[Gmod-help] Re: GBrowse/Bioperl problem
Zhiliang Hu
zhu at iastate.edu
Fri Aug 29 17:20:08 EDT 2008
Scott and Dave,
Many thanks again!
I will now spend time to read tutorials/ manuals/ class notes for configurations... Hopefully will report to you more success stories :)
Best regards,
Zhiliang
At 05:11 PM 8/29/2008 -0400, Scott Cain wrote:
>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
More information about the Gmod-help
mailing list