[Bioperl-l] How to install 1.6.2

[Chris Fields]

Note that is a branch, not a tagged release.  We created a new branch for the eventual 1.6.2 release due to problems cherry-picking commits over the last year or so.  It's not really different from master, with the exception that we'll be merging code in from the recent evo hackathon soon to master and NOT to the release.

chris

On Feb 4, 2011, at 10:33 AM, Scott Cain wrote:

> OK, the seqfeature_load script in that branch has the summary feature
> option in it.  Are you sure that the script you have doesn't?
> 
> Scott
> 
> 
> On Fri, Feb 4, 2011 at 11:27 AM, Minh Bui <buiduyminh at gmail.com> wrote:
>> I got it from here
>> https://github.com/bioperl/bioperl-live/tree/release-1-6-2
>> 
>> 
>> 
>> On Fri, Feb 4, 2011 at 11:23 AM, Scott Cain <scott at scottcain.net> wrote:
>>> 
>>> Hi Minh,
>>> 
>>> Where did you get BioPerl 1.6.2 from?  It hasn't been released yet.
>>> You need to be BioPerl from git hub to use summary features:
>>> 
>>>  https://github.com/bioperl/bioperl-live
>>> 
>>> and click the download link on the right and select either tar.gz or
>>> zip file to download.
>>> 
>>> Scott
>>> 
>>> 
>>> On Fri, Feb 4, 2011 at 11:14 AM, Minh Bui <buiduyminh at gmail.com> wrote:
>>>> HI Scott,
>>>> 
>>>> I installed it anyway but the terminal (i am using Ubuntu 10.10) and it
>>>> says
>>>> that bp_seqfeature_load.pl (unchanged) --> I still can't use --summary
>>>> feature.
>>>> 
>>>> Is there other way to use this feature?
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Fri, Feb 4, 2011 at 11:09 AM, Scott Cain <scott at scottcain.net> wrote:
>>>>> 
>>>>> Hi Minh,
>>>>> 
>>>>> I don't know why that test failed, but if you don't need to parse or
>>>>> produce EMBL files, it doesn't matter (and even if you do, it still
>>>>> may not matter, depending on what the test was).  I suggest
>>>>> installing.
>>>>> 
>>>>> Scott
>>>>> 
>>>>> 
>>>>> On Fri, Feb 4, 2011 at 11:05 AM, Minh Bui <buiduyminh at gmail.com> wrote:
>>>>>> Oh
>>>>>> One more thing, I just downloaded Bioperl 1.6.2 and
>>>>>> 
>>>>>> When I tried to run perl Build.PL, i got this message.
>>>>>> *
>>>>>> Checking whether your kit is complete...
>>>>>> WARNING: the following files are missing in your kit:
>>>>>>    .shipit
>>>>>> Please inform the author.
>>>>>> 
>>>>>> Checking prerequisites...
>>>>>> Install [a]ll optional external modules, [n]one, or choose
>>>>>> [i]nteractively?
>>>>>> [n]
>>>>>> *
>>>>>> 
>>>>>> Then I ran ./Build test but it failed.
>>>>>> 
>>>>>> Test Summary Report
>>>>>> -------------------
>>>>>> t/SeqIO/embl.t                             (Wstat: 512 Tests: 85
>>>>>> Failed:
>>>>>> 0)
>>>>>>  Non-zero exit status: 2
>>>>>>  Parse errors: Bad plan.  You planned 95 tests but ran 85.
>>>>>> Files=350, Tests=22459, 96 wallclock secs ( 2.78 usr  0.66 sys +
>>>>>> 79.46
>>>>>> cusr
>>>>>> 4.21 csys = 87.11 CPU)
>>>>>> Result: FAIL
>>>>>> Failed 1/350 test programs. 0/22459 subtests failed.
>>>>>> 
>>>>>> Is there anyway to install 1.6.2 because I really need it. Thank you
>>>>>> for
>>>>>> your help.
>>>>>> 
>>>>>> On Fri, Feb 4, 2011 at 10:44 AM, Minh Bui <buiduyminh at gmail.com>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I am trying to use the "summary" feature in  bp_seqfeature_load.pl
>>>>>>> (for
>>>>>>> Gbrowse) but it requires Bioperl 1.6.2. I have been trying to
>>>>>>> install
>>>>>>> 1.6.2 but no luck.
>>>>>>> 
>>>>>>> First, I used GIT :
>>>>>>> 
>>>>>>> git clone git://github.com/bioperl/bioperl-live.git
>>>>>>> 
>>>>>>> and I got this error:
>>>>>>> *
>>>>>>> "github.com[0: 207.97.227.239]: errno=Connection timed out
>>>>>>> fatal: unable to connect a socket (Connection timed out)"
>>>>>>> 
>>>>>>> *
>>>>>>> Then, I downloaded snapshot Core Modules on this page
>>>>>>> http://www.bioperl.org/wiki/Getting_BioPerl but it doesn't work
>>>>>>> either.
>>>>>>> 
>>>>>>> 
>>>>>>> could someone please show me how to install 1.6.2 or if there is
>>>>>>> anyway
>>>>>>> to use summary feature, please let me know.
>>>>>>> 
>>>>>>> Thank you very much,
>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> Minh Bui.
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> Minh Bui.
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> 
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>>> dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>> 
>>>> 
>>>> 
>>>> --
>>>> Minh Bui.
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>> 
>> 
>> 
>> --
>> Minh Bui.
>> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> 
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