[Gmod-help] Re: GBrowse/Bioperl problem

Scott Cain cain.cshl at gmail.com
Fri Aug 29 17:11:38 EDT 2008 

Good!  Yes you can display multiple organisms.  Typically, each
organism would be in its own mysql (or RDMS of your choice) database
and each organism would have its own configuration file.  You can see
for example 14 different databases being served by the same GBrowse
instance at WormBase:

  http://wormbase.org/db/seq/gbrowse/c_elegans/

Scott


On Fri, Aug 29, 2008 at 5:07 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
> 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
>
>



-- 
------------------------------------------------------------------------
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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