[Bioperl-l] dependencies in emboss.pm

[Florent Angly]

Hi Yoshiro,
Please keep messages on the list. The Bioperl-Run package is available on
CPAN (http://search.cpan.org/dist/bioperl-run/). It can be installed in a
similar way to Bioperl (Bioperl-live), which is explained here:
http://www.bioperl.org/wiki/Installing_BioPerl
Best,
Florent


On Fri, Mar 7, 2014 at 8:41 PM, Yoshiro Nagao <ng999 at yahoo.co.jp> wrote:

> Hi Florent
> It seems that I just installed the core.
> How can I install bioperl-run?
>
> Yoshiro
>
> --- On Fri, 2014/3/7, Florent Angly <florent.angly at gmail.com> wrote:
>
> >
> >
> >
> >
> > Yoshiro,
> > The module Bio::Emboss::Methods is located in the bioperl-run package.
> Have you installed bioperl-run in addition to bioperl-live?
> > Best,
> > Florent
> >
> >
> >
> >
> > On Fri, Mar 7, 2014 at 7:10 PM, Yoshiro Nagao <ng999 at yahoo.co.jp> wrote:
> > First, please let me apologize to you for this primitive question about
> installation (if there is more proper mailing list for this sort of
> question,
> > please let me know one).
> >
> > I tried to run the following tutorial script on my Ubuntu 12:
> >
> >
> https://github.com/bioperl/bioperl-live/blob/master/examples/align/aligntutorial.pl
> >
> > Since Bio::Factory::Emboss was not installed in my Ubuntu,
> > I downloaded and installed Bio-Emboss-5.0.0.1.tar.gz from
> > http://search.cpan.org/dist/Bio-Emboss/Emboss.pm
> >
> > Then, I modified the aligntutorial.pl as in:
> >
> > use lib "/home/usr/Bio-Emboss-5.0.0.1";
> > use Emboss;
> > #use Bio::Factory::Emboss;
> >
> > However, when I ran the aligntutorial.pl, another error message
> >   Can't locate Bio/Emboss/Methods.pm
> > appeared.
> >
> > Perhaps, I 'installed' the emboss very wrongly.
> >
> > How can I install the emboss module nicely, so that
> > I do not have to rewrite the aligntutorial.pl or modules, or
> > whatever other scripts on the GitHub site?
> >
> > Sorry for the silly question.
> >
> > Yoshiro
> >
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>