Free to run software for linux

Locale::Maketext::Extract::Run is a Perl module interface to xgettext.pl.

SYNOPSIS

use Locale::Maketext::Extract::Run xgettext;
xgettext(@ARGV);

virtbench is a set of benchmarks for virtualization environments / hypervisors. The project is designed to be easy to run and easy to extend. The main audience will be people developing hypervisors.

KriptDoc project extracts metadata from any Word file and quickly converts Word documents into txt.

In order to run KriptDoc youll need AntiWord, Perl and kommander.

Bio::Tools::Run::JavaRunner is a Perl module that can run java programs.

SYNOPSIS

my $runner = Bio::Tools::Run::JavaRunner->new(-jar => $jar);
$runner->run();

This module is probably incomplete. It is intended to be a wrapper for running java programs.

run adds a service menu for all file types. This service menu will just call the file in the command line using the active folder as work folder.

Makes running some scripts and applications much easier (Some require work folder to be the same where they are located so double-clicking does not work).

Maybe a good fix would be to make it available only for files that have the executable permission

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

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.