[Bioperl-l] Bioperl installation doubt

Chris Fields cjfields at illinois.edu
Mon Mar 28 09:27:38 EDT 2011


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 That is *way* out of date.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 superseded at this point by other docs and is not current.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