[Bioperl-l] Bioperl installation doubt

Dave Messina David.Messina at sbc.su.se
Mon Mar 28 07:51:41 EDT 2011


>
> 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 That is *way* out of date.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superseded at this point by other docs and is not current.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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