Free runs software for linux

Ophcrack is a Windows password cracker based on rainbow tables. It is a very efficient implementation of rainbow tables done by the inventors of the method.

This projetc comes with a GTK+ Graphical User Interface and runs on ,Linux Mac OS X (Intel CPU) as well as on Windows.

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

IPC::Run::Simple is a simple system() wrapper.

SYNOPSIS

# Run a command and check whether it failed
use IPC::Run::Simple;
run("echo Hello, O Cruel World")
or die "Command failed";

# Describe the failure
use IPC::Run::Simple qw($ERR);
run("echo Hello, O Cruel World")
or die "Command failed: $ERR";

# Use the :all tag instead of explicitly requesting $ERR
use IPC::Run::Simple qw(:all);
run("echo Hello, O Cruel World")
or die "Command failed: $ERR";

# Die with error message if command does not return 0
use IPC::Run::Simple qw(:Fatal);
run("echo Hello, O Cruel World");

# Allow other exit values without dying
use IPC::Run::Simple qw(:Fatal);
run(command => [ "echo", "Hello, O Cruel World!" ],
allowed => [ 1, 2, 5 ]);

This module is intended to be a very simple, straightforward wrapper around the system() call to make it behave more like other builtins.

run() will return a true value if the command was executed and return a successful status code, and false otherwise. The reason for the failure will be stored in the $IPC::Run::Simple::ERR variable (which is just $ERR if you import either $ERR or :all). The description of the reason was pulled almost directly from the system() documentation.
Optionally, you can import the :Fatal tag, which will cause run() to die() with an appropriate message if the command fails for any reason.

If you wish to allow nonzero exit values but still want to trap unexpected errors, you may use an expanded call syntax. Call run() with a set of key=>value pairs. The two implemented keys are command (an array reference containing the command to run) and allowed (an array reference of exit values that are allowed without causing run() to return false or throw an exception.)

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

Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods. A workflow is defined by a set of methods which all instanciate the class PiseApplication.

SYNOPSIS

# First, create a Bio::Tools::Run::AnalysisFactory::Pise object:
my $factory = new Bio::Tools::Run::AnalysisFactory::Pise();
# Then create the application objects (Pise::Run::Tools::PiseApplication):
my $clustalw = $factory->program(clustalw);
$clustalw->infile($my_alignment_file);
my $protpars = $factory->program(protpars);

# You can specify different servers for different applications :
my $protdist = $factory->program(protpars
-remote => http://kun.homelinux.com/cgi-bin/Pise/5.a//protpars.pl,
-email => your_email);

# Create a new workflow object :
my $workflow = Bio::Tools::Run::PiseWorkflow->new();

# Define the workflows methods using the application objects:
# the application method $protpars will receive the output of
# type readseq_ok_alig from the application method $clustalw.
$workflow->addpipe(-method => $clustalw,
-tomethod => $protpars,
-pipetype => readseq_ok_alig);

# The application method $clustalw will be piped to a second
# application method ($protdist) using the output of type readseq_ok_alig.
$workflow->addpipe(-method => $clustalw,
-tomethod => $protdist,
-pipetype => readseq_ok_alig);

# The application method $protpars will be piped to the application
# method $consense using the output of type phylip_tree.
my $consense = $factory->program(consense);
$workflow->addpipe(-method => $protpars,
-tomethod => $consense,
-pipetype => phylip_tree);

# Run the workflow.
$workflow->run();

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search.

Parameters:

fasta (Excl)
Fasta program

query (Sequence)
Query sequence File
pipe: seqfile

seqtype (Excl)
Is it a DNA or protein sequence (-n)

protein_db (Excl)
Protein Database

nucleotid_db (Excl)
Nucleotid Database

break_long (Integer)
Break long library sequences into blocks (-N)

ktup (Integer)
ktup : sensitivity and speed of the search (protein:2, DNA:6)

optcut (Integer)
OPTCUT : the threshold for optimization. (-c)

gapinit (Integer)
Penalty for gap initiation (-12 by default for fasta with proteins, -16 for DNA) (-f)

gapext (Integer)
Penalty for gap extention (-2 by default for fasta with proteins, -4 for DNA) (-g)

high_expect (Float)
Maximal expectation value threshold for displaying scores and alignments (-E)

low_expect (Float)
Minimal expectation value threshold for displaying scores and alignments (-F)

nucleotid_match (Integer)
Reward for a nucleotid match (-r)

nucleotid_mismatch (Integer)
Penalty for a nucleotid mismatch (-r)

matrix (Excl)
Scoring matrix file (-s)

X_penalty (Integer)
Penalty for a match to X (independently of the PAM matrix) (-x)

frameshift (Integer)
Penalty for frameshift between codon (fast[xy]/tfast[xy])(-h)

frameshift_within (Integer)
Penalty for frameshift within a codon (fasty/tfasty)(-j)

threeframe (Switch)
Search only the three forward frames (tfasta) (-3)

invert (Switch)
Reverse complement the query sequence (all tfasta) (-i)

genetic_code (Excl)
Use genetic code for translation (tfasta/tfast[xy]/fast[xy]) (-t)

band (Integer)
band-width used for optimization (-y)

swalig (Switch)
unlimited Smith-Waterman alignment for DNA (-A)

noopt (Switch)
no limited optimization (-o)

stat (Excl)
Specify statistical calculation. (-z)

random (Switch)
Estimate stat parameters from shuffled copies of each library sequence (-z)

histogram (Switch)
No histogram (-H)

scores (Integer)
number of similarity scores to be shown (-b)

alns (Integer)
number of alignments to be shown (-d)

html_output (Switch)
HTML output (-m)

markx (Excl)
Alternate display of matches and mismatches in alignments

init1 (Switch)
sequences ranked by the z-score based on the init1 score (-1)

z_score_out (Excl)
Show normalize score as (-B)

showall (Switch)
both sequences are shown in their entirety in alignments (fasta only) (-a)

linlen (Integer)
output line length for sequence alignments (max. 200) (-w)

offsets (String)
Start numbering the aligned sequences at position x1 x2 (2 numbers) (-X)

info (Switch)
Display more information about the library sequence in the alignment (-L)

statfile (OutFile)
Write out the sequence identifier, superfamily number, and similarity scores to this file (-R)

filter (Switch)
Lower case filtering (-S)

outfile (OutFile)
pipe: mview_input

html_outfile (OutFile)

Bio::Tools::Run::PiseApplication::freak is a Perl module.

Bio::Tools::Run::PiseApplication::freak
Bioperl class for:

FREAK Residue/base frequency table or plot (EMBOSS)


Parameters:

(see also:
http://bioweb.pasteur.fr/seqanal/interfaces/freak.html
for available values):


freak (String)

init (String)

seqall (Sequence)
seqall -- any [sequences] (-seqall)
pipe: seqsfile

letters (String)
Residue letters (-letters)

step (Integer)
Stepping value (-step)

window (Integer)
Averaging window (-window)

plot (Switch)
Produce graphic (-plot)

graph (Excl)
graph (-graph)

outfile (OutFile)
outfile (-outfile)

auto (String)

psouput (String)