[Bioperl-l] Old docs cleanup (was Re: Bioperl installation doubt)

Dave Messina David.Messina at sbc.su.se
Thu Mar 31 15:43:14 EDT 2011


Hi,

Just to clarify:

Brian, is it okay with you if I go ahead and remove the Core/ directory from
the website? (and okay with everyone else, too, for that matter? I haven't
heard any nays so far.)


Dave



On Tue, Mar 29, 2011 at 00:40, Chris Fields <cjfields at illinois.edu> wrote:

> Brian,
>
> I think this was started:
>
> http://www.bioperl.org/wiki/Bptutorial.pl
>
> It certainly could be cleaned up, organized, and updated (that and the
> FAQ).  Makes sense to have it as a HOWTO or maybe split it into several
> HOWTOs.  Maybe even combine it with the beginner's HOWTO into various
> sections?
>
> chris
>
> On Mar 28, 2011, at 3:43 PM, Brian Osborne wrote:
>
> > Chris,
> >
> > I'll get started on dissembling bptutorial. There's certainly useful text
> in there but there's also duplicated or outdated material. Looks like there
> are 3 options for any given section:
> >
> > - put it into an existing HOWTO
> > - make it into a new HOWTO
> > - delete it
> >
> > BIO
> >
> > On Mar 28, 2011, at 9:27 AM, Chris Fields wrote:
> >
> >> Dave,
> >>
> >> +1 on removing old docs to prevent confusion.  Or, alternatively, +1 to
> syncing those to current docs (though I think decreasing the replication
> effort in keeping docs up-to-date is probably the best tact).
> >>
> >> chris
> >>
> >> On Mar 28, 2011, at 6:51 AM, Dave Messina wrote:
> >>
> >>>>
> >>>> Thank you very much. It is working. I got the program code from the
> >>>> following link.
> >>>>
> >>>> http://www.bioperl.org/Core/Latest/bptutorial.html
> >>>
> >>>
> >>> Aha, okay. You got there from Google, I guess? That is *way* out of
> date.
> >>>
> >>> To the other core devs, in order to prevent this confusion in the
> future,
> >>> I'd like to delete the Core/ directory from our website since it's been
> >>> superseded at this point by other docs and is not current. I intend to
> put
> >>> up a ticket at Redmine, but I will wait a bit before doing so to allow
> time
> >>> for people to see this and comment — please do speak up if there's good
> >>> reason to keep it.
> >>>
> >>>
> >>> Could you please give me the link to join this forum to see other
> >>>> discussions, which would be more helpful to me?
> >>>>
> >>>
> >>> Sure, you can sign up for the mailing list here:
> >>>
> >>> <http://lists.open-bio.org/mailman/listinfo/bioperl-l>
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>> And the archives are also searchable:
> >>>
> >>>  http://news.gmane.org/gmane.comp.lang.perl.bio.general
> >>>
> >>>
> >>> Please let me know if you have any suggestion for me to keep learning
> the
> >>>> bioperl.
> >>>
> >>>
> >>> I would also suggest reading the (current) tutorial and HOWTOs at
> >>> www.bioperl.org . Lots of good links on the main page there,
> particularly
> >>> under the Documentation heading.
> >>>
> >>>
> >>> Dave
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>> With regards,
> >>>> Ravi.
> >>>>
> >>>>
> >>>> 2011/3/28 Dave Messina <David.Messina at sbc.su.se>
> >>>>
> >>>>> Hi Ravi,
> >>>>>
> >>>>> Please make sure to "Reply All" so that everyone on the mailing list
> can
> >>>>> follow (and add to) the discussion.
> >>>>>
> >>>>> If you read the first line of the exception, you'll see it states
> what the
> >>>>> error is:
> >>>>> "WebDBSeqI Error — check query sequences!"
> >>>>>
> >>>>> You'd have no way of knowing this, but that ID and database
> combination is
> >>>>> not functioning anymore, so that's why in this case you're getting an
> error.
> >>>>> Please try using the example in the tutorial here:
> >>>>>
> >>>>>
> >>>>>
> http://www.bioperl.org/wiki/BioPerl_Tutorial#Quick_getting_started_scripts
> >>>>>
> >>>>> which has been updated to a different ID which should work.
> >>>>>
> >>>>> Sorry for the confusion! So that we can prevent other people from
> having
> >>>>> the same issue, could you tell me where you got that example code?
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> 2011/3/28 ¶•●๋•இரவிяανι●๋••¶ <ravimbt at gmail.com>
> >>>>>
> >>>>>> Hi Dave,
> >>>>>>
> >>>>>> Thanks a lot for your reply. It is really helpful. Please find the
> >>>>>> screenshot after making the change you pointed out. But I am getting
> >>>>>> "Exception: Bio::Root::Exception" error. I think I have to set the
> >>>>>> environment variables but I am not sure how to do that. Could you
> please
> >>>>>> guide me on this too.
> >>>>>>
> >>>>>> I can go to the "Environment Variable" Window in my pc. But I dont
> know
> >>>>>> what to enter once I click "New" on that window.
> >>>>>>
> >>>>>> Thanks in advance.
> >>>>>>
> >>>>>> With regards,
> >>>>>> Ravi.
> >>>>>>
> >>>>>>
> >>>>>> 2011/3/27 Dave Messina <David.Messina at sbc.su.se>
> >>>>>>
> >>>>>>> Hi Ravi,
> >>>>>>>
> >>>>>>> The get_sequence and write_sequence methods are in the Bio::Perl
> module,
> >>>>>>> not Bio::Seq. So your first line
> >>>>>>>
> >>>>>>> use Bio::Seq;
> >>>>>>>
> >>>>>>> should be replaced with
> >>>>>>>
> >>>>>>> use Bio::Perl;
> >>>>>>>
> >>>>>>>
> >>>>>>> More examples in the BioPerl Tutorial here:
> >>>>>>> http://www.bioperl.org/wiki/BioPerl_Tutorial
> >>>>>>>
> >>>>>>>
> >>>>>>> Dve
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> 2011/3/24 ¶•●๋•இரவிяανι●๋••¶ <ravimbt at gmail.com>
> >>>>>>>
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> Could you please help me installing bioperl-db, bioperl-run &
> other
> >>>>>>>> packages
> >>>>>>>> using ppm on windows 7? Please find the attachment for the error
> >>>>>>>> message I
> >>>>>>>> get. I would really appreciate if you help me fix this issue.
> >>>>>>>>
> >>>>>>>> Thanks,
> >>>>>>>>
> >>>>>>>> With regards,
> >>>>>>>> Ravi.
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> Bioperl-l mailing list
> >>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>



More information about the Bioperl-l mailing list