[Bioperl-l] Help installing BioPerl

[Michael Robeson]

Ok, thanks guys. Must have been sleepy when installing on that last 
computer! :-)

When I get back to that computer tonight I will try it again w/o the 
correct files in the right order. I'll keep you posted as to the 
results.

- Thanks for your help! I am sure I'll be back soon.
- Mike (Bioperl newbie)


On Sep 13, 2004, at 12:04 PM, Remo Sanges wrote:

> On Sep 13, 2004, at 7:47 PM, Michael Robeson wrote:
>
>> Hmm, seems like I should just write things from scratch rather than 
>> use BioPerl. Much less troubleshooting, ehh? Naa, I'd still rather 
>> try installing/using BioPerl   :-)
>>
>> Sorry, about this but I am trying to learn. I am trying to follow 
>> along with the "perl for bioinformatics" books but they are of no use 
>> when it comes to trouble shooting bio::perl.
>
> I' m not sure but it seems that you are triyng to install bioperl-run
> before than bioperl, rigth?
> They are two different packages and you should install them in
> the rigth order...
>
> if you perform a search in cpan you will find:
>
> cpan> i /bioperl/
> Bundle          Bundle::BioPerl 
> (C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz)
> Distribution    A/AL/ALLENDAY/bioperl-microarray-0.1.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-0.05.1.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-0.6.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-0.7.0.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.0.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.0.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.2.1.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.2.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.2.3.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.4.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-db-0.1.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-gui-0.7.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-run-1.2.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-run-1.4.tar.gz
> Distribution    C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz
> Module          Bio::LiveSeq::IO::BioPerl 
> (B/BI/BIRNEY/bioperl-1.2.3.tar.gz)
>
> So you should install in this order:
>
> - Bundle::BioPerl
> - bioperl-1.4.tar.gz
> and then
> - bioperl-run-1.4.tar.gz
>
> Consider always as a reference:
>
> - the bioperl website http://bioperl.org/
> - the bioperl tutorial 
> http://www.bioperl.org/Core/Latest/bptutorial.html
> - the bioperl how-to http://bioperl.org/HOWTOs/
>
>
> HTH
>
> Remo
>