuntu system.

Step 1. Open Software Centre

Step 2. Search for ‘mrbayes’ and hit enter

Step 3. Click ‘Install’

Or, alternatively, open a terminal and type ‘sudo apt-get install mrbayes’. And to run MrBayes, open up a terminal and type ‘mb’. That’s it. I just spent 15 minutes downloading and compiling the software from source, when it was already done for me. Oh well.

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pdflatex errors and R

I was getting an error checking packages in R on an Ubuntu 10.10 machine using the ‘R CMD check’ command saying:

LaTeX errors when creating PDF version. This typically indicates Rd problems.

I have no idea what R’s problem with pdflatex was (I’ve been using pdflatex for writing papers just fine) but once I installed the texlive-full package (a metapackage that installed all sorts of other packages) the check ran without any errors. If in doubt, this package seems to install everything that might be missing (along with the kitchen sink).

ape and geiger in R

Just a quick tip if you want to use the geiger package in R on an Ubuntu system, there are a few things you need to make sure you do. First, make sure you’ve installed the gfortran package and lapack-dev package in order to build the source packages. As well, you may need to reinstall the r-base package after you’ve done this. I was getting an error message like this:

/usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv

It seemed to go away after I reinstalled r-base and restarted the R session, although I’m not sure I needed to do both. Either way, it works now.

64-bit MrBayes

Just a quick note: if you’re running a 64-bit install of MrBayes in parallel, you will probably need to use this page to apply some patches to the source code:

http://technical.bestgrid.org/index.php/Bioinformatics_applications_at_University_of_Canterbury_HPC#Installing_MrBayes

I was having problems getting MrBayes to work on a workstation running 64-bit Ubuntu, but once I started fresh and first applied those patches, things seemed to work without throwing a ‘segmentation fault’ error during the ‘sump’ function.

Field computing solutions

I have been eyeing up the Nokia n810 tablet recently, thinking about how useful it might be in a field setting.  The n810 is essentially a small, slimmed down computer running on an ARM processor (versus your typical Intel chip in most computers). ARM chips are used in most low-power devices such as mobile phones, where battery life is an important consideration. Likewise, out in the field we don’t always have easy access to electricity, although we have started to experiment with solar panels and battery packs. There are similar (and likely more computationally powerful) devices that use Intel chips, but at this point their price is a fair bit higher, and from what I could see the power draw is greater as well. The thing about the n810 is that it can be charged from a USB port, versus the much higher power requirements of something like a laptop. While the n810 comes with a Linux distribution called Maemo, people have recently managed to port Ubuntu to the device (as well, Ubuntu has been working up an ARM distribution). By using something like Ubuntu on the n810, we have a full suite of applications that we can use, from word processing (although I think OpenOffice on it would be a little unwieldy) to GIS.

While ths seems like a neat idea, the question becomes also, why? While some of the things like GIS might be nice, so that we could be updating our databases in the field, they’re probably not necessary. I have thought about whether it would be useable for reading pdfs or books, to cut down on weight, but how much weight would we really cut out if we need portable power solutions? I still would like to try it out for writing things like manuscripts, but the small keyboard size may make this a problem too.

Nonetheless, I think that it could be a worthwhile thing to try, as the costs to try it out are always coming down.

Portable OS

Lifehacker (and a few other places) have a story on Portable Ubuntu, a take on the more popular Portable Apps suite of programs. This makes me start thinking about how far off we are to a truly portable operating system. With Portable Apps at the moment, I can take all my programs and settings with me and use it on any computer (provided it runs Windows, which in my family is actually pretty rare). However, my ideal scenario, which may never occur, is to have a full OS-on-a-stick that I can insert in virtually any computer, whether it be Mac, Windows or Linux, and use it just like I would the native system. This would include things like a mapping suite, some version of R, as well as all the other typical office programs. In some way, this could be the ultimate stripped down laptop; super portable, useable almost anywhere you can find a computer. Thinking of it again, having the stick be a mirrored image of (most) of my laptops hard drive would be great as well, so I can take my work with me and not have to worry about what version I’m working on. Of course, for that I could always use Google Docs or something, but until they have internet access in the field, I need a non-cloud solution.