installing repeatmasker

there are few pre-requisite things to install repeatmasker..

repeatmasker is the first step involved in the est assembly pipeline

the prerequisites are

----perl
----sequence search engine
        you can install one of the three search engines present
         -cross-match
         -rm blast  ( i am using this one)  http://www.repeatmasker.org/RMBlast.html
         -abblast/wublast (these requires licensing )


Try 1. Download pre-compiled versions

$ wget http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
$ tar zxvf rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
$ cd rmblast-1.2-ncbi-blast-2.2.23+
$ cd bin
$ ./rmblastn
./rmblastn: error while loading shared libraries: libpcre.so.0: cannot open shared object file:
No such file or directory

I am unable to install this library. Things i found out, i may be wrong

* libpcre is part of the 32-bit libraries
* on ubuntu i was unable to find the library, maybe because of the repository.

Try 2. Download RMBlast source

$ wget http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
$ tar zxvf rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
$ cd rmblast-1.2-ncbi-blast-2.2.23+-src/c++
$ ./configure --with-mt --prefix=/usr/local/rmblast --without-debug
$ make
$ sudo make install

This installed good without any problem Modify ~/.bashrc to include the line below

export PATH=$PATH:/usr/local/rmblast/bin

To check installation

$ source ~/.bashrc
$ rmblastn
BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified

If you get the above message then RMBlast is installed

---- tanden repeat finder (trf) is needed

The TRF download will contain a single executable file. You will need to rename the file from whatever it is to just 'trf' (all lower case). Make TRF executable by typing chmod +x+u trf. You can then move this file wherever you want. I just put it in the /RepeatMasker directory.

the next step is installing repeat database...... it takes 2 days to get registered soo temporarily this process would be out of service.................

after 1 day..........

----Repeatmasker database

* url: http://www.repeatmasker.org/RMDownload.html
* download latest release version

$ cd /usr/local
$ wget http://www.repeatmasker.org/RepeatMasker-open-3-2-9.tar.gz
$ tar zxvf RepeatMasker-open-3-2-9.tar.gz

* It requires RepeatMasker Libraries
o url: http://www.girinst.org/
o Go to Downloads > RepeatMasker libraries > RepeatMasker edition: local:

$ tar zxvf repeatmaskerlibraries-20090604.tar.gz
$ rm -rf repeatmaskerlibraries-20090604.tar.gz
$ mv Libraries/RepeatMaskerLib.embl /usr/local/RepeatMasker/Libraries/.



download RepeatMasker
unpack it
install RepeatMasker libraries..copy them into RepeatMasker main folder

now configure the RepeatMasker script by using
perl ./configure

while configuring it would ask for so many where abouts ??
perl path
trf path

after finishing installation
check whether its working or not by typing the command

RepeatMasker in terminal..

Repeat masker

5.  Install RepeatMasker. Download from http://www.repeatmasker.org
	a.  The most current version of RepeatMasker requires a program called TRF.
	This can be downloaded from http://tandem.bu.edu/trf/trf.html
	b.  The TRF download will contain a single executable file.  You will need to
	rename the file from whatever it is to just 'trf' (all lower case).
	c.  Make TRF executable by typing chmod +x+u trf.  You can then move this file
	wherever you want.  I just put it in the /RepeatMasker directory.
	d.  Unpack RepeatMasker to the directory of your choice (i.e. /usr/local).
	e.  If you do not have WuBlast installed, you will need to install the program
	RMBlast.  We do not recomend using cross_match, as RepeatMasker
	performance will suffer.
	f.  Now in the RepeatMasker directory type perl ./configure in the command
	line. You will be asked to identify the location of perl, wublast, and
	trf.  The script expects the paths to the folders containing the
	executables (because you are pointing to a folder the path must end in a
	'/' character or the configuration script throws a fit).
	g.  Add the location where you installed RepeatMasker to your PATH variable in
	.bash_profile (i.e. export PATH="/usr/local/RepeatMasker:$PATH").
	h.  You must register at http://www.girinst.org and download the Repbase
	repeat database, Repeat Masker edition, for RepeatMasker to work.
	i.  Unpack the contents of the RepBase tarball into the RepeatMasker/Libraries
	directory.

had presentation on swarm........

spend sometime going through the teragrid resources and how to run jobs in them.
Following are websites I used a lot :

https://www.teragrid.org/web/user-support/gram

https://portal.teragrid.org/home;jsessionid=CC8F5DE3F54FAB3B727A972DA8E1B5B1.jvm1

est assembling

applications present in swarm..

what are they ???
where are they ???
how to run them ???


raw data -> repeat masker -> pace -> cap3 -> blast

repeat masker is used to eliminate the junk est's

pace is used to cluster the est's (organizing the est's into groups)......learn about talon

cap3 is used to create a sequence from the cluster .

blast is used to compare the sequence with the data present in database and intimate what kind of sequence it is. which gene it is ..........

had problem in site with route.php

it gives some error -- warning 2 the following is already sent at...

this occurs if we had kept some space after ending the php code

like <php

> after this there should be no spaces

started my work on bov and deploying some other applications

the problem for not working of hyperlink was due to apache..

configure mode-rewrite  and now the site is back and its working good

the site is working but the hyperlink to the other pages is giving a problem

i found some matter regarding controllers in cakephp

its at app/controllers/page_controller.php

tried working on it.. everything is ok with the page_controller.php but i dont know why it still giving me the same problem

checking out for somethingin
app/config/routes.php


this too is configured correctly...
still the problem continues..................... :)-

upload .sql files using
mysql> source file path

or

using phpmyadmin

got problem with cakephp.

deployed it in apache2 but the script is not running getting some errors....

installig tomcat6

http://www.ubuntugeek.com/how-to-install-tomcat-6-on-ubuntu-9-04-jaunty.html











apache2 has to be installed to run cakephp files..

now it has been succesfully installed

Apache2 has the concept of sites, which are separate configuration files that Apache2 will read. These are available in /etc/apache2/sites-available. By default, there is one site available called default this is what you will see when you browse to http://localhost or http://127.0.0.1. You can have many different site configurations available, and activate only those that you need.

As an example, we want the default site to be /home/user/public_html/. To do this, we must create a new site and then enable it in Apache2.

To create a new site:

• 
  
  
  Copy the default website as a starting point. sudo cp /etc/apache2/sites-available/default /etc/apache2/sites-available/mysite 
• 
  
  
  Edit the new configuration file in a text editor "sudo nano" on the command line or "gksudo gedit", for example: gksudo gedit /etc/apache2/sites-available/mysite
• 
  
  
  Change the DocumentRoot to point to the new location. For example, /home/user/public_html/
• 
  
  
  Change the Directory directive, replace <Directory /var/www/> to <Directory /home/user/public_html/>
• 
  
  
  You can also set separate logs for each site. To do this, change the ErrorLog and CustomLog directives. This is optional, but handy if you have many sites
• Save the file

Now, we must deactivate the old site, and activate our new one. Ubuntu provides two small utilities that take care of this: a2ensite (apache2enable site) and a2dissite (apache2disable site).

sudo a2dissite default && sudo a2ensite mysite

Finally, we restart Apache2:

sudo /etc/init.d/apache2 restart

If you have not created /home/user/public_html/, you will receive an warning message

To test the new site, create a file in /home/user/public_html/:

echo '<b>Hello! It is working!</b>' > /home/user/public_html/index.html

Finally, browse to http://localhost/


 https://help.ubuntu.com/community/ApacheMySQLPHP