Autarchy of the Private Cave

CLANS (CLuster ANalysis of Sequences).
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I love Debian, too.

Though I prefer ‘testing’ (which is currently codenamed Lenny) over ‘stable’ (aka Etch).

If you get Segmentation fault when trying to run fgl_glxgears in your Debian desktop environment, most often this would mean that 3D acceleration isn’t enabled.

For the case of ATI (and ATI Mobility) Radeon series, the easiest procedure would be (doing all as root, or prepending sudo to all commands):

1. aptitude update, to ensure you’ve got the list of latest packages
2. aptitude install fglrx-driver fglrx-control fglrx-kernel-src, for the actual driver; I also installed fglrx-atieventsd and fglrx-glx (these are driver-recommended packages)
3. aptitude install module-assistant, required for building the kernel module
4. module-assistant prepare, to verify that you have everything needed for the module build procedure
5. module-assistant update
6. module-assistant auto-install fglrx, to build and install the fglrx kernel module
7. depmod -a
8. modprobe fglrx, to load the fglrx kernel module
9. aticonfig ––initial, to configure ATI’s device section in /etc/X11/xorg.conf (for more options, see aticonfig ––help)
10. reboot

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For the COTRASIF tool, I’ve been using the Ensembl Compara database (since release 47) to automatically import into COTRASIF gene orthology mappings.

However, with the E!50 release, the Compara database was dropped.

Looking for another option to get orthologs from Ensembl (using martservice, via biomart.org), I tried using the standard query – selecting “Homologs” group on the “Attributes” page for a single species database, and then selecting appropriate second species to get orthology mappings.

Imagine my surprise, when not only in the interface, but also in the generated XML file I found attribute names like “cow_ensembl_gene” :-O

I only need 11 species at the moment, and excluding the sufficiently unique name mappings like “zebrafish – danio rerio”, there is a number of questionable mappings: “yeast” for S. cerevisiae (could be S.pombe), “rat” for R. norvegicus (could be R.rattus), “anopheles” for A.gambiae (could be some other Anopheles). Other mappings might be also non-unique, especially for people working with different species of the same genus.

Am I missing some system in this naming “convention”, or am I the only one who finds it strange?

Is there a way not to use “common species names” when importing orthology data from Ensembl with the help of martservice?

To cut the long story short: for the final evaluation, I had this line of control panels:

• SysCP
• Domain Technologie Control, DTC
• Virtualmin (also Webmin, Usermin)
• ISPConfig
• RavenCore (no longer developed)
• GNUPanel

SysCP: looks good to me (though demo isn’t functional), has customer billing module. Unsure as to where it is used, but most probably sponsors are also the users of SysCP. Majority of support forums are in German.

DTC: has no demo, only some screenshots. Has a set of packages for Debian lenny (which is a huge plus for maintenance and future upgrades). DTC is being developed by GPLHost, and is also used by GPLHost – so this is a live (used) distribution. Seems quite feature-rich.

Virtualmin claims to be the “world’s most powerful and flexible web server control panel”. Virtualmin offers 4 means to control it: Web, mobile device, command line, and remote API. There are both screenshots and demo. Has both GPL and Professional versions. GPL version has a number of limitations, comparing to Pro version. From what I’ve read about Webmin (all three – Virtualmin, Webmin, Usermin – are just different “layers” of server control), it is a framework with a number of “interface scripts”, which allow to control various services. As such, it is easily extendible, but is not monolithic – in the sense of module inter-dependencies and action triggers.

RavenCore was a promising CP.

GNUPanel is a year-old control panel, but has a news item on the front page (dated August, 17) promising new, completely rewritten release somewhere in October. By the feature list, looks promising. However, I need the panel right now, and even in October, that will be quite a rough release, not really used/tested anywhere, so not a good option as well. But GNUPanel is a panel to check in half a year for progress.

As the final choice, I had ISPConfig (which seems to be the best by people’s comments), and which is also quite widely used, and is easy to install onto Debian (at least the Perfect setup: Debian Etch says so), and DTC. I discarded Virtualmin (for the poor functionality of the GPLed version), RavenCore (for the lack of current descriptions and non-functioning demo), GNUPanel (which just isn’t ready yet), and SysCP (because ISPConfig seems better ).

As DTC has Debian packages (and will be easier to maintain/upgrade), I decided to try it first. I already have it installed (that’s easy, esp. if you first read the DTC Debian Express Setup). Later I might post my impressions from using DTC.

Update: DTC is indeed easy and pleasant to use. I had problems allowing FTP and SSH access using MySQL authorization, but at least FTP was an easy one to fix (SSH access with MySQL authorization is still unconfigured, but that’s a low priority for me). There is a minor concern about the files and directory permissions setup, but thanks to chrooted environment that is only minor concern. Use of a single Apache installation for hosting admin and serving user sites might be a sub-optimal decision, but it works. Traffic and disk space accounting are plain superb! Server memory use for the dtc-toaster installation is troublesome, but for a powerful RAM-my server that is not a problem (I now have about 800-900MiB RAM occupied, but that includes the XCache’s cache, quite big MySQL cache, and loads of Apache and PHP modules).

But I’m still willing to try other control panels. As I expected, GNUPanel hasn’t released anything yet; Ravencore‘s online demo is still unfunctional; ISPConfig has recently released RC (and their demo is working as it should and as it used to); SysCP is also up and running fast. If my little hosting service starts pouring in some cash, then I’ll try SysCP on my second server – to compare it with DTC, and choose one of them for further support/extension/localization.

There’s a how-to on the topic at howtoforge.com.

Note, that for the suggested solution to work, NAT/firewall should be “transparent” for outgoing ssh connections.

2008 South Ossetia war