How To Install BioPerl Without Root Privileges in Ubuntu/Linux

First step: Install local::lib so that you can install bioperl without root privileges

perl -MCPAN -Mlocal::lib -e 'CPAN::install(local::lib)'

Second step: Download latest bioperl from github

make dir /home/shg047/software/
cd /home/shg047/software/
git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
perl Build.PL
./Build test

Step 3. build test error?? Don't worry, test them one by one and install missed package, such as

./Build test --test_files t/LocalDB/Taxonomy/sqlite.t --verbose
./Build test --test_files t/Root/RootIO.t --verbose

Step 4: install the failed library according build test result. maybe huge number of library need to be installed according to your own situation. For me 25 packages were installed by myself.

perl -MCPAN -Mlocal::lib -e 'CPAN::install(DBI)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(DBD::SQLite)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(LWP::UserAgent)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(LWP::UserAgent)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(Bio::Phylo)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(Bio::DB::Sam)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(Graph::Directed)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(XML::Twig)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(Bio::Ext::Align)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(XML::Parser::PerlSAX)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(XML::Simple)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(HTML::TableExtract)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(IO::Scalar)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(XML::SAX)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(Bio::SeqIO::staden::read)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(XML::Parser::PerlSAX)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(Bio::SeqIO::staden::read)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(XML::LibXML)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(Convert::Binary::C)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(XML::SAX::Writer)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(XML::Writer)'
perl -MCPAN -Mlocal::lib -e 'CPAN::install(Bio::SeqIO::staden::read)'

step 5. test again

./Build test 

Step 6: Test bioperl installation (you should get a version number)

perl -MBio::Root::Version -le 'print $Bio::Root::Version::VERSION'

Step 7: Install bioperl with the last kick!

./Build install

Now, Use it. Use it. Bioperl is still deserve to make deep exploration.

By the way, If you want install Bio::DB::Sam to use samtools in bioperl, you need recompile samtools again with the following method.

cd /home/shg047/software/samtools-1.3.1
make clean
make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC
> cpan
install Bio::DB::Sam

OK. Now, You can use Bio::DB::Sam in your perl script

use Bio::DB::Sam;
my $sam = Bio::DB::Sam->new(-bam  => $infile);