[Bioperl-l] Bioperl installation doubt

Brian Osborne bosborne11 at verizon.net
Mon Mar 28 16:43:51 EDT 2011


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 There's certainly useful text in there but there's also duplicated or outdated material.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 That is *way* out of date.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 superseded at this point by other docs and is not current.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