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

Chris Fields cjfields at illinois.edu
Thu Mar 31 15:49:08 EDT 2011


+1 from me.  Go ahead.  Old misleading documentation is bad to have around.

chris

On Mar 31, 2011, at 2:43 PM, Dave Messina wrote:

> 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 in there but there's also duplicated or outdated material.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 superseded at this point by other docs and is not current.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
>>> 
>> 
>> 
> 
> _______________________________________________
> 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