[Bioperl-l] Installation of bioperl on Ubuntu

Andrea Edwards edwardsa at cs.man.ac.uk
Thu Oct 28 16:52:58 EDT 2010


Hi

I'm new to Perl and linux and I think I may have messed up my 
installation of Bioperl.

I followed the instructions on this page verbatim
http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server

However the

./Build test


command failed and I noticed a lot of modules were missing from the 
output of the test. I then used CPAN to install these modules. One of 
them was Bio::FeatureIO. When I installed this it seemed to be 
installing lots of BioPerl 1.6.1 files. However when i downloaded the 
bioperl as instructed here

wget -N http://bioperl.org/DIST/current_core_unstable.tar.bz2

the version that I got was 1.5.2_102

I am confused by the presence of 2 different version numbers and don't 
know how to proceed. It looks as if I have installed a lot of BioPerl 
1.6.1 and if i carry on with the make test/install instructions from the 
website I will then install version 1.5.

When i looked at the files installed in the Bio folder in my perl 
libraries there were 88 files and the only files missing compared to my 
other BioPerl installations were:
ANSI directory
BioEntry.pm
ConfigData.pm

I looked at some of the modules to try and see which version they were 
but they all had different version numbers. I think I have inadvertently 
used CPAN to install 1.6.1. What do you think?

many thanks


More information about the Bioperl-l mailing list