[Bioperl-l] new Bio::Installer modules in bioperl-run

[avilella]

On Mon, 2004-03-01 at 13:56, Todd Harris wrote:
> Hi Albert - 
> 
> This would be a nice convenience.
> 
> Do these handle the (potentially) many system-dependent issues as well?

Nope. It only checks for:

($^O =~ /dec_osf|linux|unix|bsd|solaris|darwin/i)

or strictly:

/linux/

at the points where it does system-dependent calls... for the moment.

Has bioperl an estimate of XX% of OSes where is mostly installed/used?

>   Or
> can yo

> u just generically pass configure/make/test/install paramaters to the
> installer object? Also, a superclass would be nice that creates an installer
> factory for those wishing to build lots of things from a single script.

There is a Bio::Installer::Generic for the common calls, like ("tar xzf
package.tar.gz")... But very "simplistic" right now...

http://www.ebi.ac.uk/cvs/cvspublic/wallace/bioperl-run/Bio/Installer/

Still tweaking and adding some bits,

    Albert.

> 
> todd
> 
> > On 3/1/04 7:33 AM, avilella wrote:
> 
> > Hi,
> > 
> > I've been playing with a set of modules to make the installation of
> > bioperl external programes easier.
> > 
> > These are modules with methods to basically download, decompress,
> > compile and install the program that is meant to be called by bioperl.
> > 
> > For example, for TCoffee, there would be a script in bioperl-run/scripts
> > like:
> > 
> > install_tcoffee.PLS
> > -------------------
> > use strict;
> > use Bio::Installer::TCoffee;
> > 
> > # Install in the directory where the script is called
> > use Cwd;
> > my $destination_install_dir = getcwd;
> > my $installer = new Bio::Installer::TCoffee(
> >                                           -destination_install_dir =>
> > $destination_install_dir);
> > $installer->download();
> > $installer->install();
> > 
> > 1;
> > --------------------
> > 
> > that would download, decompress and compile TCoffee to the preferred
> > directory.
> > 
> > Feedback is welcomed,
> > 
> > Thanks,
> > 
> >   Albert.
> > 
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> > 
>