rpy2 for Ubuntu

# 1. install all dependence packages

sudo apt-get build-dep r-base

# 2. Install R with shlib 

        make distclean
        ./configure --enable-R-shlib
        make
        make install 

# 3. install rpy2 

   sudo easy_install rpy2

R install ubuntu

INSTALLATION

To obtain the latest R packages, add an entry like

  deb http://cran.cnr.Berkeley.edu/bin/linux/ubuntu lucid/

   sudo apt-get update
   sudo apt-get install r-base

public key trouble

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys <KEY NUMBER>

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 51716619E084DAB9

Bioperl Parsing_BLAST

http://www.bioperl.org/wiki/Parsing_BLAST_HSPs

http://www.bioperl.org/wiki/Parsing_BLAST_results_into_per-query_files


CPAN: Automatically install dependencies without confirmation 

perl -MCPAN -e shell 

o conf prerequisites_policy follow
o conf commit 

PREPARING TO INSTALL

This is optional, but regardless of your subsequent choice of installation method, it will help to carry out the following steps. They will increase the likelihood of installation success (especially of optional dependencies).

• Upgrade CPAN:

>perl -MCPAN -e shell
cpan>install Bundle::CPAN
cpan>q

• Install/upgrade Module::Build, and make it your preferred installer:

>cpan cpan>install Module::Build
cpan>o conf prefer_installer MB
cpan>o conf commit
cpan>q

>tar xvfz BioPerl-1.6.1.tar.gz
>cd BioPerl-1.6.1

Now issue the build commands:

>perl Build.PL
>./Build test 

>./Build install