Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    How to: enable metadata duplication on an existing btrfs filesystem

    30th December 2016

    Just one command: sudo btrfs balance start -v -mconvert=dup /toplevel/
    where /toplevel/ is your mountpoint of the btrfs root, -v is there for verbosity (not too verbose, don’t worry), and -mconvert=dup literally says act on metadata only, convert data profile to DUP.

    This will duplicate both metadata and btrfs system data.
    Verify with: sudo btrfs fi df /toplevel:

    Data, single: total=10.00GiB, used=3.88GiB
    System, DUP: total=64.00MiB, used=4.00KiB
    Metadata, DUP: total=512.00MiB, used=286.18MiB
    GlobalReserve, single: total=96.00MiB, used=0.00B

    Explanation: on SSDs, mkfs.btrfs creates metadata in single mode (because of widely spread SSD deduplication algorithms negating duplicate entries). However, second copy of metadata increases recovery chances, especially so if your SSD does not deduplicate writes. Hence the desire to add metadata/systemdata duplication after the filesystem is created.

    Posted in *nix, how-to, Notepad, Software | No Comments »

    Raspberry Pi Colocation service

    29th December 2016

    Exactly what the title says: Raspberry Pi colocation service, yay! At only 30 EUR/year as of this writing.

    Posted in Links | No Comments »

    Mail-in-a-box, Sovereign, Modoboa, iRedMail, etc

    28th December 2016

    Preparing to dismantle my physical server (and move different hosted things to one or more VPS),
    I’ve realized that an email server is necessary: to send website-generated emails, and also
    receive a few rare contact requests arriving at the websites.

    My current email server was configured eons ago, it works well,
    but I have no desire to painfully transfer all the configuration…
    Better install something new, shiny and exciting, right? :)

    I had 3 #self-hosted, #mail-server bookmarks:

    (Sovereign, the 4th one, was addded after reading more about Mail-in-a-box.)

    Here are my notes on what seemed important about these 4.
    Read the rest of this entry »

    Posted in *nix, Comparison, Links, Notepad, Software, Web | No Comments »

    The sugar conspiracy

    19th June 2016

    A long but interesting read: The Sugar Conspiracy.

    Posted in Links, Misc, Science, Society | No Comments »

    How to: install Windows 7 on a recent laptop/PC from a bootable USB drive

    12th June 2016

    If you had ever seen the not-so-descriptive error message
    A required CD/DVD drive device driver is missing,
    then you have been trying to install Windows 7 (possibly using a bootable flash drive) on a recent laptop or desktop.

    There are two major obstacles for a somewhat-dated Windows 7 when it sees modern hardware:

    • USB 3.0
    • SSDs and newer disk drives in general

    Fortunately, both problems are easy to fix.
    Just follow the steps below; skip steps 1 and 2 if you already have a bootable Win7 flash drive.
    Read the rest of this entry »

    Posted in how-to | No Comments »

    TSW-friendly task and note management software

    5th June 2016

    A while ago I was looking for GTD/TSW-compatible android app.
    I ended up using Trello, Keep, and Calendar.

    But I always keep looking for new/improved tools, as right now I feel the best one does not exist…
    (If the best one can exist at all – requirements and conditions change all the time, so there is no fixed perfect immovable target.)

    I have been contemplating trying out the TSW methodology, but neither Keep nor Trello are quite there yet.
    I ended up using Evernote; after recent management changes and actually trying to become profitable it may as well last long enough.

    Everything was fine and calm until I have found workflowy yesterday.
    In essence, it is very similar to the text-file-based system that I have been using for at least half a year.

    Briefly, it is a web-based text editor on steroids, with possibly infinite nesting lists and seemingly full keyboard shortcuts control – no mouse needed.
    I recommend that you try the demo – it seems to be fully functional, and there is no need to sign up.

    This discovery made me read through pages and pages of this class of software tools.
    Here is a very brief summary of my findings: Read the rest of this entry »

    Posted in Links, Misc, Notepad, Software | No Comments »

    Practical comparison of NGS adapter trimming tools

    1st June 2016

    I used to work with sequencing providers who were giving me fairly clean data.
    It was already barcode-separated, and had no over-represented adapter sequences.
    The only thing I had to do was to (optionally) quality-trim the reads, and check for biological contamination.

    Recently, however, I have come across some real-world data, which not only had contamination in it, but also quite a noticeable percentage of adapters.
    I did a quick test of multiple tools to see if they fit my requirements:

    • should be easy/logical to use: no arcane/convoluted command lines or config files
    • should detect adapters automatically, either using its own database or a provided plain FASTA file
    • should be reasonably fast
    • must leave no adapter traces behind: I prefer aggressive trimming

    I have tried the following tools:

    • fastq-mcf from the ea-tools package
    • skewer
    • TrimmomaticPE
    • cutadapt: haven’t used it directly, but it is used by some of the compared tools
    • bbduk from BBMAP
    • autoadapt
    • TrimGalore!

    Read the rest of this entry »

    Posted in Bioinformatics | 2 Comments »