[Gmod-help] Re: GBrowse/Bioperl problem

[Zhiliang Hu]

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1.5.2 are just too out of date.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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