New Laptop, and how to get science / phylogenetics crucial software onto Ubuntu

About a week ago I finally bit and bought a new laptop, a Dell Inspiron 11 3162, as my old netbook has grown old, slow, and of short battery life.

Yes, this is not exactly high-end, but the point is, I don't want high-end. A really good, high performance, cutting edge laptop would come with two downsides. First, it would be optimised for being high performance and not for being light and small; and I really want something that travels easily. Second, it would be expensive; and I want something cheap - we are talking less than AUD400 here - so that it will not be too painful if it gets damaged or stolen during field work or a conference trip.

The new machine came with Windows 10. I think it is a psychological defect on my part, but whenever I try to use Windows 8 or 10 even just for a few minutes I get really upset. Not trying to proselytise here, just my personal problem. A real problem, however, is that this model of laptop comes with storage of only 32 G on a card, no hard-drive. I assume the idea is that many people use the cloud these days (I don't), but still this is a tad on the ridiculous side. Windows 10 took up very nearly half of that space, so install a few things and get a few security updates and you hit the wall.

Having considered these two issues, I carpet-bombed Windows and installed Ubuntu 16.04. By itself this operating system takes up about 3.3 G without and now c. 8 G with various programs and packages I installed on top of it, still only half of what Windows did by itself. So, yeah. Also, I can now click on something and the computer does not have to think for 3-4 seconds before it reacts. As a colleague sardonically commented on the performance issues of Windows, "Intel giveth, and Microsoft taketh away." I also bought a micro card to fit into the little slot on the left side of the laptop, and it works nicely as additional storage, contrary to some comments I have seen on the web. It merely had to be formatted for Ubuntu.

Mostly I use my laptop for simple things, like Skype, checking eMails, writing on a manuscript, etc., but generally not to run time-consuming analyses. That being said, I like to have some analysis software on there too in case it becomes necessary during travel. It has to be admitted that one of the disadvantages of Ubuntu is still that it is not always trivial to find and install specialised software. As I just had to do exactly that, I thought I would use this post to collect my recent experiences. Perhaps somebody will find it useful before it is too much out of date.

First, the software centre was weirdly empty. Here I found a post on the ask ubuntu forum helpful.

If you have the same problem, open terminal and run:

sudo apt update
sudo apt upgrade -y

Now for my personal must-haves and how I got them:

Inkscape
(Vector graphics program, e.g. for editing figures for a manuscript.)

No problem installing from Software Centre.

GIMP
(Pixel graphics editor, for photos.)

No problem installing from Software Centre.

R
(Statistics software.)

There are probably different ways of doing it, but I followed the instructions from digitalocean.

rstudio
(GUI for R.)

Download the relevant .deb file from the program website, right-click and select to open it with the software centre.

Java
(Required to run several of the other programs here.)

I got JDK instead of merely JRE, just to be on the safe side. Open terminal and run:

sudo apt-get update
sudo apt-get install default-jdk

Source of information: digitalocean.

Acrobat PDF Reader
(Sadly it seems to be the only PDF reader on Linux that can edit complex PDFs such as used for grant proposals by some funding agencies. Only a very old version is available as Acrobat has discontinued Linux support.)

Open terminal and run:

sudo apt-get install libatk1.0-0 libc6 libfontconfig1 libgcc1 libgdk-pixbuf2.0-0 libglib2.0-0 libgtk2.0-0 libidn11 libpango1.0-0 libstdc++6 libx11-6 libxext6 libxml2 libxt6 zlib1g lsb-release debconf

wget http://archive.canonical.com/pool/partner/a/acroread/acroread-bin_9.5.5-1raring1_i386.deb

sudo dpkg -i acroread-bin_9.5.5-1raring1_i386.deb

Source of information: ask ubuntu forum.

In my case, however, I experienced some errors. Apparently Acrobat Reader requires some outdated packages to run, and Ubuntu does not want to install them because it has got the newer versions. The system itself then kindly suggested to me to run a command to fix the problem. I hope I remember correctly, but I think it was simply:

sudo apt-get upgrade -f

The f parameter is supposed to fix broken dependencies. That command (or one very much like it) solved the problem for me, and I was able to start the reader.

AliView
(Sequence alignment editor.)

Following the instructions on the program website should have worked, in principle. However, I realised only then that Java was not yet installed, and AliView obviously wouldn't work without it. Download the aliview.install.run file, change its file preferences to make it executable, open terminal, go to relevant folder, run:

sudo ./aliview.install.run

MAFFT
(In my eyes the best sequence alignment tool, can also be called by AliView.)

After experiencing some problems trying to install from the rpm file that is available on the program homepage I found an entry on howtoinstall.co that simplified things. Open a terminal and run simply:

sudo apt-get update
sudo apt-get install mafft

That was easy.

PAUP test versions
(Phylogenetics software implementing various methods.)

This comes as an executable. Obtain Linux distribution from program website, unpack, set file preferences to allow the program being executed, done.

TNT
(Parsimony phylogenetics software.)

Obtain Linux distribution from program website, unpack, set file preferences to allow the program being executed, done. When running the program the first time you will have to accept the license agreement, as opposed to during an installation.

MrBayes
(Bayesian phylogenetics software.)

Available on github and sourceforge. I downloaded and unpacked it, opened a terminal, navigated to the relevant folder, and followed the instructions for compiling that are given in the appropriately named text file. Worked beautifully, only I had to disable Beagle, as prompted during compilation.

FigTree
(Phylogenetic tree viewer.)

Java program, so simply get it from the program website, unpack, and set the JAR file to be executable in its preferences. It should then be run by Java whenever it is opened. I find it useful to create a link on the desktop for easier access.

Tracer
(To examine the results of MrBayes runs.)

Java program, so simply get it from the program website, unpack, and set the JAR file to be executable in its preferences. It should then be run by Java whenever it is opened. I find it useful to create a link on the desktop for easier access.

jModelTest
(Model testing for Likelihood and Bayesian phylogenetics. For larger datasets I would not use the laptop, of course, as it takes forever and benefits greatly from parallel processing.)

Java program, so simply get it from the program website, unpack, and set the JAR file and the PhyML program (!) to be executable in their preferences. It should then be run by Java whenever it is opened. I find it useful to create a link on the desktop for easier access.

WINE
(Windows emulator, just in case)

No problem installing from Software Centre.

SciTE
(Text editor with many useful functions, for data files etc.)

No problem installing from Software Centre.

Skype
(Video calls.)

Download the .deb file from the program website, right-click and select to open it with the software centre.

ClamTK
(Virus scanner.)

No problem installing from Software Centre.