Monday, January 13, 2014

How To Install BioPerl Without Root Privileges

I've seen this question asked and partially answered all around the web. As with anything related to Perl, I'm sure there is more than one way to do it. Here's how I do it with Perl 5.10.1 on CentOS 6.4.

First, install local::lib with bootstrapping method as described here.



## Install local::lib with boostrapping technique
wget http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/local-lib-1.008018.tar.gz #download the tarball
tar -zxvf local-lib-1.008018.tar.gz # unpack
cd local-lib-1.008018
mkdir -p ~/perl5 # default installation path
perl Makefile.PL --bootstrap
make test && make install


Next, put this in your .bashrc so that it's executed every time you log in:

# Put this in your .bashrc:
echo 'eval $(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)'


Log out then log back in, then download and install BioPerl, answering "yes" to any question asking you to download and install dependencies when necessary:

## Install bioperl
wget http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz # get the tarball
tar -zxvf BioPerl-1.6.1.tar.gz # extract
cd BioPerl-1.6.1
perl Build.PL
./Build test
./Build install
## Test bioperl installation (you should get a version number)
perl -MBio::Root::Version -le 'print $Bio::Root::Version::VERSION'


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Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.