4th December 2010
Here’s a simple and clear guide for gmail, which also definitely works with other relay hosts. I’ve used it to configure my ISP’s mail relay (they block outgoing port 25) on a Debian Squeeze laptop.
Posted in *nix, how-to, Links, Notepad, Software | No Comments »
16th November 2010
Imagine you need to get a few lines from a group of files with missing identifier mappings. I have a bunch of files with content similar to this one:
ENSRNOG00000018677 1368832_at 25233
ENSRNOG00000002079 1369102_at 25272
ENSRNOG00000043451 25353
ENSRNOG00000001527 1388013_at 25408
ENSRNOG00000007390 1389538_at 25493
In the example above I need '25353', which does not have corresponding affy_probeset_id in the 2nd column.
It is clear how to do that:
CODE:sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}'
This outputs a column of required IDs (EntrezGene in this example):
116720
679845
309295
364867
298220
298221
25353
However, I need these IDs as a comma-separated list, not as newline-separated list.
There are several ways to achieve the desired result (only the last pipe commands differ):
CODE:sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | gawk '$1=$1' ORS=', '
CODE:sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | tr '\n' ','
CODE:sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | sed ':a;N;$!ba;s/\n/, /g'
CODE:sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | sed ':q;N;s/\n/, /g;t q'
CODE:sort -u *_affy_ensembl.txt | grep -v '_at' | awk '{print $2}' | paste -s -d ","
These solutions differ in efficiency and (slightly) in output. sed will read all the input into its buffer to replace newlines with other separators, so it might not be best for large files. tr might be the most efficient, but I haven't tested that. paste will re-use delimiters, so you cannot really get comma-space ", " separation with it.
Sources: linuxquestions 1 (explains used sed commands), linuxquestions 2, nixcraft.
Posted in *nix, Bioinformatics, how-to, Notepad, Software | No Comments »
11th November 2010
Just came across Skype Call Recorder - an awesome in its functionality+simplicity tool to record skype calls. Highly recommended!
It worked immediately for me, and default settings are good enough not to bother tweaking. Well, I know that because I did tweak a few to get more nerdiness, but normal people don't need that.
SCR download page has packages for Ubuntu, Debian/i386, Xandros, RPM-based distributions, Gentoo - and as its free, you can of course just use the fsource, Luke!
At the time of writing, a package for Debian/amd64 was not available, but it is really easy to build one.
Here's mine: skype-call-recorder-debian_0.8_amd64.deb
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16th October 2010
In my previous post on CUE sheet support in Linux music players I mentioned DeaDBeeF. Unfortunately, DeaDBeeF is not yet available as a Debian package.
Fortunately, Alexey Smirnov (the author of DeaDBeeF) maintains a github repository deadbeef-debian which has simple instructions on installing DeaDBeeF in Debian (citing with minor edits): Read the rest of this entry »
Posted in Links, Software | 3 Comments »
3rd October 2010
Recently I finally managed to configure remote (aka off-site) backup for my Debian server. As always, I started with a comparison of existing solutions.
Debian has a number of packages enabling remote (over the network) backup: backupPC, backupninja, backup-manager, dirvish, duplicity, luckybackup, rdiff-backup, and some others.
Read the rest of this entry »
Posted in *nix, Links, Software | 1 Comment »
16th July 2010
In short: sudo mkswap -L new_swap_label -U old_swap_UUID /dev/sd_swap_device.
If you don't care about the UUID: just sudo mkswap -L new_swap_label /dev/sd_swap_device.
Step-by-step:
Read the rest of this entry »
Posted in *nix, how-to | No Comments »
30th April 2010
Last updated: 2011-12-13
- Clementine music player
- DeaDBeeF (as in 0xDEADBEEF) is an audio player for GNU/Linux systems with X11 (though now it also runs in plain console without X, in FreeBSD, and in OpenSolaris) with CUE sheets support
- AudioPlayer51 is a free, open-source, cross-platform audio player written to handle FLAC files and CUE sheets (exclusively). If you don't use FLAC files and CUE sheets, you won't find AudioPlayer51 very useful.
- Amarok: only for WAV+CUE, doesn't currently support FLAC+CUE; version 2.3.1 is promised to fully support CUE sheets
- Audacious (through the .cue plugin)
- QMMP (haven't tested this one)
- XMMS through mp3cue (also untested)
- foobnix (untested, suggested in this comment)
- cueplay
Some extra links:
Posted in *nix, Links, Software | 6 Comments »