[Gmod-help] Re: GBrowse/Bioperl problem

[Scott Cain]

The message about "Bio::Graphics version 0" means that the GBrowse
installer couldn't find bioperl at all.  Are you sure you installed
it?  Is it in the normal path for perl?  There is no separate
installer for Bio::Graphics; it is part of bioperl.  What happens if
you do this on the command line:

  perl -MBio::Graphics::Panel -e 'print Bio::Graphics::Panel->api_version'

Scott


On Fri, Aug 29, 2008 at 2:16 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
> Dave - Good to hear from you!  (Sorry that means I didn't read hard enough -- I've been struggling with bioperl-1.5.2_200 all this morning ;-)
>
> Now I installed "bioperl-live".  The "Build test" show few failed tests:
>
>   Failed 5/258 test programs. 9/18624 subtests failed.
>
> -- which perhaps mostly from the error I saw "Count sequence n02" or something like that. I hope this is minor.
>
> Now, I deleted all previous expanded "Generic-Genome-Browser-1.69" folder/files, made a trial on newly uncompressed GBrowse-1.69: "perl Makefile.PL", it complains the same:
>
> ----------------------------------
> Installed Bio::Graphics version 0 is less than desired version 1.7.
> You need to update your BioPerl installation to greater than version 1.5.2.
>
> Can't locate object method "api_version" via package "Bio::Graphics::Panel" at (eval 6) line 2, <STDIN> line 5.
>        ...propagated at Makefile.PL line 266, <STDIN> line 5.
> ----------------------------------
>
> I am look for separate tar ball for "Bio::Graphics" so I can do a manual install and have not found one yet...
>
> Will keep you updated :)
>
> Zhiliang
>
>
> At 10:32 AM 8/29/2008 -0700, you wrote:
>>Hi Zhiliang,
>>
>>It's good to hear from you!  Your e-mail caused me to look at the
>>BioPerl page on the GMOD web site AND UPDATE IT.
>>
>>  http://gmod.org/wiki/BioPerl
>>
>>For GBrowse 1.69 you actually need BioPerl-live.  BioPerl 1.4 and
>>1.5.2 are just too out of date.  There are pointers on the BioPerl
>>page to the BioPerl website, or you can just download it from
>>BioPerl.org at
>>
>> http://www.bioperl.org/DIST/nightly_builds/
>>
>>Dave C.
>>GMOD Help Desk
>>
>>> From: Zhiliang Hu <zhu at iastate.edu>
>>> Date: Thu, Aug 28, 2008 at 7:51 PM
>>> Subject: GBrowse/Bioperl problem
>>> To: Dave Clements <clements at nescent.org>
>>>
>>>
>>> Dear Dave,
>>>
>>> I think this might be a small problem so I ask you directly without getting
>>> to GMOD user group --
>>>
>>> I got Chado installed successfully, and came to install GBrowse.  I made
>>> sure I installed the needed bioperl -- the latest version available:
>>>
>>> cpan[1]> d /bioperl/
>>> cpan[2]> install BIRNEY/bioperl-1.4.tar.gz
>>>
>>> But when come to build GBrowse for install "perl Makefile.PL" (on it's
>>> latest release v.1.69) it complains that I don't have the right bioperl:
>>> ----------------------------------------------
>>>                File Paths
>>>
>>>         CONF /usr/local/apache/conf
>>>       HTDOCS /usr/local/apache/doc
>>>       CGIBIN /usr/local/apache/cgi-bin
>>>  GBROWSE_ROOT gbrowse
>>>          LIB
>>>          BIN
>>>          YES
>>>       PREFIX
>>>        DO_XS 1
>>>      NONROOT
>>>      SELINUX
>>>
>>> (Run perl Makefile.PL -h for help on changing)
>>> ----------------------------------------------
>>>
>>> Installed Bio::Graphics version 0 is less than desired version 1.7.
>>> You need to update your BioPerl installation to greater than version 1.5.2.
>>>
>>> Can't locate object method "api_version" via package "Bio::Graphics::Panel"
>>> at (eval 6) line 2, <STDIN> line 5.
>>>        ...propagated at Makefile.PL line 266, <STDIN> line 5.
>>> ------------------------------------------------------------
>>>
>>> I also checked the "Bio::Graphics" module source, and found it's bundled in
>>> bioperl and no separate downloads available.  How may I solve this problem?
>>>
>>> Thanks in advance!
>>>
>>> Zhiliang
>>>
>>>
>>>
>>
>>--
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>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory