The Debian Administrator’s Handbook

Written by two Debian developers — Raphaël Hertzog and Roland Mas — the Debian Administrator’s Handbook started as a translation of their French best-seller known as Cahier de l’admin Debian (published by Eyrolles).

It’s a fantastic resource for all users of a Debian-based distribution.

Accessible to all, this book teaches the essentials to anyone who wants to become an effective and independant Debian GNU/Linux administrator.

Given that traditional editors did not want to take the risk to make this translation, we decided to do the translation ourselves and to self-publish the result. After a successful crowdfunding campaign, we managed to complete this translation between December 2011 and May 2012.

To live up to our free software ideals, we wanted the book to be freely available (that is under the terms of a license compatible with the Debian Free Software Guidelines of course). There was a condition though: a liberation fund had to be completed to ensure we had a decent compensation for the work that the book represents. This fund reached its target of €25K in April 2012.

via The Debian Administrator’s Handbook.

How can I determine if my CPU supports PAE?

While in your (GNU/Linux) shell, simply type:

grep pae /proc/cpuinfo

If PAE extensions are available, you’ll see a string for each core available:

flags : fpu vme de pse tsc msr PAE mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe pebs bts cid xtpr
flags : fpu vme de pse tsc msr PAE mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe pebs bts cid xtpr
flags : fpu vme de pse tsc msr PAE mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe pebs bts cid xtpr
flags : fpu vme de pse tsc msr PAE mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe pebs bts cid xtpr

(the capital PAE is due to my editing, for visibility reasons)

This becomes useful if you need to install RedHat/CentOS 6 on your hardware to support >3GB of RAM on 32bit CPU and more…

EL34 – The home of Eddie

Eddie is a programmers editor for MacOSX and Gnome Linux. Inspired by the Macintosh Programmers Workshop, Eddie brings some of it’s powerful features into a modern lightweight and capable programmer’s editor. Eddie is ideal for C/C++ development using makefiles and shell tools but can also be used with XCode projects. The Worksheet in Eddie is a full-featured shell that combines the power of bash and the ease of editing in a normal text window-like mode. Eddie is equally capable at editing HTML, JavaScript, Python, Ruby, Lua and many other languages.
Originally written for BeOS, it is currently actively developed for MacOSX and Gnome Linux.

Bio-Linux: Ubuntu and bioinformatics

Bio-Linux: Ubuntu and bioinformatics

Hi! Today I’d like to spend some words on a particular Open Source project which aims to make know, test and finally use the available tools for molecolar biology, bio-technologies and bio-informatics in general. This world is overwhelmed by a number of “tools” divided in an ocean of productors, licences, repositories and kind of package (rpm, deb, Z, tar.gz, plain code…). Enter Bio-Linux.

The Bio-Linux project starts from a branch of UK’s NERC (National Environment Research Council) dealing with biology. This NEBC proudly has took in hand this shattered cosmo of open source software for bioinformatics under his own “umbrella” and then has gone further … has created a full GNU/Linux distribution, building over the solid core of Ubuntu (on it’s Long Term Support 8.04 release). Today Bio-Linux 5 is:

  • a LiveCD operating system;
  • a fully functional operating system running on desktop and servers alike;
  • a bioinformatics repository for Ubuntu

and all this is fully supported and given the news on the NEBC and NERC there’s money to guarrantee that for the expectable future. Personally at work I’ve had chance to appreciate this distro in all the flavours listed above and also as a VMware’s appliance.

If you’ve already running an Ubuntu 8.04 box in this wiki page you’ll find how-to add the biolinux repository to your sources.list. There it’s also stated that there’s some kind of compatibility with Debian and also with the latest 9.04 release, even if for a couple of software there are occasional bugs. But, on the workplace, expecially when the user has to USE his desktop and not work to make it run, Ubuntu 8.04 (with an updated copy of OpenOffice and a couple of backports) it THE way go, at least for me.

As a personal, final note, I must regret on the strickt control of the repository … I’ve witnessed a similar Biolinux project, focused on the RPM world being abandoned in 2007 supporting ancient distros like Fedora6 and RedHat 9 … I’d prefer a strong team in the Ubuntu (or $distro) community claiming “we will take care of all things bioinformatics, like it’s done for Compitz or other focused projects in the past. A change of menthality is needed so, when the Public Administration (or a private) invests on an open source technology the RoI must be seen in the product itself (and/or on how it facilitates works or makes you make more money increasing the productivity) and not in a self-owned fancy site claiming “I MADE IT, I AM BIG, GIMME MORE MONEY”. Don’t you think so?