Free to run josiah leming software for linux

Run a web server inside LAN is a simple script to run a WWW server inside a Local Area Network. Run a web server inside LAN script assume all iptables features are compiled statically in the kernel, or all modules are loaded.

Otherwise you may encounter some surprises trying to utilize the more featureful and creative commandlines that Ive come up with.

Sample:

#external and internal interfaces
EXT=eth0
INT=eth1

# clear everything, and create my cascading chains
iptables -F
iptables -N e0
iptables -N tcpin
iptables -N udpin

# e0 is the name of our chain for eth0
iptables -I INPUT -i $EXT -j e0

# OUTPUT Chain
iptables -A OUTPUT -o $EXT -j DROP -p icmp --icmp-type ! echo-request

# remote gnutella queries were really pissing me off one day
# iptables -A OUTPUT -o $EXT -j DROP -p tcp ! --syn --dport 6346
# iptables -A OUTPUT -o $EXT -j DROP -p tcp ! --syn --sport 6346

# $EXT Chain
# a single rule to accept SYN Packets for multiple ports (up to 15)
iptables -A tcpin -j ACCEPT -p tcp --syn -m multiport --destination-ports 873,993,995,143,80,113,21,22,23,25,53

# stateful connection tracking is wonderful stuff
# ESTABLISHED tcp connections are let through
# If we send a SYN out, the ACK is seen as RELATED
# then further communication is accepted by the ESTABLISHED rule
iptables -A e0 -j ACCEPT -m state --state ESTABLISHED
iptables -A e0 -j ACCEPT -m state --state RELATED

# certain ports I simply DROP
iptables -A tcpin -j DROP -p tcp --syn -m multiport --destination-ports 6346,139

# UDP rules...
iptables -A udpin -j DROP -p udp -m multiport --destination-ports 137,27960

# I run a DNS server, so we must accept UDP packets on port 53
iptables -A udpin -j ACCEPT -p udp -m state --state NEW --destination-port 53

# lets log NEW udp packets on ports 1024:65535, then let them through
iptables -A udpin -j LOG -p udp -m state --state NEW --destination-port 1024:65535 --log-level debug --log-prefix UDPNEW --log-ip-options
iptables -A udpin -j ACCEPT -p udp -m state --state NEW --destination-port 1024:65535

# lets log NEW tcp packets on ports 1024:65535, then let them through
iptables -A tcpin -j LOG -p tcp --syn --destination-port 1024:65535 --log-level debug --log-prefix TCPNEW --log-tcp-options --log-ip-options
iptables -A tcpin -j ACCEPT -p tcp --syn --destination-port 1024:65535

# lets log INVALID or NEW tcp packets on priveleged ports, then DROP
# (remember I have certain ACCEPT rules higher up the chain)
iptables -A tcpin -j LOG -p tcp -m state --state INVALID,NEW --destination-port 1:1023 --log-level warn --log-prefix TCPPRIV --log-tcp-options --log-ip-options
iptables -A tcpin -j DROP -p tcp -m state --state INVALID,NEW --destination-port 1:1023

iptables -A e0 -p tcp -j tcpin
iptables -A e0 -p udp -j udpin
iptables -A e0 -j LOG --log-level debug --log-prefix NETFILTER --log-ip-options -m state --state INVALID,NEW
iptables -A e0 -j DROP

# NAT Rules
# I run a web server inside...
iptables -t nat -A PREROUTING -p tcp -i eth0 --dport 80 -j DNAT --to-destination 192.168.1.4:80

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.)

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

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

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

CHARGE Protein charge plot (EMBOSS)


Parameters:

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


charge (String)

init (String)

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

window (Integer)
Window (-window)

aadata (String)
Amino acid property data file name (-aadata)

plot (Switch)
Produce graphic (-plot)

graph (Excl)
graph (-graph)

outfile (OutFile)
outfile (-outfile)

auto (String)

psouput (String)

Python in Scheme is a scheme library that allows you to run Python code within Scheme.

Python in Scheme project uses the Python/C API to embed a Python interpreter.

EthGraph provides a Qt-based graphical network device traffic monitor.
Installation instructions for ethgraph.
1) Download and untar/ungzip the source
2) Edit the makefile as necessary for paths on your system
3) Run "make"
4) Run "make install" as root
For help, run "ethgraph --help".
Enhancements:
- Bugfix: fix scaling of bars on graph (not dependent on refresh rate)
- Enlarge widget to fix clipping of text on other systems
- Create an INSTALL doc

Bio::Tools::Run::PiseApplication::align2model is a Bioperl class for align2model - create a multiple alignment of sequences to an existing model.

Parameters:

align2model (String)

run (String)
Run name

db (Sequence)
Sequences to align (-db)

model_file (InFile)
Model (-i)
pipe: sam_model

id (String)
Sequence identifier(s) selection (separated by commas) (-id)

nscoreseq (Integer)
Maximum number of sequences to be read (-nscoreseq)

adpstyle (Excl)
Dynamic programming style (-adpstyle

SW (Excl)
Sequence scoring (-SW)

auto_fim (Switch)
Add FIMs automatically (-auto_fim)

jump_in_prob (Float)
Probability cost of jumping into the center of the model (-jump_in_prob)

jump_out_prob (Float)
Probability cost of jumping out the center of the model (-jump_out_prob)

a2mdots (Switch)
Print dots to fill space need for other sequences insertions (-a2mdots)

dump_parameters (Excl)
(-dump_parameters)

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)