Summary
Getting Linux
Try ![[WWW]](http://wikispot.org/wiki/eggheadbeta/img/sycamore-www.png){kind=small}
Ubuntu. You can test it out on a live-cd, install it on a separate partition, or install it in a virtual environment inside Windows or OSX. Alternatively, give PhyLIS a try.
Getting Started
gedit is the standard text editor on Ubuntu. While graphical user interfaces have become common and polished for most Linux applications, it always helps to learn to use the terminal. Ubuntu provides an excellent introduction.
Compiling from Source
Most software is available as a binary — a program that has already been compiled to run on a particular architecture of computer (such as OSX or Windows, or some flavor of Linux). Whether or not you use Linux, at some point you may find software that you have to compile from source. In general this can be very tricky, but here are a couple pointers that might help you get started.
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Download and extract the archive (.zip, .tgz or whatever it might be).
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Look inside that folder for any file called README or INSTALL, they are the best place to get started, but aren't always provided.
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The standard install sequence is:
./configure make sudo make install
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configure scripts are often not provided for bioinformatics software, so chances are the first command won't work. This script searches your computer to find what kind of compilers, etc are available for installation. Often this isn't necessary, hence it is ignored.
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make is the most important command. This runs a script that tells the software how to compile. If it runs successfully, you should end up with an executable binary file. You can now run the program using
./executable_name
from a terminal window inside the directory.
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A make install routine often isn't provided either. All this does is add the binary to your path, so you can call the program from the terminal regardless of what directory you are working in. You can do this by hand using:
sudo cp executable_name /usr/bin
Installing Software
Java Programs
Java programs are cross-platform, you'll just need the java runtime environment. Install the Sun Java 6 Runtime environment: sudo apt-get install sun-java-jre
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BEAST
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Tracer
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FigTree
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Mesquite
C / C++ programs
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RaxML — C, just run the gcc version of the makefile. Haven't tried the MPI version.
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BEST — C compiles fine with make.
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Brownie — C++ won't compile.
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Garli — C++, requires Nexus Class Library installed (C++ library which installs fine with configure, make, make install).
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Phylocom — R, C (go to src directory and type make),
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MrBayes — Compiles fine with make, but is also in the Ubuntu universe repositories. just: sudo apt-get install mrbayes
R programs
Install R: sudo apt-get install r-base
all packages install fine from within R: install.packages("package_name")
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ape
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ade4
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ouch
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geiger
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laser
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