[Bioperl-l] Bioperl installation doubt

Thu Apr 14 17:06:40 EDT 2011

Chris,

I've done a bit of work on http://www.bioperl.org/wiki/Bptutorial.pl, I'd say it's now about one quarter of its original size. Most of the text has gone into new or existing HOWTOs.

BIO

On Mar 28, 2011, at 6:40 PM, Chris Fields 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 There's certainly useful text in there but there's also duplicated or outdated material.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 That is *way* out of date.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 superseded at this point by other docs and is not current.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
>>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
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>>> 
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