[Bioperl-l] Fwd: [Gmod-ajax] Jbrowse on mac os 10.5

Chris Fields cjfields at illinois.edu
Wed Mar 18 14:11:34 EDT 2009


On Mar 18, 2009, at 11:35 AM, Isabelle Phan wrote:

> Hello Chris
>
>> The following, from the INSTALL file, alludes to the use of
>> 'sudo' but
>> could be made clearer:
>
> Perhaps I've missed something, but we seem to be writing at cross  
> purposes:
>
> I am running the build with 'sudo' and I have admin privileges on my  
> machine. I am not installing any modules that the bioperl Build  
> flags as optional.

My question is where do HTML::Tagset and Digest::MD5 sneak in during  
the installation.  They are not listed as prereqs for BioPerl

> My question was:
>
> Do I have to issue the Build command? I understand from the INSTALL  
> that I have to. Your previous message seems to imply I do NOT have to.

If you are installing using the package tarball, you would use:

sudo perl Build.PL
./Build
./Build test
sudo ./Build install

if you want the Build.PL script to install the required modules (it  
uses CPAN.pm to do this), and if you want to install to a location  
that requires admin privileges.  The four modules absolutely required  
are: DB_File, Data::Stag, IO::String, Scalar::Util.

> It would help me immensely to get a clear answer: after I unpack the  
> Bioperl tarball, do I have to run the Build, Yes or No?
>
> Many thanks for your patience,
>
> Isabelle


As Hilmar points out, you don't have to actually install BioPerl (his  
reasons for not installing are the same as mine).  If you have your  
env set up it correctly you could use it from wherever (maybe even a  
copy within a secure folder for web apps, for instance).

chris


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