[Gmod-help] Re: GBrowse/Bioperl problem

Zhiliang Hu zhu at iastate.edu
Fri Aug 29 17:07:15 EDT 2008 

Bravo!
It's now up running: http://www.animalgenome.org/cgi-bin/gbrowse/yeast/

MANY THANKS to you all!

One other question -- I think it is important in the early stage of set up:

Can I use one GBrowse installation to display several different genomes? (I mean to show independently, as if they are separate installations; I knew "comparative" thing will be something for the future).  I apologize in advance if this is already covered somewhere and I am too lazy to look it up!

Have a nice weekend!

Zhiliang


At 04:52 PM 8/29/2008 -0400, Scott Cain wrote:
>OK--now we're making progress.  That tells me you have a really old
>bioperl installed somewhere, and when you try to install GBrowse it is
>getting the old bioperl.  Try rerunning the Build install command, but
>add the uninstall option, like this:
>
>  sudo ./Build install --uninst 1
>
>which will remove old bioperl modules from where ever they are.  If
>that doesn't work (ie, the perl command still doesn't find the right
>Bio::Graphics::Panel), double check that you really have bioperl-live
>and not something else (I don't really know what that something else
>might be--I'm running out of options :-)
>
>Oh, and the thing about symlinks doesn't have anything to do with
>this.  It is trying (and probably succeeding) to make a symlink for a
>script it is installing so it can be excuted with either its real name
>or the linked name.  It says "trying" because it doesn't work under
>Windows.
>
>Scott
>
>
>On Fri, Aug 29, 2008 at 4:45 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>> Scott,
>>
>> I am sorry, I had an alias 'perl -p -i.bak -e' on.
>>
>> Now it says:
>>> perl -MBio::Graphics::Panel -e 'print Bio::Graphics::Panel->api_version'
>> Can't locate object method "api_version" via package "Bio::Graphics::Panel" at -e line 1.
>>
>> I have sent you a mail about the "Bio::Graphics" locations... perhaps on this system (linux) some symbolic links are missing? - Because I notice at the end of "./Build install" there is a line:
>>
>> /usr/local/bin/perl maintenance/symlink_script.pl
>> Will try to install symlinks to /usr/local/bin
>>
>> Not sure what does "will try to" mean, and links from where to where...
>>
>> Zhiliang
>>
>> At 04:19 PM 8/29/2008 -0400, you wrote:
>>>Hi Zhiliang,
>>>
>>>Did you copy and paste that command?  I just checked it on both my
>>>Ubuntu and Mac OS 10.5 computers and it gives the expected answer
>>>("1.7", but with no line feed, so it looked like this: "1.7sloan:~
>>>cain$", where the command prompt is "sloan:~ cain$").  Since you are
>>>installing in /usr/local, I would expect to find the bioperl modules
>>>in /usr/local/lib/perl/5.8.8/Bio/ or similar.
>>>
>>>Scott
>>>
>>>
>>>On Fri, Aug 29, 2008 at 4:13 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>>>> Thank Scott - that's a useful info!
>>>>
>>>> This command line produced an error:
>>>>> perl -MBio::Graphics::Panel -e 'print Bio::Graphics::Panel->api_version'
>>>>
>>>> syntax error at -e line 2, near "MBio::Graphics::Panel
>>>> print"
>>>> Execution of -e aborted due to compilation errors.
>>>>
>>>>
>>>> On the installation -- I do find over 60+ bioperl programs got copied to /usr/local/bin/bp_* today.
>>>>
>>>> I will look into if the "Bio::Graphics" parts got into the system locations...
>>>>
>>>> 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
>>
>>
>
>
>
>-- 
>------------------------------------------------------------------------
>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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