Autarchy of the Private Cave

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    Archive for the '*nix' Category

    MultiParanoid vs. QuickParanoid: pro et contra for each

    9th July 2013


    Here we present a new proteome-scale analysis program called MultiParanoid that can automatically find orthology relationships between proteins in multiple proteomes. The software is an extension of the InParanoid program that identifies orthologs and inparalogs in pairwise proteome comparisons. MultiParanoid applies a clustering algorithm to merge multiple pairwise ortholog groups from InParanoid into multi-species ortholog groups.


    QuickParanoid is a suite of programs for automatic ortholog clustering and analysis. It takes as input a collection of files produced by InParanoid and finds ortholog clusters among multiple species. For a given dataset, QuickParanoid first preprocesses each InParanoid output file and then computes ortholog clusters. It also provides a couple of programs qa1 and qa2 for analyzing the result of ortholog clustering.

    So… both use InParanoid… Are there any differences? Let me list those which I’ve found.

    Read the rest of this entry »


    Posted in *nix, Bioinformatics, Software | 2 Comments »

    Hands-on examination of Linux disk caching effects

    8th July 2013

    LinuxAteMyRAM :) (also as a PDF: Linux disk caching effects)

    To examine the behavior of your Linux box disk caching under specific loads, see Linux write cache mystery (PDF).

    To understand what is going on, see also The Linux Page Cache and pdflush (PDF) by the same author, Gregory Smith.

    Another useful resource is OpenSUSE’s Tuning the Memory Management Subsystem, which nicely explains some of the kernel cache/memory-related configuration options.


    Posted in *nix, Software | No Comments »

    Free private git repository hosting

    29th August 2012

    Github is awesome and still improving, but sometimes I’d prefer to have some of my repositories hidden from the eyes of the public – not so much because of the code value (though that is also important sometimes), but rather because those repositories are all “work in progress” or “short-lived” and may have so much junk in them at some moments in time that it would simply be too embarrassing to publish this untidiness.

    Previously, I’ve used gitosis to setup git repository hosting on my server. I’m still using it for long-living projects, but I’m now lazy enough to dislike the steps needed to setup a new repo (and I’m creating more and more new repos, some of which are likely to die very young). Some kind of GUI would help, but gitweb seems not that useful to me (here’s how to make it work with gitosis, and another recipe, or maybe just try gitosis-web or gitosis-web-admin).

    Another downside is that gitosis is no longer actively maintained and was even removed from ubuntu repositories. Suggested course of action for gitosis users is to migrate to gitolite. However, basic design of gitolite is the same, so personally (looking for something easier to use) I see only minor gains in this migration (which I’ll have to perform anyway sooner or later).

    Another interesting self-hosted option is girocco. Too bad I have absolutely no experience with, so it’s hard to tell if girocco is convenient to use or not… Comments are welcome.

    Using dropbox for git repositories (also here) seems a nice and fairly easy option, with only a few downsides: it’ll eat your dropbox space (which is still much more than you get from free git hosters), and it isn’t that easy in a multi-user environment. Also, you will have to setup dropbox on your headless servers where you may want to run your code, which isn’t exactly what I’d want to do. Same arguments apply to git on google drive.

    An alternative to various self-hosted systems would be to use an existing system with free private projects. Git wiki has a list of hosts to start with.

    Here’s a brief summary of the options I’ve found relatively attractive (see below for my experience with 3 of the listed services). (See also this recent comparison.)

    Providers \ Features
    Paid plans?
    AssemblaUnlimitedUnlimited1 GB+
    GIT EnterpriseUnlimited101 GB+
    ProjectLocker120.2 GB+

    Initially, I found GIT Enterprise and Assembla to be the most attractive options to try. After trying both, I found Assembla faster and generally more attractive to work with. It wasn’t immediately obvious how to create more than one source repository, but after figuring that out everything is smooth.

    However, after trying BitBucket, I had immediately switched all my assembla repositories to it :) BitBucket is just like github, but with free private repositories. It also has an issues tracker and a wiki. It even allows small teams to work on private repositories!


    Posted in *nix, Links, Software | 1 Comment »

    tudu: a beautiful ncurses to-do list application

    11th October 2011

    tudu is just what it says in the title, and is written in C.
    All the functions are mapped to keys. Extremely flexible: you can use it either as a simple to-do list, or utilize a bunch of optional features (priorities, schedules, deadlines, categories, tags, maybe something else).

    If you (like me) love ncurses – you will love tudu :) Just give it a try.

    Screenshot copyright: Ruben Pollan (tudu author).


    Posted in *nix, Software | No Comments »

    Good advice: /bin/false is not security

    1st October 2011

    SSH Security and You – /bin/false is *not* security.


    Posted in *nix, Links, Security | No Comments »

    How to remotely convert live 1xHDD/LVM Linux server to 2xHDD RAID1/LVM (GRUB2, GPT)

    17th May 2011


    • current HDD is /dev/sda, it has a GPT (with bios_grub being /dev/sda1), separate /boot partition (/dev/sda2), and a physical LVM volume (/dev/sda3), where LVM holds all the remaining partitions (root, /home, /srv, …); LVM is properly configured, and system reboots with no problems
    • your new drive is /dev/sdb, it is identical to /dev/sda, and it comes empty from the manufacturer (this is important! wipe the drive if it is not empty, especially if it used to be a part of another RAID)
    • your system is Debian or Debian-based; in this exact example I’ve been using Ubuntu Server 10.04
    • your LVM volume group is named vg0
    • make sure you understand what each command does before executing it
    • you do have an external backup of all your important data, and you do understand that the following operations are potentially dangerous to your data integrity

    Inspired by: Debian Etch RAID guide, serverfault question.
    Read the rest of this entry »


    Posted in *nix, how-to, Software | 6 Comments »

    Generate .mood moodbar files for your whole music collection

    10th April 2011

    Amarok moodbar wiki page has 2 nice scripts to generate .mood files for your whole music collection (to be displayed by amarok when playing).

    Read the rest of this entry »


    Posted in *nix, Links, Notepad, Software | 3 Comments »