Installing bioperl without root access

In order to give our users the maximum freedom, we are not installing perl modules systemwide, but the modules have to be installed on a per user basis, unless the modules are of such importance and wide use by our user basis, that it justifies a system wide installation. Here is a tutorial how to install perl modules by yourself without having root access:

1) start cpan and config. defaults are ok.
   downloadsites set: 11 9 4
   takes a while -> quit

2) create local perl module directory:
 > mkdir ~/myperl
 
3) start cpan and set the following options:

 > cpan
 cpan> o conf makepl_arg "LIB=~/myperl/lib \
  INSTALLMAN1DIR=~/myperl/man/man1 \
  INSTALLMAN3DIR=~/myperl/man/man3 \
  INSTALLSCRIPT=~/myperl/bin \
  INSTALLBIN=~/myperl/bin"

 cpan> o conf mbuildpl_arg "--lib=~/myperl/lib \
  --installman1dir=~/myperl/man/man1 \
  --installman3dir=~/myperl/man/man3 \
  --installscript=~/myperl/bin \
  --installbin=~/myperl/bin"

 cpan> o conf mbuild_install_arg "--install_path lib=~/myperl"
 cpan> o conf prerequisites_policy automatically
 cpan> o conf commit
 cpan> quit

then you can install whatever modules you like in your local directory.
For example, for bioperl you would need:

 cpan>d /bioperl/
 CPAN: Storable loaded ok
 Going to read /home/bosborne/.cpan/Metadata
 Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
 
 ....
 
 Distribution B/BI/BIRNEY/bioperl-1.2.tar.gz
 Distribution B/BI/BIRNEY/bioperl-1.4.tar.gz
 Distribution C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz

Now install:

 cpan> force install C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz

in case the download is slow, then edit the file ~/.cpan/CPAN/MyConfig.pm and insert the following line
into $CPAN::Config :

'dontload_hash' => { "Net::FTP" => 1, "LWP" =>1 },

in case something goes wrong you can delete ~/.cpan and start over again.

very helpful is the perl shell which you can obtain by installing:
cpan> install Psh
cpan> install IO::String

it is then available under ~/myperl/bin/psh
e.g. try out 
psh% use Bio::Perl;
psh% $seq_object = get_sequence('genbank',"ROA1_HUMAN");
psh% write_sequence(">roa1.fasta",'fasta',$seq_object);