Install Perl from source

 cd /opt

 wget http://www.cpan.org/src/5.0/perl-5.14.2.tar.gz

 tar -zxf perl-5.14.2.tar.gz

 cd perl-5.14.2

 ./Configure -h

 ./Configure -Dusethreads -Dprefix=/usr

 make

 make test

 make install

 perl -V

 which perl 

To see the status of perl installation 

make install > install.log

To install Perl modules using CPAN:

perl -MCPAN -e shell

Then install lets say if we want to install BioGraphics module.

install Bio::Graphics

Usefull command for test running jobs

fg - run jobs in the foreground

May be you will need to install following dependencies

sudo apt-get install libreadline-dev

Python BeautifulSoup scraper script

Beautiful Soup written in Python.Which is  HTML / XML parser, it can handle non-standard tags and generate inside parse tree. Also provides a simple and commonly used in navigation , search and modify the operation.
Recently i tried BeautifuSoup module inorder to parse html class libraries, Here is the simple scrapy code for extracting informaton from Apple website.

 #! /usr/bin/python  
 print 'Content-type: text/plain\r\n'  
 from BeautifulSoup import BeautifulSoup   
 import urllib   
 webpage = urllib.urlopen(r"http://store.apple.com/us/browse/home/shop_iphone/family/iphone/iphone4s");   
 soup = BeautifulSoup(webpage.read())   
 tags = soup('ul',{'class':'selection-options all-models'})   
 tags = tags[0](lambda tag : len(tag.attrs) == 1 and tag.name in ['span'] and   
            tag['class'] in ['shipping','price','color','title'])   
 for tag in tags :   
   print tag.text   
   print '-' * 30   

Results:

16GB2
------------------------------
black
------------------------------
From$199
------------------------------
In Stock
------------------------------
16GB2
------------------------------
black
------------------------------
From$199
------------------------------
In Stock

Setup Galaxy production server on Ubuntu and Apache environment

1.) Create user called galaxy with password galaxy

 admin@myserver:~# adduser galaxy  
 Adding user `galaxy' ...  
 Adding new group `galaxy' (1007) ...  
 Adding new user `galaxy' (1008) with group `galaxy' ...  
 Creating home directory `/home/galaxy' ...  
 Copying files from `/etc/skel' ...  
 Enter new UNIX password:  
 Retype new UNIX password:  
 passwd: password updated successfully  
 Changing the user information for galaxy  
 Enter the new value, or press ENTER for the default  
     Full Name []:  
     Room Number []:  
     Work Phone []:  
     Home Phone []:  
     Other []:  
 Is the information correct? [Y/n] Y  
 admin@myserver:~#  

2.) Change user to galaxy and clone galaxy production version

 admin@myserver: su galaxy  
 galaxy@myserver:/home/admin$ cd   
 galaxy@myserver: hg clone https://bitbucket.org/galaxy/galaxy-dist  

3.) If you don't have mercurial client for clone galaxy use following step

 admin@myserver:sudo apt-get install mercurial  

4.) Set the $TEMP environment variable to Galaxy's new_files_path directory

 galaxy@myserver:~$ export TEMP=/home/galaxy/galaxy-dist/database/tmp  

5.) We need clean python interpreter with correct python path

 galaxy@myserver:wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py  
 galaxy@myserver:/usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env  

6.) Now we need to setup new database for galaxy.I am going to create PostgreSQL database

 galaxy@myserver:~/galaxy-dist$ psql -h localhost -d postgres -U postgres  
 postgres=#CREATE DATABASE galaxy_prod;  
 postgres=# CREATE USER galaxy_prod_user WITH PASSWORD 'galaxy';  
 postgres=# GRANT ALL PRIVILEGES ON DATABASE galaxy_prod to galaxy_prod_user;  
 postgres=# \q  

7.) Then we need to configure Galaxy default server settings to our server details

 galaxy@myserver:cd galaxy-dist/  
 galaxy@myserver:~/galaxy-dist$ chmod -R 777 universe_wsgi.ini  
 galaxy@myserver:~/galaxy-dist$ vi universe_wsgi.ini  

8.) Here is the basic changes for universe_wsgi.ini file.

 host = xxx.xxx.23.123 [IP ADDRESS]  
 debug = False  
 use_interactive = False  
 database_connection = postgres://galaxy_prod_user:galaxy@localhost:5432/galaxy_prod  

9.) There are many more changes we can do for galaxy by customizing niverse_wsgi.ini for instance adding tracks,user privileges, ftp upload e.t.c.Galaxy has its own server but there are pages with static contents therefore we can setup proxy to enhance efficiency

 admin@myserver:vi /etc/httpd/conf/httpd.conf  

10.) Add following lines to httpd.conf

 <VirtualHost *:80>  
 ServerName xxx.xxx.23.123 [IP ADDRESS]  
 RewriteEngine on  
 #RewriteLog "/etc/httpd/logs/rewrite_log"  
 #RewriteLogLevel 9  
 RewriteRule ^/galaxy$ /galaxy/ [R]  
 #RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]  
 #RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]  
 #RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]  
 #RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L]  
 #RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]  
 RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]  
 </VirtualHost>  

11.) Now we need to restart proxy server.

 admin@myserver:/etc/init.d/httpd restart  

12.) Finally we can run galaxy

 galaxy@myserver:~/galaxy-dist$ sh ./run.sh --daemon  

13.) We can stop or see the status by using following commands

 galaxy@myserver:~/galaxy-dist$ sh ./run.sh --stop-daemon  
 galaxy@myserver:~/galaxy-dist$ sh ./run.sh --status  

14.) Done! 

Ubuntu folder/file permission

chmod -R 754 /www/test

7 – Owner(current user)
5 – Group(set by owner)
4 – anyone else

Basic numbers make persmission settings as follows

0 – no permission, this person cannot read, write or execute
1 – execute only
2 – write only
3 – execute and write only (1 + 2)
4 – read only
5 – execute and read only (1 + 4)
6 – write and read only (2 + 4)
7 – execute, write and read (1 + 2 + 3)

Log calculator

The log base

of

Install ProFTP server for Galaxy

Its not wise to use user sudo apt-get install proftpd or proftpd-basic because there are no postgres modules in default package.but if you have GUI interface udo apt-get install gadmin-proftpd is important
chanaka@localhost:~# wget ftp://ftp.proftpd.org/distrib/source/proftpd-1.3.4a.tar.gz
chanaka@localhost:~# tar xfvz proftpd-1.3.4a.tar.gz
chanaka@localhost:~/proftpd-1.3.4a#
chanaka@localhost:~/proftpd-1.3.4a# ./configure --disable-auth-file --disable-ncurses               \
        --disable-ident --disable-shadow --enable-openssl           \
        --with-modules=mod_sql:mod_sql_postgres:mod_sql_passwd
chanaka@localhost:~/proftpd-1.3.4a# make
chanaka@localhost:~/proftpd-1.3.4a# make install

Then create PostgreSQL user called galaxyftp with least privileges.
chanaka@localhost:~$  createuser -SDR galaxyftp
chanaka@localhost:~$ psql galaxy_prod
psql (8.4.9)
Type "help" for help.

galaxy_prod=# ALTER ROLE galaxyftp PASSWORD '[password]';
ALTER ROLE
galaxy_prod=# GRANT SELECT ON galaxy_user TO galaxyftp;
GRANT
galaxy_prod=# \q

Here is the final proftd.conf (/usr/local/proftpd/proftpd.conf)
# Basics, some site-specific
ServerName                      "myserver.org"
ServerType                      standalone
DefaultServer                   on
Port                            21
Umask                           077
SyslogFacility                  DAEMON
SyslogLevel                     debug
MaxInstances                    30
User                            nobody
Group                           nogroup
DisplayConnect                  /ftp/proftpd_welcome.txt
# Passive port range for the firewall
PassivePorts                    30000 40000
# Cause every FTP user to be "jailed" (chrooted) into their home directory
DefaultRoot                     ~
# Automatically create home directory if it doesn't exist
CreateHome                      on dirmode 700
# Allow users to overwrite their files
AllowOverwrite                  on
# Allow users to resume interrupted uploads
AllowStoreRestart               on
# Bar use of SITE CHMOD
<Limit SITE_CHMOD>
  DenyAll
</Limit>
# Bar use of RETR (download) since this is not a public file drop
<Limit RETR>
  DenyAll
</Limit>
# Do not authenticate against real (system) users
<IfModule mod_auth_pam.c>
AuthPAM                         off
</IfModule>
# Set up mod_sql_password - Galaxy passwords are stored as hex-encoded SHA1
SQLPasswordEngine               on
SQLPasswordEncoding             hex
# Set up mod_sql to authenticate against the Galaxy database
SQLEngine                       on
SQLBackend                      postgres
SQLConnectInfo                  galaxy_prod@myserver.org galaxyftp [password]
SQLAuthTypes                    SHA1
SQLAuthenticate                 users
# An empty directory in case chroot fails
SQLDefaultHomedir               /ftp/proftpd
# Define a custom query for lookup that returns a passwd-like entry.  UID and GID should match your Galaxy user.
SQLUserInfo                     custom:/LookupGalaxyUser
SQLNamedQuery                   LookupGalaxyUser SELECT "email,password,'512','512','/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'"

Note! Don't forget to configure  pg_hba.conf entry for host "XXXXX", Also check the firewall for ftp usually 21,We need to use galaxy user like 512. Done!

We can see the errors by using following
chanaka@localhost:~# cd /usr/local/sbin
chanaka@localhost:~/usr/local/sbin# ./proftpd -nd9
or check PostgreSQL or proftpd log files

If you get "Fatal: unknown configuration directive 'AuthPAM' " error use following solution.

<IfModule mod_auth_pam.c>
AuthPAM                         off
</IfModule>

Also following lines may useful to you:(/usr/local/sbin)
chanaka@localhost:~#ps aux | grep proftpd
chanaka@localhost:~#Kill [pid]
chanaka@localhost:~#Where is proftpd

To start
sudo /etc/init.d/proftpd start

Add multiple columns to Advanced Data Grid

Since three days I was trying to add multiple columns to Flex ADG Finally end up with one line solution amazing!
here is the 72 hours work :)
//tl add the column number
ADG.validateNow();

thanks to http://riaflex.blogspot.com/2008/05/dynamic-advanceddatagrid-columns.html