牧羊人

1. Upgrade CPAN
1.1. >perl -MCPAN -e shell
1.2. cpan>install Bundle::CPAN
1.3. cpan>q

2. Install/upgrade Module::Build
2.1. >cpan
2.2. cpan>install Module::Build
2.3. cpan>o conf prefer_installer MB [prefer_installer   [MB]]
2.4. cpan>o conf commit [commit: wrote '/etc/perl/CPAN/Config.pm']

3 Install bioperl
3.1. >sudo wget http://bioperl.org/DIST/current_core_unstable.tar.gz
3.2. >sudo tar -zxvf current_core_unstable.tar.gz
3.3. >cd bioperl-1.5.2_102/
3.4. >sudo perl Makefile.PL (***If choosing 'a' instead of 'n': Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] a***)
3.5. >./Build test
3.6. >./Build install

4. may occurs some following ERRORS

......
Install [a]ll optional external modules
......
What do you want to build?

  1) Interface to Ace socket server and local databases (pure Perl)
  2) The above plus XS optimizations (requires C compiler)
  3) The above plus RPC server interface (requires C compiler)

Enter your choice:  [1]

Do you want to install Ace::Browser?  [n]
......

Install bioperl by cpan
1. >sudo su- [http://linux.vbird.org/linux_basic/0410accountmanager.php#sudo]
2. >cpan [get into cpan interface]
2.1. cpan> o conf [find out where config.pm is]
　　CPAN::Config options from /etc/perl/CPAN/Config.pm
2.2. cpan>q [quit cpan]
2.3. vi /etc/perl/CPAN/Config.pm [add available ftp url into config.pm]
　　'urllist' => [q[ftp://cpan.nctu.edu.tw/], q[ftp://ftp.perl.org/pub/CPAN/]],
3. >perl -MCPAN -e shell [Upgrade CPAN]
4. >cpan
5. cpan>install S/SE/SENDU/bioperl-1.5.2_102.tar.gz [2008.0418: bioperl-1.5.2_102.tar.gz]
file: $CPAN/authors/id/S/SE/SENDU/bioperl-1.5.2_102.tar.gz
size: 5919092 bytes
md5: 4890481c5beb33e129b65b922fb0c126
'bioperl-1.5.2_102.tar.gz' => {
'md5' => '4890481c5beb33e129b65b922fb0c126',
'md5-ungz' => '575cd48e80c3e864e46f2add6c045ddc',
'mtime' => '2007-02-14',
'sha256' => '277c74c785afc05ad1d9dbe938677639c33130487d15bdc4a7a10e033137bada',
'sha256-ungz' => 'd070644aa42f876f9d2cfc5fd727df7f4663f4bca7dd9cfae034a74762453d4a',
'size' => '5919092'
}
Install bioperl by cpan

[ERROR]
Error: Can't locate the perl binary used to run this script in...
Solution: http://rt.cpan.org/Public/Bug/Display.html?id=19465 [unset LANG]

[ERROR]
t/SeqFeature.................ok 76/211                                      
-------------------- WARNING ---------------------
MSG: [1/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
---------------------------------------------------
chmod 666 /root/.cpan/build/bioperl-1.5.2_102-ldCKbN/blib/lib/Bio/Ontology/DocumentRegistry.pm
vi /root/.cpan/build/bioperl-1.5.2_102-ldCKbN/blib/lib/Bio/Ontology/DocumentRegistry.pm
    change Line 85 & 86:
        ontology => 'http://umn.dl.sourceforge.net/sourceforge/song/sofa.ontology',
        definitions =>'http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition',
        to [http://www.movoin.com/index.php/archives/171]
        ontology => 'http://heanet.dl.sf.net/sourceforge/song/sofa.ontology',
        definitions =>'http://heanet.dl.sf.net/sourceforge/song/sofa.definition',
chmod 444 /root/.cpan/build/bioperl-1.5.2_102-ldCKbN/blib/lib/Bio/Ontology/DocumentRegistry.pm
chmod 666 /root/.cpan/build/bioperl-1.5.2_102-ldCKbN/Bio/Ontology/DocumentRegistry.pm
    change Line 85 & 86 [Dead Link]:
        ontology => 'http://umn.dl.sourceforge.net/sourceforge/song/sofa.ontology',
        definitions =>'http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition',
        to [http://www.movoin.com/index.php/archives/171]
        ontology => 'http://heanet.dl.sf.net/sourceforge/song/sofa.ontology',
        definitions =>'http://heanet.dl.sf.net/sourceforge/song/sofa.definition',
chmod 444 /root/.cpan/build/bioperl-1.5.2_102-ldCKbN/Bio/Ontology/DocumentRegistry.pm
t/HtSNP......................Can't use string ("9") as an ARRAY ref while "strict refs" in use at /root/.cpan/build/bioperl-1.5.2_102-ldCKbN/blib/lib/Bio/PopGen/HtSNP.pm line 1075.

[Solution]
Ctrl + C to terminate the process here
chmod 666 /root/.cpan/build/bioperl-1.5.2_102-O63JGV/blib/lib/Bio/PopGen/HtSNP.pm
vi /root/.cpan/build/bioperl-1.5.2_102-O63JGV/blib/lib/Bio/PopGen/HtSNP.pm
    change Line 1075: foreach my $value (@{@$aref} ){
        to: foreach my $value (@$aref){ and save
chmod 444 /root/.cpan/build/bioperl-1.5.2_102-O63JGV/blib/lib/Bio/PopGen/HtSNP.pm

Install the CPAN module Class::Inspector
[http://www.bioperl.org/wiki/FAQ#Why_can.27t_I_easily_get_a_list_of_all_the_methods_a_object_can_call.3F]
1. >cpan
2. cpan> install A/AD/ADAMK/Class-Inspector-1.22.tar.gz
Create a perl script with the following code, put it into your path, and run it, e.g, >perl Inspector.pl Bio::Seq
#!/usr/bin/perl -w
use Class::Inspector;
$class = shift || die "Usage: methods perl_class_name\n";
eval "require $class";
print join ("\n", sort @{Class::Inspector->methods($class,'full','public')}), "\n";

http://doc.bioperl.org/releases/bioperl-1.0.1/Bio/SeqIO.html

perl Inspector.pl Bio::SeqIO
[
Bio::Root::IO::catfile
Bio::Root::IO::close
Bio::Root::IO::dup
Bio::Root::IO::exists_exe
Bio::Root::IO::file
Bio::Root::IO::flush
Bio::Root::IO::gensym
Bio::Root::IO::mode
Bio::Root::IO::noclose
Bio::Root::IO::qualify
Bio::Root::IO::qualify_to_ref
Bio::Root::IO::rmtree
Bio::Root::IO::tempdir
Bio::Root::IO::tempfile
Bio::Root::IO::ungensym
Bio::Root::Root::confess
Bio::Root::Root::debug
Bio::Root::Root::throw
Bio::Root::Root::verbose
Bio::Root::RootI::carp
Bio::Root::RootI::deprecated
Bio::Root::RootI::stack_trace
Bio::Root::RootI::stack_trace_dump
Bio::Root::RootI::throw_not_implemented
Bio::Root::RootI::warn
Bio::Root::RootI::warn_not_implemented
Bio::SeqIO::DESTROY
Bio::SeqIO::PRINT
Bio::SeqIO::READLINE
Bio::SeqIO::TIEHANDLE
Bio::SeqIO::alphabet
Bio::SeqIO::fh
Bio::SeqIO::location_factory
Bio::SeqIO::new
Bio::SeqIO::newFh
Bio::SeqIO::next_seq
Bio::SeqIO::object_factory
Bio::SeqIO::sequence_builder
Bio::SeqIO::sequence_factory
Bio::SeqIO::write_seq
]

perl Inspector.pl Bio::Seq
[
Bio::AnnotatableI::croak
Bio::FeatureHolderI::get_all_SeqFeatures
Bio::IdentifiableI::lsid_string
Bio::IdentifiableI::namespace_string
Bio::PrimarySeqI::moltype
Bio::PrimarySeqI::revcom
Bio::PrimarySeqI::translate
Bio::PrimarySeqI::trunc
Bio::Root::Root::confess
Bio::Root::Root::debug
Bio::Root::Root::throw
Bio::Root::Root::verbose
Bio::Root::RootI::carp
Bio::Root::RootI::deprecated
Bio::Root::RootI::stack_trace
Bio::Root::RootI::stack_trace_dump
Bio::Root::RootI::throw_not_implemented
Bio::Root::RootI::warn
Bio::Root::RootI::warn_not_implemented
Bio::Seq::DESTROY
Bio::Seq::accession
Bio::Seq::accession_number
Bio::Seq::add_SeqFeature
Bio::Seq::all_SeqFeatures
Bio::Seq::alphabet
Bio::Seq::annotation
Bio::Seq::authority
Bio::Seq::can_call_new
Bio::Seq::desc
Bio::Seq::description
Bio::Seq::display_id
Bio::Seq::display_name
Bio::Seq::feature_count
Bio::Seq::flush_SeqFeature
Bio::Seq::flush_SeqFeatures
Bio::Seq::get_SeqFeatures
Bio::Seq::id
Bio::Seq::is_circular
Bio::Seq::length
Bio::Seq::namespace
Bio::Seq::new
Bio::Seq::object_id
Bio::Seq::primary_id
Bio::Seq::primary_seq
Bio::Seq::remove_SeqFeatures
Bio::Seq::seq
Bio::Seq::species
Bio::Seq::subseq
Bio::Seq::top_SeqFeatures
Bio::Seq::validate_seq
Bio::Seq::version
Bio::SeqI::write_GFF
]