Facundo Muñoz, MSc in Mathematics, PhD in Statistics from University of Valencia. He is currently a postdoc researcher at the french Institute National de la Recherche Agronomique (INRA). His main research field is spatial (Bayesian) statistics applied to environmental and biostatistical problems. He is currently working on statistical methodologies for the analysis of forest genetic resources.
Being a busy biostatistician, I spend plenty of time glued to my computer. As an immediate consequence, every once in a while I need to set up my working station from zero. Either when I change job (I have done twice this year!), or when I want to update my OS version (upgrades rarely go perfect), or when I get a new laptop.
This involves, you know, installing the OS, the main programs I need for work like R and LaTeX, some related software like a good Control Version System, a couple of Integrated Development Environments for coding and writing, and a dozen of other ancillary tools that I use every now and then.
Furthermore, I need to configure everything to run smoothly, set up my preferences, install plugins, and so on.
Last time I did this manually, I spent a week setting everything up, and in the following days I always had something missing. Then I thought I should have got this process scripted.
Last week I set up my working environment in my new job. In a few hours I had everything up and running exactly the way I like. I spent an aditional day updating the script with new software, updated versions, and solving some pending issues.
I thought this script might be useful for others as well, hence this post. It is version-controled in a google code repository, where you can download the main script.
It is not very general, as installation details changes a lot from system to system. I use Linux Mint, but I believe it should go pretty straightforward with any derivative of Ubuntu, or Ubuntu itself (those distros using the APT package management). Other Linux branches (Arch, RedHat, Suse, Mac’s Darwin) users would need to make significant changes to the script, but still the outline might help. If you use Windows, well… don’t.
Of course, you will not be using the same software as I do, nor the same preferences or configurations. But it might serve as a guide to follow line by line, changing things to suit your needs.
In particular, it provides an almost-full installation (without unnecessary language packages) of the very latest LaTeX version (unlike that in the repos), and takes care of installing it correctly. It also sets up the CRAN repository and installs the latest version of R.
The script also installs the right GDAL and Proj4 libraries, which are important in case you work with maps in R or a GIS.
Finally, it installs some downloadable software like Kompozer (for web authoring), the Dropbox application, and more. It scrapes the web in order to fetch the latest and right versions of each program.
I hope it helps someone. And if you have alternative or complementary strategies, please share!