Friday, September 28, 2012

linux, Mac, perl, RedHat, Unix, Windows

PERLCC MODULE

1:03 PM Unknown No comments

1. List-MoreUtils-0.33.tar.gz

2. ExtUtils-MakeMaker-6.62.tar.gz

3. Perl-OSType-0.005.tar.gz

4. Module-Metadata-1.000011.tar.gz

5. PathTools-3.33.tar.gz

6. Locale-Maketext-Simple-0.21.tar.gz

7. Module-CoreList-2.73.tar.gz

8. Module-Load-0.22.tar.gz

9. Params-Check-0.36.tar.gz

10. Module-Load-Conditional-0.54.tar.gz

11. IPC-Cmd-0.78.tar.gz

12. ExtUtils-CBuilder-0.280205.tar.gz

13. ExtUtils-ParseXS-3.15.tar.gz

14. Test-Simple-0.98.tar.gz

15. Perl-OSType-1.002.tar.gz

16. Test-Harness-3.25.tar.gz

17. Compress-Raw-Bzip2-2.055.tar.gz

18. Compress-Raw-Zlib-2.056.tar.gz

19. IO-Compress-2.055.tar.gz

20. IO-Zlib-1.10.tar.gz

21. Package-Constants-0.02.tar.gz

22. Algorithm-Diff-1.1902.tar.gz

23. Text-Diff-1.41.tar.gz

24. Archive-Tar-1.90.tar.gz

25. ExtUtils-Install-1.54.tar.gz

26. Module-Build-0.4003.tar.gz

27. Config-IniFiles-2.77.tar.gz

28. DBD-Oracle-1.50.tar.gz

29. DBI-1.622.tar.gz

Perl [ Generate executables from Perl / Binary file]

7:03 AM Unknown No comments

File Hello.pl
---------------------------------------------
#!/usr/bin/perl
use strict;
use warnings;

print "Hei man !!! \n";
---------------------------------------------

[root@localhost Desktop]# perlcc -o Hello Hello.pl
[root@localhost Desktop]# chmod +x Hello
[root@localhost Desktop]# ./Hello
Hei man !!!
[root@localhost Desktop]# less Hello
"Hello" may be a binary file. See it anyway?

Wednesday, September 19, 2012

Command Line, Data Base, DB, linux, Oracle, RedHat, Unix

Perl - Info about the module [ DBD/DBI ] Oracle

7:11 AM Unknown 1 comment

[root@localhost Desktop]# perl -e 'use DBD::Oracle; print $DBD::Oracle::VERSION,"\n";'
1.50
[root@localhost Desktop]# perl -e 'use DBI; print $DBI::VERSION,"\n";
1.622

Data Base, DB, linux, Oracle, RedHat, Unix

Install [ Oracle 11g XE on Red Hat ]

6:37 AM Unknown 1 comment

#rpm -i oracle-xe-11.2.0-1.0.x86_64.rpm
Executing post-install steps...
You must run '/etc/init.d/oracle-xe configure' as the root user to configure the database.

[root@localhost Disk1]# /etc/init.d/oracle-xe configure

Oracle Database 11g Express Edition Configuration
-------------------------------------------------
This will configure on-boot properties of Oracle Database 11g Express
Edition. The following questions will determine whether the database should
be starting upon system boot, the ports it will use, and the passwords that
will be used for database accounts. Press <Enter> to accept the defaults.
Ctrl-C will abort.

Specify the HTTP port that will be used for Oracle Application Express [8080]:

Specify a port that will be used for the database listener [1521]:

Specify a password to be used for database accounts. Note that the same
password will be used for SYS and SYSTEM. Oracle recommends the use of
different passwords for each database account. This can be done after
initial configuration:
Confirm the password:

Do you want Oracle Database 11g Express Edition to be started on boot (y/n) [y]:y

Starting Oracle Net Listener...Done
Configuring database...Done
Starting Oracle Database 11g Express Edition instance...Done
Installation completed successfully.

----------------------------------------------------------------------------------------------------------

Edit .bashrc

[root@localhost ~]# vim .bashrc
# User specific aliases and functions

alias rm='rm -i'
alias cp='cp -i'
alias mv='mv -i'

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

#ORACLE CONFIG
ORACLE_HOSTNAME=localhost.localdomain; export ORACLE_HOSTNAME
ORACLE_UNQNAME=DB11G; export ORACLE_UNQNAME
ORACLE_BASE=/u01/app/oracle; export ORACLE_BASE
ORACLE_HOME=$ORACLE_BASE/product/11.2.0/xe; export ORACLE_HOME
ORACLE_SID=XE; export ORACLE_SID
NLS_LANG=`$ORACLE_HOME/bin/nls_lang.sh`; export NLS_LANG
ORACLE_TERM=xterm; export ORACLE_TERM
PATH=/usr/sbin:$PATH; export PATH
PATH=$ORACLE_HOME/bin:$PATH; export PATH

LD_LIBRARY_PATH=$ORACLE_HOME/lib:/lib:/usr/lib; export LD_LIBRARY_PATH
CLASSPATH=$ORACLE_HOME/JRE:$ORACLE_HOME/jlib:$ORACLE_HOME/rdbms/jlib; export CLASSPATH

if [ $USER = "oracle" ]; then
if [ $SHELL = "/bin/ksh" ]; then
    ulimit -p 16384
    ulimit -n 65536
else
    ulimit -u 16384 -n 65536
fi
fi

----------------------------------------------------------------------------------------------------------
[root@localhost ~]# sqlplus

SQL*Plus: Release 11.2.0.2.0 Production on Wed Sep 19 10:52:11 2012

Copyright (c) 1982, 2011, Oracle. All rights reserved.

Enter user-name: system
Enter password:

Connected to:
Oracle Database 11g Express Edition Release 11.2.0.2.0 - 64bit Production

SQL>

Tuesday, September 18, 2012

linux, RedHat, Unix

Linux - Sudoers file

7:21 AM Unknown 1 comment

Login redhat

[redhat@localhost ~]$ sudo su -l
redhat is not in the sudoers file. This incident will be reported.
[redhat@localhost ~]$

Login root

vim /etc/sudoers

root ALL=(ALL) ALL
redhat ALL=(ALL) ALL

Login redhat

[redhat@localhost ~]$ sudo su -l
[sudo] password for redhat:
[root@localhost ~]#

Friday, September 14, 2012

Bioinformatic, Command Line, Data Base, DB, linux, Mac, perl, Unix

Bioinformatics BIT/LGMB

11:29 AM Unknown No comments

Bioinformatics BIT/LGMB

Data validation IC/TCC

Jobs ...

Find the error !!!

Thanks all ...

Prof. Wilson, Prof. Israel, Daniel, Marcelo, Rodrigo, Meire, Jorge, Rippel, Burger, Thais, Erico, Alonso, Gilson.

Google [ Chart Tools ]

11:17 AM Unknown No comments

<html>
<head>
<script type="text/javascript" src="https://www.google.com/jsapi"></script>
<script type="text/javascript">
google.load("visualization", "1", {packages:["corechart"]});
google.setOnLoadCallback(drawChart);
function drawChart() {
var data = google.visualization.arrayToDataTable([

['ASW Africano/EUA', 1],
['CEU Utah/Europeia', 1],
['CHB Pequim/China', 1],
['CHD Chinesa/Colorado', 1],
['GIH Guzerate, Texas', 1],
['JPT Toquio/Japao', 1],
['LWK Luhya/Quenia', 1],
['MXL Mexicana/Los Angeles,California', 1],
['MKK Maasai/Kinyawa, Quenia', 1],
['TSI Toscani/Italia', 1],
['YRI Ioruba/Nigeria', 1]
]);

var options = {

};

var chart = new google.visualization.PieChart(document.getElementById('chart_div'));
chart.draw(data, options);
}
</script>
</head>
<body>
<div id="chart_div" style="width: 900px; height: 500px;"></div>
</body>
</html>
---------------------------------------------------------------------------------------------------------

fonte : https://developers.google.com/chart/

Wednesday, September 12, 2012

Command Line, Data Base, linux, Oracle, perl, Unix, Windows

Perl - [ Create | Insert - DB Oracle ]

10:13 PM Unknown No comments

use strict;
use warnings;
use DBD::Oracle qw(:ora_types);
use DBI;

use constant SqlOracle => 'C:\oraclexe\app\oracle\product\10.2.0\server\BIN\sqlplus.exe\\';
use constant User => 'system';
use constant Pass => '12345';
use constant DB => 'XE';

print "Test Show Valeu : $0\n";

my $dbh = DBI->connect("dbi:Oracle:".DB,User,Pass) or die $!;

my $CreateTable = "CREATE TABLE EMPREGADO (codigo number(6) primary key, nome varchar2(25) not null, salario number(11,2))";

my $sth = $dbh->prepare($CreateTable);

$sth->execute();

$sth = $dbh->prepare( q{INSERT INTO EMPREGADO (codigo,nome,salario) VALUES(?,?,?)}) or die $dbh->errstr;

open(IN,"pessoas.txt") or die $!;

while(<IN>){
chomp;
my($codigo,$nome,$salario) = split (/\t/,$_);
$sth->execute($codigo,$nome,$salario) or die $dbh->errstr;

}
close(IN);

$dbh->disconnect;

------------------------------------------------------------------------------------------------------------

SQL> desc empregado;
Nome Nulo? Tipo
----------------------------------------- -------- ----------------------------

CODIGO NOT NULL NUMBER(6)
NOME NOT NULL VARCHAR2(25)
SALARIO NUMBER(11,2)

SQL> select * from empregado;

CODIGO NOME SALARIO
---------- ------------------------- ----------
1 joao 10
2 maria 80
3 jose 60

------------------------------------------------------------------------------------------------------------

pessoas.txt

1 joao 10
2 maria 80
3 jose 60

Command Line, DB, linux, Mac, Oracle, perl, Unix, Windows

Perl - [ Perl DBI Oracle connect from Windows ]

6:05 PM Unknown No comments

Tuesday, September 11, 2012

Command Line, linux, Mac, perl, Unix

Perl - [ File Exists ]

5:10 PM Unknown No comments

#!/usr/bin/perl
use strict;
use warnings;

my $file = $ARGV[0];

die "This File ($file) Exists ! " if (-e "$file");

Result

$ perl tmp.pl tmp.pl
This File (tmp.pl) Exists ! at tmp.pl line 7.

linux, Mac, perl, Unix

Perl - [ Exists Dir ]

5:05 PM Unknown No comments

#!/usr/bin/perl
use strict;
use warnings;

my $dir = $ARGV[0];

die "This ($dir) is not a directory" if (-d $dir);

Result

$ perl tmp.pl Music/
This (Music/) is not a directory at tmp.pl line 7.

Command Line, linux, Mac, perl, Unix

Perl - [ Exists File | System Command ]

2:41 PM Unknown No comments

#!/usr/bin/perl
use strict;
use warnings;

if(-e "tmp.pl"){

print "File exists tmp.pl\n";

system("echo Yes File > tmp.txt");
}else{

print "File not exists tmp.pl\n";

system("echo No File > tmp.txt");
}

Command Line, linux, Mac, perl

Perl - USE [ Copy | Move | Constant ]

2:28 PM Unknown No comments

#!/usr/bin/perl
use strict;
use warnings;

use File::Copy;
use constant WORK=>'/Users/als/';

copy(WORK."tmp.txt",WORK."tmp.txt.copy") or die "Copy failed $!";

move(WORK."tmp.txt",WORK."Desktop/tmp.txt") or die "Move failed $!";

print "Print constant\t:",WORK;

Monday, September 10, 2012

Command Line, HTML, linux, Mac, perl, Unix, Web

Perl - [ Create INDEX.HTML ]

9:40 AM Unknown No comments

#!/usr/bin/perl
use strict;
use warnings;

&Usage if $#ARGV<0;

my $REGEX = shift;

print "
<html>
    <head>
        <title></title>
        </head>
        <body>
                <center><h1></h1></center>

                                                        ";
foreach my $file (glob ("*.html")){

        my $text = $file;
        $text =~ s/\.$REGEX.*//g;

        print "\t\t<a href=\"$file\">$text</a><br/>\n";
}
print "
        </body>

</html>

";

sub Usage(){

    print "\nUsage: perl CreatePageIndex.pl fastq > index.html\n";
        exit(1);
}

----------------------------------------------------------------------------------------------------

-bash-4.0$ ll
total 2356
-rw-r--r-- 1 andre users 326585 2012-09-10 10:57 Phix.sort.bam.html.html
-rw-r--r-- 1 andre users 350366 2012-09-10 10:57 polipo11p.sort.bam.html.html
-rw-r--r-- 1 andre users 336857 2012-09-10 10:57 polipo17p.sort.bam.html.html
-rw-r--r-- 1 andre users 345978 2012-09-10 10:57 polipo45p.sort.bam.html.html
-rw-r--r-- 1 andre users 342493 2012-09-10 10:57 tumor11t.sort.bam.html.html
-rw-r--r-- 1 andre users 344666 2012-09-10 10:57 tumor17t.sort.bam.html.html
-rw-r--r-- 1 andre users 351703 2012-09-10 10:57 tumor45t.sort.bam.html.html
-bash-4.0$perl CreatePageIndex.pl

Usage: perl CreatePageIndex.pl fastq > index.html

-bash-4.0$ perl CreatePageIndex.pl sort

<html>
    <head>
        <title></title>
        </head>
        <body>
                <center><h1></h1></center>

                                                                        <a href="Phix.sort.bam.html.html">Phix</a><br/>
                <a href="polipo11p.sort.bam.html.html">polipo11p</a><br/>
                <a href="polipo17p.sort.bam.html.html">polipo17p</a><br/>
                <a href="polipo45p.sort.bam.html.html">polipo45p</a><br/>
                <a href="tumor11t.sort.bam.html.html">tumor11t</a><br/>
                <a href="tumor17t.sort.bam.html.html">tumor17t</a><br/>
                <a href="tumor45t.sort.bam.html.html">tumor45t</a><br/>

        </body>

</html>

Command Line, Data Base, linux, perl, Unix

Perl - Info DBI

8:31 AM Unknown No comments

$ perl -e 'use DBI; print $DBI::VERSION,"\n";'

$ perl -e 'use DBD::Oracle; print $DBD::Oracle::VERSION,"\n";'

http://search.cpan.org/~pythian/DBD-Oracle-1.50/lib/DBD/Oracle.pm

Command Line, linux, perl, Unix

Perl - [ VIM | headers | pl ]

8:04 AM Unknown No comments

less ~/.vim/headers/pl

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;

my ($output_dir,$number,$input_dir);

&Usage("Too few arguments") if $#ARGV<0;

GetOptions(

        'o|out_dir=s'    => \$output_dir,
        'i|input_dir=s'    => \$input_dir,
        'n|number=i'     => \$number

)or &Usage("Wrong arguments");

&process();

sub process(){

        foreach my $file (glob("*.")){

                open(IN,"$file")or die $!;

                while(<IN>){
                        chomp;
                        my @line = split(/\t/,$_);
                        print "$line[1]\n";
                        die;
                }
        }
}

sub Usage(){

        my($msg) = @_;

        print "\nUsage: perl script.pl -o out_dir/ -i input_dir/ -n 1

        $msg!

        Argument(s):

        -out_dir|-o
        -number|-n
        -input_dir|-i\n";
        exit(1);
}

Command Line, linux, Mac, perl, Unix

Perl [ Net::FTP ]

7:13 AM Unknown No comments

#!/usr/bin/perl
use strict;
use warnings;

use Net::FTP;

my $ftp = Net::FTP->new("ftp.suse.com", Debug => 0, Timeout => 3) or die "Cannot connect to ftp.suse.com: $@";

if ( $ftp->login('anonymous','')){

    my @dirs = $ftp->dir();

    foreach my $dir (@dirs){

            my ($permission,$number1,$user,$group,$number2,$months,$day,$year,$name_path) = split(/\s+/,$dir);

            print "Name path:\t$name_path\n";

            my @sub_dir = $ftp->ls("$name_path/*.txt");

            print "Name file *.txt:\t$sub_dir[0]\n";

            my $file_txt = $ftp->get($sub_dir[0]);

            print "Name file GET $file_txt:\t$sub_dir[0]\n";

            print "Copy $file_txt to LocalHost\n";

            `cp $file_txt ftp.txt`;

            $ftp->quit();
    }
}
-----------------------------------------------------------------------------------------------

Result

perl ftp.pl
Name path:      pub
Name file *.txt:        pub/README.txt
Name file GET README.txt:       pub/README.txt
Copy README.txt to LocalHost
less ftp.txt

Google Chart Tools

8:32 AM Unknown No comments

Font : https://developers.google.com/chart/image/docs/chart_wizard

Font : http://www.toprated.com.br/crie-graficos-de-maneira-rapida-e-facil-com-o-google-chart-tools-parte-1

Command line

Friday, September 28, 2012

PERLCC MODULE

Tuesday, September 25, 2012

Perl [ Generate executables from Perl / Binary file]

Wednesday, September 19, 2012

Perl - Info about the module [ DBD/DBI ] Oracle

Install [ Oracle 11g XE on Red Hat ]

Tuesday, September 18, 2012

Linux - Sudoers file

Friday, September 14, 2012

Bioinformatics BIT/LGMB

Google [ Chart Tools ]

Wednesday, September 12, 2012

Perl - [ Create | Insert - DB Oracle ]

Perl - [ Perl DBI Oracle connect from Windows ]

Tuesday, September 11, 2012

Perl - [ File Exists ]

Perl - [ Exists Dir ]

Perl - [ Exists File | System Command ]

Perl - USE [ Copy | Move | Constant ]

Monday, September 10, 2012

Perl - [ Create INDEX.HTML ]

Perl - Info DBI

Perl - [ VIM | headers | pl ]

Perl [ Net::FTP ]

Thursday, September 6, 2012

Google Chart Tools

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