[Bioperl-l] Installation of bioperl on Ubuntu

Chris Fields cjfields at illinois.edu
Thu Oct 28 17:28:17 EDT 2010


On Oct 28, 2010, at 3:52 PM, Andrea Edwards wrote:

> 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

Ugh, that's not good; that should be removed (we're now at v 1.6.1 stable, but about 10 months past that release now and sorely due for another).  For the latest 'unstable' code, you can go to github:

http://github.com/bioperl/bioperl-live

Click on the 'Downloads' button.

Just a warning, but FeatureIO will likely disappear from the github bioperl-live repo master branch.  We're breaking out chunks of code that can be released independently, FeatureIO being one.

> 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

ConfigData is only for the installation.  Not sure about the others.

> 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

Since we moved to github this past May we no longer have different revision numbers per module (git doesn't support them, but so far we haven't seen many actually missing them).  

chris


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