[Bioperl-l] Bioperl installation doubt

Chris Fields cjfields at illinois.edu
Mon Mar 28 18:40:39 EDT 2011


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 There's certainly useful text in there but there's also duplicated or outdated material.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 That is *way* out of date.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 superseded at this point by other docs and is not current.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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