Problem migrating to Gbrowse 2.46, database undefined.
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Hi all,
I tried to migrate a current Gbrowse 2.39 installation to a new server running CentOS 6.2 with Gbrowse 2.46. Such migration worked fine for a different site, but I encountered problem with a particular site, I am getting such errors Use of uninitialized value $symbolic_db_name in join or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 920., Unknown database defined for general at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 926., Could not open database: Can't call method "new" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., Has anyone seen such issue before? I could not figure out which "database" the error message refers to? It has mysql database and Bio::DB::Sam databases. I would like to hear suggestions on how to track down this problem. Thank you. ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Problem migrating to Gbrowse 2.46, database undefined.
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Hi Zhi-Wei, On Saturday, March 24, 2012 11:18 AM, Zhi-Wei Lu wrote: > I tried to migrate a current Gbrowse 2.39 installation to a new server > running CentOS 6.2 with Gbrowse 2.46. Such migration worked fine for a > different site, but I encountered problem with a particular site, I am > getting such errors > > Use of uninitialized value $symbolic_db_name in join or string at > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 920., > Unknown database defined for general at > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 926., > Could not open database: Can't call method "new" on an undefined value > at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., I can't help you much because I had the same problem. :-( Like you, I tested it on another server and the upgrade seemed to go ok. Then, it failed with the server which I wanted to upgrade. Both are running Ubuntu 11.10. Given the same OS version and configuration files (the first server is actually the "prototype server" of the second; I've tried hard to mirror their settings and hope I was successful), I guessed the source of the problem is that the Perl modules aren't being updated properly. I can't think of anything else that could be the problem. Anyway, in the end, I gave up and left it at 2.39. I think I will wait for the next Ubuntu upgrade to upgrade GBrowse...seems safer and easier than doing so from source. Good luck and I hope someone else can help you! Ray ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Thank you, Raymond for sharing your experience.
Does anyone know how I can set up debug mode so that I know where in the configuration file that I am encountering trouble? How can I downgrade gbrowse? I installed Gbrowse 2.46 from source. Thank you. On 03/25/2012 01:33 AM, Raymond Wan wrote: > Hi Zhi-Wei, > > > On Saturday, March 24, 2012 11:18 AM, Zhi-Wei Lu wrote: >> I tried to migrate a current Gbrowse 2.39 installation to a new server >> running CentOS 6.2 with Gbrowse 2.46. Such migration worked fine for a >> different site, but I encountered problem with a particular site, I am >> getting such errors >> >> Use of uninitialized value $symbolic_db_name in join or string at >> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 920., >> Unknown database defined for general at >> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 926., >> Could not open database: Can't call method "new" on an undefined value >> at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., > > I can't help you much because I had the same problem. :-( Like you, I tested > it on another server and the upgrade seemed to go ok. Then, it failed with the > server which I wanted to upgrade. > > Both are running Ubuntu 11.10. Given the same OS version and configuration > files (the first server is actually the "prototype server" of the second; I've > tried hard to mirror their settings and hope I was successful), I guessed the > source of the problem is that the Perl modules aren't being updated properly. > I can't think of anything else that could be the problem. > > Anyway, in the end, I gave up and left it at 2.39. I think I will wait for the > next Ubuntu upgrade to upgrade GBrowse...seems safer and easier than doing so > from source. > > Good luck and I hope someone else can help you! > > Ray > > > > ------------------------------------------------- > This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk > -- Zhi-Wei Lu Bioinformatics Core Genome Center University of California, Davis (530) 752-2698 ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Problem migrating to Gbrowse 2.46, database undefined.
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In reply to this post by zwluxx
See what happens when you explicitly define the default database:
[GENERAL] database = my_default_database # ... and later on ... [my_default_database:database]
db_adaptor = foo... db_args = bar... Lincoln
On Fri, Mar 23, 2012 at 11:18 PM, Zhi-Wei Lu <[hidden email]> wrote: Hi all, Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <[hidden email]> ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Thanks, Lincoln.
I have tried that, it didn't work. I ended up re-writing the configuration files from the one that worked for other site. This time, it worked fine, however, I have not migrate many other options from the original file yet, therefore, I don't know which option(s) prevented it from working. I would probably stay with version 2.39 for now, until this particular bug or feature is resolved. Thank you. On 03/26/2012 08:22 PM, Lincoln Stein wrote: See what happens when you explicitly define the default database: ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Problem migrating to Gbrowse 2.46, database undefined.
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This is very puzzling. How complicated is the config file in question?
Lincoln
On Tue, Mar 27, 2012 at 12:37 AM, Zhi-Wei Lu <[hidden email]> wrote:
Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <[hidden email]> ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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It is not a very complicated configuration file at all. Is there
anyway that I can get more debug output for parsing the
configuration file?
I turned on debug=1, but it didn't give any more information than before. Thank you. On 03/26/2012 09:55 PM, Lincoln Stein wrote:On 03/26/2012 09:55 PM, Lincoln Stein wrote: This is very puzzling. How complicated is the config file in question? -- Zhi-Wei Lu Bioinformatics Core Genome Center University of California, Davis (530) 752-2698This is very puzzling. How complicated is the config file in question?-- Zhi-Wei Lu Bioinformatics Core Genome Center University of California, Davis (530) 752-2698 ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Problem migrating to Gbrowse 2.46, database undefined.
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A little awkward, but you can do this:
Send the result from error.log to me to have a look. Lincoln On Tue, Mar 27, 2012 at 11:43 AM, Zhi-Wei Lu <[hidden email]> wrote:
Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <[hidden email]> ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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I am getting these error messages, the "uninitialized value in
numeric ge .." message is new, the other messages were the same as
before.
[Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of uninitialized value in numeric ge (>=) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 752., referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of uninitialized value in numeric ge (>=) at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 752., referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] track = general at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 910., referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of uninitialized value $symbolic_db_name in join or string at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 922., referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Unknown database defined for general at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 928., referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Could not open database: Can't call method "new" on an undefined value at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Premature end of script headers: gbrowse, referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] File does not exist: /var/www/gbrowse2/htdocs/favicon.ico On 03/27/2012 08:57 AM, Lincoln Stein wrote: A little awkward, but you can do this: -- Zhi-Wei Lu Bioinformatics Core Genome Center University of California, Davis (530) 752-2698 ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Problem migrating to Gbrowse 2.46, database undefined.
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I suspect you have a bug in your conf file that is preventing the name
of the track (from the [dbname:database] section) from being set. Can you send the configuration file? Scott On Tue, Mar 27, 2012 at 2:07 PM, Zhi-Wei Lu <[hidden email]> wrote: > I am getting these error messages, the "uninitialized value in numeric ge > .." message is new, the other messages were the same as before. > > > [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of > uninitialized value in numeric ge (>=) at > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 752., > referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ > [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of > uninitialized value in numeric ge (>=) at > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 752., > referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ > [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] track = general > at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 910., > referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ > [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of > uninitialized value $symbolic_db_name in join or string at > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 922., > referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ > [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Unknown database > defined for general at > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 928., > referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ > [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Could not open > database: Can't call method "new" on an undefined value at > /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., referer: > http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ > [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Premature end of > script headers: gbrowse, referer: > http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ > [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] File does not > exist: /var/www/gbrowse2/htdocs/favicon.ico > > > > On 03/27/2012 08:57 AM, Lincoln Stein wrote: > > A little awkward, but you can do this: > > Find the installed file Bio/Graphics/Browser2/DataSource.pm > Find this bit of code around line 900: > > if ($track =~ /:database$/) { > > > $symbolic_db_name = $track > > > } elsif (my $d = $self->semantic_fallback_setting($track => 'database', > $length)) { > > $symbolic_db_name = "$d:database"; > > > } elsif ($self->semantic_setting($track=>'db_adaptor',$length)) { > > > $symbolic_db_name = $track; > > > } elsif ($self->semantic_fallback_setting($track => 'db_adaptor', > $length)) { > > $symbolic_db_name = 'general'; > > > } > > > Add this debugging statement just before the block of code in question: > > warn "track = $track"; > > > Send the result from error.log to me to have a look. > > Lincoln > > On Tue, Mar 27, 2012 at 11:43 AM, Zhi-Wei Lu <[hidden email]> wrote: >> >> It is not a very complicated configuration file at all. Is there anyway >> that I can get more debug output for parsing the configuration file? >> >> I turned on debug=1, but it didn't give any more information than before. >> >> Thank you. >> >> >> >> On 03/26/2012 09:55 PM, Lincoln Stein wrote:On 03/26/2012 09:55 PM, >> Lincoln Stein wrote: >> >> This is very puzzling. How complicated is the config file in question? >> >> Lincoln >> >> On Tue, Mar 27, 2012 at 12:37 AM, Zhi-Wei Lu <[hidden email]> wrote: >>> >>> Thanks, Lincoln. >>> >>> I have tried that, it didn't work. I ended up re-writing the >>> configuration files from the one that worked for other site. This time, it >>> worked fine, however, I have not migrate many other options from the >>> original file yet, therefore, I don't know which option(s) prevented it from >>> working. >>> >>> I would probably stay with version 2.39 for now, until this particular >>> bug or feature is resolved. >>> >>> Thank you. >>> >>> >>> On 03/26/2012 08:22 PM, Lincoln Stein wrote: >>> >>> See what happens when you explicitly define the default database: >>> >>> [GENERAL] >>> database = my_default_database >>> >>> # ... and later on ... >>> [my_default_database:database] >>> db_adaptor = foo... >>> db_args = bar... >>> >>> Lincoln >>> >>> On Fri, Mar 23, 2012 at 11:18 PM, Zhi-Wei Lu <[hidden email]> wrote: >>>> >>>> Hi all, >>>> >>>> I tried to migrate a current Gbrowse 2.39 installation to a new server >>>> running CentOS 6.2 with Gbrowse 2.46. Such migration worked fine for a >>>> different site, but I encountered problem with a particular site, I am >>>> getting such errors >>>> >>>> Use of uninitialized value $symbolic_db_name in join or string at >>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 920., >>>> Unknown database defined for general at >>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 926., >>>> Could not open database: Can't call method "new" on an undefined value >>>> at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., >>>> >>>> Has anyone seen such issue before? I could not figure out which >>>> "database" the error message refers to? It has mysql database and >>>> Bio::DB::Sam databases. >>>> >>>> I would like to hear suggestions on how to track down this problem. >>>> Thank you. >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> This SF email is sponsosred by: >>>> Try Windows Azure free for 90 days Click Here >>>> http://p.sf.net/sfu/sfd2d-msazure >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> [hidden email] >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Director, Informatics and Biocomputing Platform >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Renata Musa <[hidden email]> >>> >>> >> >> >> >> -- >> Lincoln D. Stein >> Director, Informatics and Biocomputing Platform >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Renata Musa <[hidden email]> >> >> >> >> -- >> Zhi-Wei Lu >> Bioinformatics Core >> Genome Center >> University of California, Davis >> (530) 752-2698 >> >> >> This is very puzzling. How complicated is the config file in question? >> Lincoln >> >> On Tue, Mar 27, 2012 at 12:37 AM, Zhi-Wei Lu <[hidden email]> wrote: >> >>> >>> >>> >>> >>> >>> Thanks, Lincoln. >>> >>> >>> >>> I have tried that, it didn't work. I ended up re-writing the >>> configuration files from the one that worked for other site. This >>> time, it worked fine, however, I have not migrate many other options >>> from the original file yet, therefore, I don't know which option(s) >>> prevented it from working. >>> >>> >>> >>> I would probably stay with version 2.39 for now, until this >>> particular bug or feature is resolved. >>> >>> >>> >>> Thank you. >>> >>> >>> >>> On 03/26/2012 08:22 PM, Lincoln Stein wrote: >>> >>> >>> See what happens when you explicitly define the >>> default database: >>> >>> >>> >>> [GENERAL] >>> >>> database = my_default_database >>> >>> >>> >>> >>> # ... and later on ... >>> >>> [my_default_database:database] >>> >>> db_adaptor = foo... >>> >>> db_args = bar... >>> >>> >>> >>> >>> Lincoln >>> >>> >>> >>> >>> On Fri, Mar 23, 2012 at 11:18 PM, >>> Zhi-Wei Lu <[hidden email]> >>> wrote: >>> >>> >>>> >>>> Hi all, >>>> >>>> >>>> >>>> I tried to migrate a current Gbrowse 2.39 installation to a >>>> new server >>>> >>>> running CentOS 6.2 with Gbrowse 2.46. Such migration worked >>>> fine for a >>>> >>>> different site, but I encountered problem with a particular >>>> site, I am >>>> >>>> getting such errors >>>> >>>> >>>> >>>> Use of uninitialized value $symbolic_db_name in join or >>>> string at >>>> >>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm >>>> line 920., >>>> >>>> Unknown database defined for general at >>>> >>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm >>>> line 926., >>>> >>>> Could not open database: Can't call method "new" on an >>>> undefined value >>>> >>>> at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm >>>> line 44., >>>> >>>> >>>> >>>> Has anyone seen such issue before? I could not figure out >>>> which >>>> >>>> "database" the error message refers to? It has mysql >>>> database and >>>> >>>> Bio::DB::Sam databases. >>>> >>>> >>>> >>>> I would like to hear suggestions on how to track down this >>>> problem. >>>> >>>> Thank you. >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> This SF email is sponsosred by: >>>> >>>> Try Windows Azure free for 90 days Click Here >>>> >>>> http://p.sf.net/sfu/sfd2d-msazure >>>> >>>> _______________________________________________ >>>> >>>> Gmod-gbrowse mailing list >>>> >>>> [hidden email] >>>> >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> Lincoln D. Stein >>> >>> Director, Informatics and Biocomputing Platform >>> >>> Ontario Institute for Cancer Research >>> >>> 101 College St., Suite 800 >>> >>> Toronto, ON, Canada M5G0A3 >>> >>> 416 673-8514 >>> >>> Assistant: Renata Musa <[hidden email]> >>> >>> >>> >>> >>> >>> >>> >>> >> >> >> >> -- >> Lincoln D. Stein >> Director, Informatics and Biocomputing Platform >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> >> 416 673-8514 >> Assistant: Renata Musa <[hidden email]> >> >> >> >> >> >> >> >> -- >> Zhi-Wei Lu >> Bioinformatics Core >> Genome Center >> University of California, Davis >> (530) 752-2698 >> >> > > > > -- > Lincoln D. Stein > Director, Informatics and Biocomputing Platform > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa <[hidden email]> > > > > -- > Zhi-Wei Lu > Bioinformatics Core > Genome Center > University of California, Davis > (530) 752-2698 > > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Gmod-gbrowse mailing list > [hidden email] > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Problem migrating to Gbrowse 2.46, database undefined.
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Here's what I would do:
At the top of you conf file, you have this: [GENERAL] description = Solanum lycopersicum db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn dbi:mysql:database=tomato:host=localhost -user me -pass mypass I would remove the db_adaptor and db_args sections since they are reproduced in you database stanza, and replace them with a database declaration, so that it looks like this: [GENERAL] description = Solanum lycopersicum database = tomato I think the problem is that you never declared what the default database was (thus the uninit warnings) and adding this database line should fix that. Scott On Tue, Mar 27, 2012 at 3:05 PM, Zhi-Wei Lu <[hidden email]> wrote: > Hi Scott, > > Here is the configuration file (with password and user names changed). > > This config file worked file with Gbrowse 2.39. > > Thank you. > > On 03/27/2012 11:45 AM, Scott Cain wrote: >> I suspect you have a bug in your conf file that is preventing the name >> of the track (from the [dbname:database] section) from being set. Can >> you send the configuration file? >> >> Scott >> >> >> On Tue, Mar 27, 2012 at 2:07 PM, Zhi-Wei Lu <[hidden email]> wrote: >>> I am getting these error messages, the "uninitialized value in numeric ge >>> .." message is new, the other messages were the same as before. >>> >>> >>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of >>> uninitialized value in numeric ge (>=) at >>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 752., >>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of >>> uninitialized value in numeric ge (>=) at >>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 752., >>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] track = general >>> at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 910., >>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of >>> uninitialized value $symbolic_db_name in join or string at >>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 922., >>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Unknown database >>> defined for general at >>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 928., >>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Could not open >>> database: Can't call method "new" on an undefined value at >>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., referer: >>> http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Premature end of >>> script headers: gbrowse, referer: >>> http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] File does not >>> exist: /var/www/gbrowse2/htdocs/favicon.ico >>> >>> >>> >>> On 03/27/2012 08:57 AM, Lincoln Stein wrote: >>> >>> A little awkward, but you can do this: >>> >>> Find the installed file Bio/Graphics/Browser2/DataSource.pm >>> Find this bit of code around line 900: >>> >>> if ($track =~ /:database$/) { >>> >>> >>> $symbolic_db_name = $track >>> >>> >>> } elsif (my $d = $self->semantic_fallback_setting($track => 'database', >>> $length)) { >>> >>> $symbolic_db_name = "$d:database"; >>> >>> >>> } elsif ($self->semantic_setting($track=>'db_adaptor',$length)) { >>> >>> >>> $symbolic_db_name = $track; >>> >>> >>> } elsif ($self->semantic_fallback_setting($track => 'db_adaptor', >>> $length)) { >>> >>> $symbolic_db_name = 'general'; >>> >>> >>> } >>> >>> >>> Add this debugging statement just before the block of code in question: >>> >>> warn "track = $track"; >>> >>> >>> Send the result from error.log to me to have a look. >>> >>> Lincoln >>> >>> On Tue, Mar 27, 2012 at 11:43 AM, Zhi-Wei Lu <[hidden email]> wrote: >>>> It is not a very complicated configuration file at all. Is there anyway >>>> that I can get more debug output for parsing the configuration file? >>>> >>>> I turned on debug=1, but it didn't give any more information than before. >>>> >>>> Thank you. >>>> >>>> >>>> >>>> On 03/26/2012 09:55 PM, Lincoln Stein wrote:On 03/26/2012 09:55 PM, >>>> Lincoln Stein wrote: >>>> >>>> This is very puzzling. How complicated is the config file in question? >>>> >>>> Lincoln >>>> >>>> On Tue, Mar 27, 2012 at 12:37 AM, Zhi-Wei Lu <[hidden email]> wrote: >>>>> Thanks, Lincoln. >>>>> >>>>> I have tried that, it didn't work. I ended up re-writing the >>>>> configuration files from the one that worked for other site. This time, it >>>>> worked fine, however, I have not migrate many other options from the >>>>> original file yet, therefore, I don't know which option(s) prevented it from >>>>> working. >>>>> >>>>> I would probably stay with version 2.39 for now, until this particular >>>>> bug or feature is resolved. >>>>> >>>>> Thank you. >>>>> >>>>> >>>>> On 03/26/2012 08:22 PM, Lincoln Stein wrote: >>>>> >>>>> See what happens when you explicitly define the default database: >>>>> >>>>> [GENERAL] >>>>> database = my_default_database >>>>> >>>>> # ... and later on ... >>>>> [my_default_database:database] >>>>> db_adaptor = foo... >>>>> db_args = bar... >>>>> >>>>> Lincoln >>>>> >>>>> On Fri, Mar 23, 2012 at 11:18 PM, Zhi-Wei Lu <[hidden email]> wrote: >>>>>> Hi all, >>>>>> >>>>>> I tried to migrate a current Gbrowse 2.39 installation to a new server >>>>>> running CentOS 6.2 with Gbrowse 2.46. Such migration worked fine for a >>>>>> different site, but I encountered problem with a particular site, I am >>>>>> getting such errors >>>>>> >>>>>> Use of uninitialized value $symbolic_db_name in join or string at >>>>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 920., >>>>>> Unknown database defined for general at >>>>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 926., >>>>>> Could not open database: Can't call method "new" on an undefined value >>>>>> at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., >>>>>> >>>>>> Has anyone seen such issue before? I could not figure out which >>>>>> "database" the error message refers to? It has mysql database and >>>>>> Bio::DB::Sam databases. >>>>>> >>>>>> I would like to hear suggestions on how to track down this problem. >>>>>> Thank you. >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> This SF email is sponsosred by: >>>>>> Try Windows Azure free for 90 days Click Here >>>>>> http://p.sf.net/sfu/sfd2d-msazure >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> [hidden email] >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>>> >>>>> >>>>> -- >>>>> Lincoln D. Stein >>>>> Director, Informatics and Biocomputing Platform >>>>> Ontario Institute for Cancer Research >>>>> 101 College St., Suite 800 >>>>> Toronto, ON, Canada M5G0A3 >>>>> 416 673-8514 >>>>> Assistant: Renata Musa <[hidden email]> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Director, Informatics and Biocomputing Platform >>>> Ontario Institute for Cancer Research >>>> 101 College St., Suite 800 >>>> Toronto, ON, Canada M5G0A3 >>>> 416 673-8514 >>>> Assistant: Renata Musa <[hidden email]> >>>> >>>> >>>> >>>> -- >>>> Zhi-Wei Lu >>>> Bioinformatics Core >>>> Genome Center >>>> University of California, Davis >>>> (530) 752-2698 >>>> >>>> >>>> This is very puzzling. How complicated is the config file in question? >>>> Lincoln >>>> >>>> On Tue, Mar 27, 2012 at 12:37 AM, Zhi-Wei Lu <[hidden email]> wrote: >>>> >>>>> >>>>> >>>>> >>>>> >>>>> Thanks, Lincoln. >>>>> >>>>> >>>>> >>>>> I have tried that, it didn't work. I ended up re-writing the >>>>> configuration files from the one that worked for other site. This >>>>> time, it worked fine, however, I have not migrate many other options >>>>> from the original file yet, therefore, I don't know which option(s) >>>>> prevented it from working. >>>>> >>>>> >>>>> >>>>> I would probably stay with version 2.39 for now, until this >>>>> particular bug or feature is resolved. >>>>> >>>>> >>>>> >>>>> Thank you. >>>>> >>>>> >>>>> >>>>> On 03/26/2012 08:22 PM, Lincoln Stein wrote: >>>>> >>>>> >>>>> See what happens when you explicitly define the >>>>> default database: >>>>> >>>>> >>>>> >>>>> [GENERAL] >>>>> >>>>> database = my_default_database >>>>> >>>>> >>>>> >>>>> >>>>> # ... and later on ... >>>>> >>>>> [my_default_database:database] >>>>> >>>>> db_adaptor = foo... >>>>> >>>>> db_args = bar... >>>>> >>>>> >>>>> >>>>> >>>>> Lincoln >>>>> >>>>> >>>>> >>>>> >>>>> On Fri, Mar 23, 2012 at 11:18 PM, >>>>> Zhi-Wei Lu <[hidden email]> >>>>> wrote: >>>>> >>>>> >>>>>> Hi all, >>>>>> >>>>>> >>>>>> >>>>>> I tried to migrate a current Gbrowse 2.39 installation to a >>>>>> new server >>>>>> >>>>>> running CentOS 6.2 with Gbrowse 2.46. Such migration worked >>>>>> fine for a >>>>>> >>>>>> different site, but I encountered problem with a particular >>>>>> site, I am >>>>>> >>>>>> getting such errors >>>>>> >>>>>> >>>>>> >>>>>> Use of uninitialized value $symbolic_db_name in join or >>>>>> string at >>>>>> >>>>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm >>>>>> line 920., >>>>>> >>>>>> Unknown database defined for general at >>>>>> >>>>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm >>>>>> line 926., >>>>>> >>>>>> Could not open database: Can't call method "new" on an >>>>>> undefined value >>>>>> >>>>>> at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm >>>>>> line 44., >>>>>> >>>>>> >>>>>> >>>>>> Has anyone seen such issue before? I could not figure out >>>>>> which >>>>>> >>>>>> "database" the error message refers to? It has mysql >>>>>> database and >>>>>> >>>>>> Bio::DB::Sam databases. >>>>>> >>>>>> >>>>>> >>>>>> I would like to hear suggestions on how to track down this >>>>>> problem. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> >>>>>> This SF email is sponsosred by: >>>>>> >>>>>> Try Windows Azure free for 90 days Click Here >>>>>> >>>>>> http://p.sf.net/sfu/sfd2d-msazure >>>>>> >>>>>> _______________________________________________ >>>>>> >>>>>> Gmod-gbrowse mailing list >>>>>> >>>>>> [hidden email] >>>>>> >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> Lincoln D. Stein >>>>> >>>>> Director, Informatics and Biocomputing Platform >>>>> >>>>> Ontario Institute for Cancer Research >>>>> >>>>> 101 College St., Suite 800 >>>>> >>>>> Toronto, ON, Canada M5G0A3 >>>>> >>>>> 416 673-8514 >>>>> >>>>> Assistant: Renata Musa <[hidden email]> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Director, Informatics and Biocomputing Platform >>>> Ontario Institute for Cancer Research >>>> 101 College St., Suite 800 >>>> Toronto, ON, Canada M5G0A3 >>>> >>>> 416 673-8514 >>>> Assistant: Renata Musa <[hidden email]> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> Zhi-Wei Lu >>>> Bioinformatics Core >>>> Genome Center >>>> University of California, Davis >>>> (530) 752-2698 >>>> >>>> >>> >>> >>> -- >>> Lincoln D. Stein >>> Director, Informatics and Biocomputing Platform >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Renata Musa <[hidden email]> >>> >>> >>> >>> -- >>> Zhi-Wei Lu >>> Bioinformatics Core >>> Genome Center >>> University of California, Davis >>> (530) 752-2698 >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF email is sponsosred by: >>> Try Windows Azure free for 90 days Click Here >>> http://p.sf.net/sfu/sfd2d-msazure >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> [hidden email] >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >> >> > > > -- > Zhi-Wei Lu > Bioinformatics Core > Genome Center > University of California, Davis > (530) 752-2698 > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Problem migrating to Gbrowse 2.46, database undefined.
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An anonymous database in which the db_adaptor and db_args options are directly under the [general] stanza is supposed to work still. I will test it.
Lincoln
On Tue, Mar 27, 2012 at 4:22 PM, Scott Cain <[hidden email]> wrote: Here's what I would do: Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <[hidden email]> ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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In reply to this post by Scott Cain
Thanks, Scott!
This was one of the test that I had done and I did it again! It still failed nevertheless. This particular config file is cursed! I have another variation of this config file produced by modifying a config file from working site for 2.46 and it worked for this site. These two files are quite similar. I have not go over line by line yet to see which line or maybe invisible character(s) in the config file caused all my headaches. On 03/27/2012 01:22 PM, Scott Cain wrote: > Here's what I would do: > > At the top of you conf file, you have this: > > [GENERAL] > description = Solanum lycopersicum > db_adaptor = Bio::DB::SeqFeature::Store > db_args = -adaptor DBI::mysql > -dsn dbi:mysql:database=tomato:host=localhost > -user me > -pass mypass > > I would remove the db_adaptor and db_args sections since they are > reproduced in you database stanza, and replace them with a database > declaration, so that it looks like this: > > [GENERAL] > description = Solanum lycopersicum > database = tomato > > I think the problem is that you never declared what the default > database was (thus the uninit warnings) and adding this database line > should fix that. > > Scott > > > On Tue, Mar 27, 2012 at 3:05 PM, Zhi-Wei Lu <[hidden email]> wrote: >> Hi Scott, >> >> Here is the configuration file (with password and user names changed). >> >> This config file worked file with Gbrowse 2.39. >> >> Thank you. >> >> On 03/27/2012 11:45 AM, Scott Cain wrote: >>> I suspect you have a bug in your conf file that is preventing the name >>> of the track (from the [dbname:database] section) from being set. Can >>> you send the configuration file? >>> >>> Scott >>> >>> >>> On Tue, Mar 27, 2012 at 2:07 PM, Zhi-Wei Lu <[hidden email]> wrote: >>>> I am getting these error messages, the "uninitialized value in numeric ge >>>> .." message is new, the other messages were the same as before. >>>> >>>> >>>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of >>>> uninitialized value in numeric ge (>=) at >>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 752., >>>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of >>>> uninitialized value in numeric ge (>=) at >>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 752., >>>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] track = general >>>> at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 910., >>>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Use of >>>> uninitialized value $symbolic_db_name in join or string at >>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 922., >>>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Unknown database >>>> defined for general at >>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 928., >>>> referer: http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Could not open >>>> database: Can't call method "new" on an undefined value at >>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., referer: >>>> http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] Premature end of >>>> script headers: gbrowse, referer: >>>> http://phytonetworks.ucdavis.edu/cgi-bin/gbrowse/yeast/ >>>> [Tue Mar 27 10:57:10 2012] [error] [client 128.120.143.71] File does not >>>> exist: /var/www/gbrowse2/htdocs/favicon.ico >>>> >>>> >>>> >>>> On 03/27/2012 08:57 AM, Lincoln Stein wrote: >>>> >>>> A little awkward, but you can do this: >>>> >>>> Find the installed file Bio/Graphics/Browser2/DataSource.pm >>>> Find this bit of code around line 900: >>>> >>>> if ($track =~ /:database$/) { >>>> >>>> >>>> $symbolic_db_name = $track >>>> >>>> >>>> } elsif (my $d = $self->semantic_fallback_setting($track => 'database', >>>> $length)) { >>>> >>>> $symbolic_db_name = "$d:database"; >>>> >>>> >>>> } elsif ($self->semantic_setting($track=>'db_adaptor',$length)) { >>>> >>>> >>>> $symbolic_db_name = $track; >>>> >>>> >>>> } elsif ($self->semantic_fallback_setting($track => 'db_adaptor', >>>> $length)) { >>>> >>>> $symbolic_db_name = 'general'; >>>> >>>> >>>> } >>>> >>>> >>>> Add this debugging statement just before the block of code in question: >>>> >>>> warn "track = $track"; >>>> >>>> >>>> Send the result from error.log to me to have a look. >>>> >>>> Lincoln >>>> >>>> On Tue, Mar 27, 2012 at 11:43 AM, Zhi-Wei Lu <[hidden email]> wrote: >>>>> It is not a very complicated configuration file at all. Is there anyway >>>>> that I can get more debug output for parsing the configuration file? >>>>> >>>>> I turned on debug=1, but it didn't give any more information than before. >>>>> >>>>> Thank you. >>>>> >>>>> >>>>> >>>>> On 03/26/2012 09:55 PM, Lincoln Stein wrote:On 03/26/2012 09:55 PM, >>>>> Lincoln Stein wrote: >>>>> >>>>> This is very puzzling. How complicated is the config file in question? >>>>> >>>>> Lincoln >>>>> >>>>> On Tue, Mar 27, 2012 at 12:37 AM, Zhi-Wei Lu <[hidden email]> wrote: >>>>>> Thanks, Lincoln. >>>>>> >>>>>> I have tried that, it didn't work. I ended up re-writing the >>>>>> configuration files from the one that worked for other site. This time, it >>>>>> worked fine, however, I have not migrate many other options from the >>>>>> original file yet, therefore, I don't know which option(s) prevented it from >>>>>> working. >>>>>> >>>>>> I would probably stay with version 2.39 for now, until this particular >>>>>> bug or feature is resolved. >>>>>> >>>>>> Thank you. >>>>>> >>>>>> >>>>>> On 03/26/2012 08:22 PM, Lincoln Stein wrote: >>>>>> >>>>>> See what happens when you explicitly define the default database: >>>>>> >>>>>> [GENERAL] >>>>>> database = my_default_database >>>>>> >>>>>> # ... and later on ... >>>>>> [my_default_database:database] >>>>>> db_adaptor = foo... >>>>>> db_args = bar... >>>>>> >>>>>> Lincoln >>>>>> >>>>>> On Fri, Mar 23, 2012 at 11:18 PM, Zhi-Wei Lu <[hidden email]> wrote: >>>>>>> Hi all, >>>>>>> >>>>>>> I tried to migrate a current Gbrowse 2.39 installation to a new server >>>>>>> running CentOS 6.2 with Gbrowse 2.46. Such migration worked fine for a >>>>>>> different site, but I encountered problem with a particular site, I am >>>>>>> getting such errors >>>>>>> >>>>>>> Use of uninitialized value $symbolic_db_name in join or string at >>>>>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 920., >>>>>>> Unknown database defined for general at >>>>>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm line 926., >>>>>>> Could not open database: Can't call method "new" on an undefined value >>>>>>> at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm line 44., >>>>>>> >>>>>>> Has anyone seen such issue before? I could not figure out which >>>>>>> "database" the error message refers to? It has mysql database and >>>>>>> Bio::DB::Sam databases. >>>>>>> >>>>>>> I would like to hear suggestions on how to track down this problem. >>>>>>> Thank you. >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> This SF email is sponsosred by: >>>>>>> Try Windows Azure free for 90 days Click Here >>>>>>> http://p.sf.net/sfu/sfd2d-msazure >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> [hidden email] >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>>> >>>>>> -- >>>>>> Lincoln D. Stein >>>>>> Director, Informatics and Biocomputing Platform >>>>>> Ontario Institute for Cancer Research >>>>>> 101 College St., Suite 800 >>>>>> Toronto, ON, Canada M5G0A3 >>>>>> 416 673-8514 >>>>>> Assistant: Renata Musa <[hidden email]> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Lincoln D. Stein >>>>> Director, Informatics and Biocomputing Platform >>>>> Ontario Institute for Cancer Research >>>>> 101 College St., Suite 800 >>>>> Toronto, ON, Canada M5G0A3 >>>>> 416 673-8514 >>>>> Assistant: Renata Musa <[hidden email]> >>>>> >>>>> >>>>> >>>>> -- >>>>> Zhi-Wei Lu >>>>> Bioinformatics Core >>>>> Genome Center >>>>> University of California, Davis >>>>> (530) 752-2698 >>>>> >>>>> >>>>> This is very puzzling. How complicated is the config file in question? >>>>> Lincoln >>>>> >>>>> On Tue, Mar 27, 2012 at 12:37 AM, Zhi-Wei Lu <[hidden email]> wrote: >>>>> >>>>>> >>>>>> >>>>>> >>>>>> Thanks, Lincoln. >>>>>> >>>>>> >>>>>> >>>>>> I have tried that, it didn't work. I ended up re-writing the >>>>>> configuration files from the one that worked for other site. This >>>>>> time, it worked fine, however, I have not migrate many other options >>>>>> from the original file yet, therefore, I don't know which option(s) >>>>>> prevented it from working. >>>>>> >>>>>> >>>>>> >>>>>> I would probably stay with version 2.39 for now, until this >>>>>> particular bug or feature is resolved. >>>>>> >>>>>> >>>>>> >>>>>> Thank you. >>>>>> >>>>>> >>>>>> >>>>>> On 03/26/2012 08:22 PM, Lincoln Stein wrote: >>>>>> >>>>>> >>>>>> See what happens when you explicitly define the >>>>>> default database: >>>>>> >>>>>> >>>>>> >>>>>> [GENERAL] >>>>>> >>>>>> database = my_default_database >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> # ... and later on ... >>>>>> >>>>>> [my_default_database:database] >>>>>> >>>>>> db_adaptor = foo... >>>>>> >>>>>> db_args = bar... >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Lincoln >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Mar 23, 2012 at 11:18 PM, >>>>>> Zhi-Wei Lu <[hidden email]> >>>>>> wrote: >>>>>> >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> >>>>>>> >>>>>>> I tried to migrate a current Gbrowse 2.39 installation to a >>>>>>> new server >>>>>>> >>>>>>> running CentOS 6.2 with Gbrowse 2.46. Such migration worked >>>>>>> fine for a >>>>>>> >>>>>>> different site, but I encountered problem with a particular >>>>>>> site, I am >>>>>>> >>>>>>> getting such errors >>>>>>> >>>>>>> >>>>>>> >>>>>>> Use of uninitialized value $symbolic_db_name in join or >>>>>>> string at >>>>>>> >>>>>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm >>>>>>> line 920., >>>>>>> >>>>>>> Unknown database defined for general at >>>>>>> >>>>>>> /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataSource.pm >>>>>>> line 926., >>>>>>> >>>>>>> Could not open database: Can't call method "new" on an >>>>>>> undefined value >>>>>>> >>>>>>> at /usr/local/lib64/perl5/Bio/Graphics/Browser2/DataBase.pm >>>>>>> line 44., >>>>>>> >>>>>>> >>>>>>> >>>>>>> Has anyone seen such issue before? I could not figure out >>>>>>> which >>>>>>> >>>>>>> "database" the error message refers to? It has mysql >>>>>>> database and >>>>>>> >>>>>>> Bio::DB::Sam databases. >>>>>>> >>>>>>> >>>>>>> >>>>>>> I would like to hear suggestions on how to track down this >>>>>>> problem. >>>>>>> >>>>>>> Thank you. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> >>>>>>> This SF email is sponsosred by: >>>>>>> >>>>>>> Try Windows Azure free for 90 days Click Here >>>>>>> >>>>>>> http://p.sf.net/sfu/sfd2d-msazure >>>>>>> >>>>>>> _______________________________________________ >>>>>>> >>>>>>> Gmod-gbrowse mailing list >>>>>>> >>>>>>> [hidden email] >>>>>>> >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Lincoln D. Stein >>>>>> >>>>>> Director, Informatics and Biocomputing Platform >>>>>> >>>>>> Ontario Institute for Cancer Research >>>>>> >>>>>> 101 College St., Suite 800 >>>>>> >>>>>> Toronto, ON, Canada M5G0A3 >>>>>> >>>>>> 416 673-8514 >>>>>> >>>>>> Assistant: Renata Musa <[hidden email]> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Lincoln D. Stein >>>>> Director, Informatics and Biocomputing Platform >>>>> Ontario Institute for Cancer Research >>>>> 101 College St., Suite 800 >>>>> Toronto, ON, Canada M5G0A3 >>>>> >>>>> 416 673-8514 >>>>> Assistant: Renata Musa <[hidden email]> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Zhi-Wei Lu >>>>> Bioinformatics Core >>>>> Genome Center >>>>> University of California, Davis >>>>> (530) 752-2698 >>>>> >>>>> >>>> >>>> -- >>>> Lincoln D. Stein >>>> Director, Informatics and Biocomputing Platform >>>> Ontario Institute for Cancer Research >>>> 101 College St., Suite 800 >>>> Toronto, ON, Canada M5G0A3 >>>> 416 673-8514 >>>> Assistant: Renata Musa <[hidden email]> >>>> >>>> >>>> >>>> -- >>>> Zhi-Wei Lu >>>> Bioinformatics Core >>>> Genome Center >>>> University of California, Davis >>>> (530) 752-2698 >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> This SF email is sponsosred by: >>>> Try Windows Azure free for 90 days Click Here >>>> http://p.sf.net/sfu/sfd2d-msazure >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> [hidden email] >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>> >> >> -- >> Zhi-Wei Lu >> Bioinformatics Core >> Genome Center >> University of California, Davis >> (530) 752-2698 >> >> >> > > -- Zhi-Wei Lu Bioinformatics Core Genome Center University of California, Davis (530) 752-2698 ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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