[Bioperl-l] dependencies in emboss.pm

[Fields, Christopher J]

Just a warning, it may require that you force install.  We try to make it easier to set up but it wouldn’t surprise us if it fails if you don’t have a particular software package installed.

(which reminds me, maybe this should be added to travis-ci…)

chris

On Mar 7, 2014, at 4:53 AM, Florent Angly <florent.angly at gmail.com> wrote:

> 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
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>> 
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