[Gmod-help] Re: GBrowse/Bioperl problem

[Zhiliang Hu]

Scott,

I found "Bio/Graphics" in multiple locations in the system path, and in
one location files are with today's date:

> find /usr/local/lib -name "Graphics*" | awk ' {print "ls -l "$1}' | sh

/usr/local/lib/perl5/site_perl/5.8.5/i686-linux/auto/Bio/Graphics
/usr/local/lib/perl5/site_perl/5.8.5/i686-linux/Bio/Graphics
/usr/local/lib/perl5/site_perl/5.8.5/Bio/Graphics.pm
/usr/local/lib/perl5/site_perl/5.8.5/Bio/Graphics <---- Today's time stamp
/usr/local/lib/perl5/site_perl/5.8.5/Ace/Graphics

The file /usr/local/lib/perl5/site_perl/5.8.5/Bio/Graphics/Panel is there
which GBroswse build complains cannot find...  All folders to that location
have 755 and files 444 permissions.  Could be something else that it didn't
look at this location?
...

Zhiliang

At 02:35 PM 8/29/2008 -0400, Scott Cain wrote:
>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
>>>>
>>>>
>>>>
>>>
>>>--
>>>Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>>
>>
>
>
>
>-- 
>------------------------------------------------------------------------
>Scott Cain, Ph. D. cain.cshl at gmail.com
>GMOD Coordinator (http://gmod.org/) 216-392-3087
>Cold Spring Harbor Laboratory