[Bioperl-l] Installation of bioperl on Ubuntu

Minh Bui buiduyminh at gmail.com
Thu Oct 28 17:07:06 EDT 2010


Hi Andrea,

You don't have to install Bioperl manually on Ubuntu.

You can go to *System* > *Administration* > "*Synaptic Package Manager*" ,
search for "Bioperl" and install it. I believe it has the latest version.

Minh.


On Thu, Oct 28, 2010 at 4:52 PM, Andrea Edwards <edwardsa at cs.man.ac.uk>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
>
> 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
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


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