Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Configuring web-server: for production and for development

    25th October 2009

    Production: see http://www.howtoforge.com/how-to-set-up-apache2-with-mod_fcgid-and-php5-on-debian-etch – it is for Debian Etch (which is old-stable), but many of the steps apply equally well to Debian Lenny (current-stable). Also, this is a very basic guide, as if you are going to host multiple sites from multiple clients, you most definitely will need some hosting control panel.

    Development: see http://www.ruzee.com/blog/2009/01/apache-virtual-hosts-a-clean-setup-for-php-developers. This setup works very well, unless you need to create several virtual hosts every day – in which case necessary actions could be partially scripted.

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    Posted in Links, Notepad, PHP, Programming, Software | No Comments »

    Debugging PHP: Eclipse PDT + XDebug + XDebug helper

    8th June 2009

    Stimulated by a bug in a complex and unfamiliar web PHP application with heaps of custom tweaks by other programmers, I decided to try a more professional approach to PHP programming and debugging than the standard var_dump() and family.

    As a result, I’m now using Eclipse PDT with Xdebug and Xdebug Helper (Firefox extension). Now I don’t understand how I used to debug my PHP programs before!

    After proper configuration (I’m using local Apache, but it is also possible to debug remotely), my work flow is rather simple:

    • use my web-app as usual, e.g. tweaking and testing here and there
    • if something server-side goes wrong: click the XDebug helper icon in Firefox, and perform some server-request action (e.g. load a page)
    • debugging is started in Eclipse PDT, where I can step through the code, set breakpoints, and examine all variables
    • as soon as the problem is fixed – click the XDebug helper icon again to continue using the site normally (w/o invoking the debugger)

    It takes some time to get used to, but then it’s a breeze.

    Some advice:

    • don’t use apt-get/aptitude to install Eclipse; it will be much easier both in the short and long run to use some all-in-one package from the Eclipse PDT site; all you need to do – download, extract, run!
    • before actually starting to do anything, tweak the eclipse.ini file by increasing heap size from 40 MiB (default) to some larger value (I used 128MiB). If you don’t do this, then at some point your debugging will become painfully sloooow, and then you’ll start getting tons of “out of heap memory” errors, each one suggesting that you quit Eclipse immediately
    • install XDebug with apt-get/aptitude – worked perfectly, and there’s /etc/php5/conf.d/xdebug.ini not to mess with php.ini
    • do read XDebug guide for PDT 2.x (I’m assuming you got the 2.x version); it should be the only document you will really need to configure everything

    I only wish Eclipse was faster – that is, written not in Java but e.g. C or C++.

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    Posted in Links, PHP, Programming, Software | 3 Comments »

    Debian-Med Project

    3rd September 2008

    There’s a Debian-Med project, aiming to

    develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research

    Debian-Med has several web sites/pages: one at Debian.org (descriptive), and the actual project’s website at debian-med.alioth.debian.org. There’s also debian-med wiki (for developers).

    As of nowadays, Debian-Med has released a number of Debian packages, which are grouped into respective Debian Med Tasks. The Biology-dev task, for example, contains MCL and libsbml packages (among many others).

    Check this project out – you might find that the software you need is already available as Debian package.

    This post was stimulated by Steffen’s comment.

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    Posted in *nix, Links, Science, Software | No Comments »

    Drupal theme development: where to start

    8th June 2008

    Simplest way to develop your custom Drupal theme is to start with some skeleton/wireframe theme.

    In this post, I’m briefly reviewing 4 themes (atck, blueprint, framework, and zen), made specifically to serve as theme developer’s starting point. All 4 are listed with their features (as per Drupal project page of each one), with my personal “impressions” (not based on actual use experience, yet). There’s also my choice and order of preference for the 4 candidates at the end.
    Read the rest of this entry »

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    Posted in Drupal, Links, Notepad, Software, Web, XHTML/CSS | 8 Comments »

    Ukrainian web-portal bigmir.net switched from own free email service to gmail

    30th October 2007

    Just a minute ago, I was shocked after logging in to mail.bigmir.net: instead of the bigmir’s own, HTML-only email interface, I got redirected at the gmail’s “Terms and conditions”, after accepting which I found my emails in the classic gmail mailbox.

    First thing to think about: at least they did transfer all my emails to the new account.

    Second: hey, they had given up their own email interface! Are they leaving the web-portal market of Ukraine? Was the part of their team (which later formed MI6) too important to handle their exodus with no consequences? Is that just a desire to give customers “better” interface and not invest anything into development?

    I hope this won’t be a trend, for every service to have Google behind their servers. Or even just behind the name, to avoid extra complexity of having a server.

    Finally, I think I’ll get used. But it was only yesterday, that I read the Google anti-utopia, where Big Brother’s name is (evidently) Google, and it’s webcams and microphones and search history define each person’s future AND guilt. Scary…

    And I wonder which will be the next service of bigmir.net, “outsourced” like their email.

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    Posted in Misc, Web | No Comments »