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
  

Installation using CPAN or manual installation

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Installation using CPAN or manual installation

   Installation using PPM is preferred since it is easier, but if you run
   into problems, or a ppm isn't available for the version/package of bioperl
   you want, or you want to choose which optional dependencies to install,
   you can install manually by downloading the appropriate package or by
   using CPAN. In fact both methods ultimately need nmake to be
   installed, CPAN to be upgraded to >= v1.81, Module::Build to be installed
   (>= v0.2805) and Test::Harness to be upgraded to >= v2.62:

           1) Download nmake

           2) Double-click to run it, which extracts 3 files. Move both
           NMAKE.EXE and the NMAKE.ERR files to a place in your PATH; if set
           up properly, you can move these to your Perl bin directory,
           normally C:\Perl\bin.

           1) Open a cmd window by going to Start >> Run and typing 'cmd'
           into the box and pressing return.

           2) Type 'cpan' to enter the CPAN shell.

           3) At the cpan> prompt, type 'install CPAN' to upgrade to the
           latest version.

           4) Quit (by typing 'q') and reload cpan. You may be asked some
           configuration questions; accepting defaults is fine.

           5) At the cpan> prompt, type 'o conf prefer_installer MB' to tell
           CPAN to prefer to use Build.PL scripts for installation. Type 'o
           conf commit' to save that choice.

           6) At the cpan> prompt, type 'install Module::Build'.

           7) At the cpan> prompt, type 'install Test::Harness'.

   You can now follow the unix instructions for installing using CPAN, or
   install manually:

           8) Download the .zip version of the package you want.

           9) Extract the archive in the normal way.

           10) In a cmd window 'cd' to the directory you extracted to. Eg. if
           you extracted to directory 'Temp', 'cd Temp\bioperl-1.5.2_100'

           11) Type 'perl Build.PL' and answer the questions appropriately.

           12) Type 'perl Build test'. All the tests should pass, but if they
           don't, let us know. Your usage of Bioperl may not be affected
           by the failure, so you can choose to continue anyway.
          
           12.5) Run 'Build installdeps' to install missing prerequisites.

           13) Type 'perl Build install' to install Bioperl.