User:Timothee Flutre/Notebook/Postdoc/2013/12/27: Difference between revisions
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== | ==About organizing a project== | ||
* | * '''Motivation''': when starting a new project, it is very handy to ''quickly'' and ''easily'' set up a ''portable'' structure allowing the project to be ''backed-up'' on other machines, ''shared'' with collaborators and the work to be ''reproduced/replicated'' by colleagues. | ||
* '''OS choice''': concerning computers, one usually has a preferred [https://en.wikipedia.org/wiki/Operating_system operating system]. Yet, in scientific projects where computing is an important aspect of research, the most frequent is [https://en.wikipedia.org/wiki/Linux GNU/Linux]. Thus, even if it's always good to know how to find our way on other operating systems, such as [https://en.wikipedia.org/wiki/Microsoft_Windows Microsoft Windows] and [https://en.wikipedia.org/wiki/OS_X Apple Mac OS X], I will focus in the following on GNU/Linux. | |||
* '''My history''': in 2006, during an internship in a bioinformatics lab, I discovered GNU/Linux. More specifically, I worked on a [https://en.wikipedia.org/wiki/Fedora_%28operating_system%29 Fedora] distribution and was able to install it on my laptop. From 2007 to 2010, during my PhD, I switched to [https://en.wikipedia.org/wiki/Debian Debian] and then [https://en.wikipedia.org/wiki/Ubuntu_%28operating_system%29 Ubuntu] for my laptop, and I used several computer clusters running with [https://en.wikipedia.org/wiki/Solaris_%28operating_system%29 Solaris] and [https://en.wikipedia.org/wiki/CentOS CentOS]. This looks like an anthology of weird names but, fundamentally, all these distributions are more or less similar to each other and can be described as [https://en.wikipedia.org/wiki/Unix-like Unix-like systems]. Please note, however, that all these are not equivalent in terms of protecting your freedom. More broadly, for instance, it is hence much worth knowing about the difference between [https://en.wikipedia.org/wiki/GNU/Linux_naming_controversy GNU and Linux] and, for those who read the [http://www.amazon.com/dp/1451648537/ biography of Steve Jobs], I highly recommend reading the [https://en.wikipedia.org/wiki/Free_as_in_Freedom:_Richard_Stallman%27s_Crusade_for_Free_Software biography of Richard Stallman] (founder of GNU). | |||
* '''Home structure''': bin/, src/, src_ext/, texmf/, tmp/, work/ | |||
* '''Project structure''': analysis/, doc/, download/, figures/, preprocessing/, scripts/, src/ | |||
* '''Editor''': emacs with org-mode | |||
* '''Backup''': rsync | |||
* '''Programming''': templates, git, Autotools, | |||
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