Free to run amok software for linux

VBox Runner 0.2 provides you with a small but very useful KRunner module which can allow you to run your VirtualBox virtual machines from KRunner. This product will be an excellent choice for everyone.

Robo Hunt is an action game where you have to run for life and plutonium.

Take all plutonium and dont be caught. The robot hunters are smart and they do not cheat.

Test-Run is an improved test harness for scripts that emit TAP (Test Anything Protocol). It was forked from Test::Harness, and it uses TAP::Parser.

The project is used to analyze the output of the scripts and present it to the user in a summarized form. Test-Run features separation of the test-running backend and the command line frontend, a "runprove" utility for running tests from the command line, a plugin-system, and colors for the summary line.

run in xterm is an servcie menu which adds "run in xterm" & "run in xterm as root" to action menu on binary files, scripts etc.

It has 2 languages: english and polish.

Installation:

copy/save this file in
~/.kde/share/apps/konqueror/servicemenus

wmtunlo is one of the useless dockapp ever made, so use it or not....
The configuration file is stored in $HOME/.clay/ directory.
There are 8 examples named wmtunlorc.example1 thru wmtunlorc.example8. To test these examples rename selected file to wmtunlorc and put it into $HOME/.clay/ directory, then run wmtunlo.
You can assign three programs to run when double-click is performed (look at options in wmtunlorc file for details).
Enhancements:
- command line options was replaced by a config file
- now, we can run up to 3 programs on double-click (based on patch by Alan Jurgensen)

Fruity Banking! is a double entry accounting system which can be used for personal or business account management.
Main features:
- GPL licensed.
- Intuitive, clear, Web-based interface
- uses the CherryPy framework to run as a self-contained application.
- Can be run via Apache/mod_rewrite or mod_python
- MySQL backend and simple database structure make it easy to write scripts in any language.
- Cross platform/portable and will run on Windows, OSX, Linux, *BSD, etc.
Enhancements:
- More presentation improvements.

CoverPrint prints the current amaroK playlist to a CD cover using easily customizable SVG templates.

Usage:

Run the script. No configuring is necessary. Rightclick in the playlist window and select Print CD Cover from the CoverPrint context menu.

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families.
SYNOPSIS
use Bio::Tools::Run::TribeMCL;
use Bio::SearchIO;
# 3 methods to input the blast results
# straight forward raw blast output (NCBI or WU-BLAST)
my @params = (inputtype=>blastfile);
# OR
# markov program format
# protein_id1 protein_id2 evalue_magnitude evalue_factor
# for example:
# proteins ENSP00000257547 and ENSP00000261659
# with a blast score evalue of 1e-50
# and proteins O42187 and ENSP00000257547
# with a blast score evalue of 1e-119
# entry would be
my @array = [[qw(ENSP00000257547 ENSP00000261659 1 50)],
[qw(O42187 ENSP00000257547 1 119)]];
my @params = (pairs=>@array,I=>2.0);
# OR
# pass in a searchio object
# slowest of the 3 methods as it does more rigourous parsing
# than required for us here
my $sio = Bio::SearchIO->new(-format=>blast,
-file=>blast.out);
my @params=(inputtype=>searchio,I=>2.0);
# you can specify the path to the executable manually in the following way
my @params=(inputtype=>blastfile,I=>2.0,
mcl=>/home/shawn/software/mcl-02-150/src/shmcl/mcl,
matrix=>/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix);
my $fact = Bio::Tools::Run::TribeMCL->new(@params);
# OR
$fact->matrix_executable(/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix);
$fact->mcl_executable(/home/shawn/software/mcl-02-150/src/shmcl/mcl);
# to run
my $fact = Bio::Tools::Run::TribeMCL->new(@params);
# Run the program
# returns an array reference to clusters where members are the ids
# for example :2 clusters with 3 members per cluster:
# $fam = [ [mem1 mem2 mem3],[mem1 mem2 mem3]]
# pass in either the blastfile path/searchio obj/the array ref to scores
my $fam = $fact->run($sio);
# print out your clusters
for (my $i = 0; $i
print "Cluster $i t ".scalar(@{$fam->[$i]})." membersn";
foreach my $member (@{$fam->[$i]}){
print "t$membern";
}
}
This clustering is achieved by analysing similarity patterns between proteins in a given dataset, and using these patterns to assign proteins into related groups. In many cases, proteins in the same protein family will have similar functional properties.
Enhancements:
- Perl