[Gmod-help] Re: GBrowse/Bioperl problem

Scott Cain cain.cshl at gmail.com
Fri Aug 29 16:41:44 EDT 2008 

Try this:

  perl -V

That gives some fairly lengthy output, but at the end it gives the
search path for installed perl modules.  Is
/usr/local/lib/perl5/site_perl in the list?  Also, did you double
check that you typed/copied that perl command from a few emails ago
correctly?  I'm beginning to fear that there is something wrong with
your perl.

Scott


On Fri, Aug 29, 2008 at 4:29 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
> 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
>
>



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

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