Error running Generic-Genome-Browser
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Error running Generic-Genome-Browser
 
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Hello there,
I have been trying to run Generic-Genome-Breowser form some time, but its not showing proper results. I am trying for the sample data given for volvox. I am attaching the result output page when i am pinging on url http://localhost/cgi-bin/gbrowse/volvox. Please kindly reply. -- MALOBI NANDI CSIR Institute of Genomics and Integrative Biology(CSIR-IGIB) Naraina, New Delhi ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Screenshot.png (158K)
Re: Error running Generic-Genome-Browser
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Hi Malobi,
Please look in the apache error_log, particularly the last few lines. It should give some indication what the problem is; of course, if it makes no sense to you, please copy it back to the mailing list. The apache error_log is usually in /var/log/apache2 or /var/log/httpd. Scott On Sat, Jun 30, 2012 at 9:20 AM, malobi nandi <[hidden email]> wrote: > Hello there, > > I have been trying to run Generic-Genome-Breowser form some time, but > its not showing proper results. I am trying for the sample data given > for volvox. I am attaching the result output page when i am pinging on > url http://localhost/cgi-bin/gbrowse/volvox. Please kindly reply. > > -- > MALOBI NANDI > CSIR Institute of Genomics and Integrative Biology(CSIR-IGIB) > Naraina, New Delhi > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > 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 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Gbrowse keeps rerouting to the demo
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I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server.
db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo psql=# ALTER USER tripaldemo SET search_path TO chado; config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF htdocs_base = /var/www/html/gbrowse2 url_base = /gbrowse2 tmp_base = /var/tmp/gbrowse2 persistent_base = /var/lib/gbrowse2 userdata_base = /var/lib/gbrowse2/userdata db_base = /var/www/cgi-bin/gb2/gbrowse However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? David Jeang This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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In reply to this post by Scott Cain
-----Original Message----- From: Jeang, David - ARS Sent: Monday, July 02, 2012 9:49 AM To: 'Scott Cain' Cc: [hidden email] Subject: Gbrowse keeps rerouting to the demo I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo psql=# ALTER USER tripaldemo SET search_path TO chado; config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF htdocs_base = /var/www/html/gbrowse2 url_base = /gbrowse2 tmp_base = /var/tmp/gbrowse2 persistent_base = /var/lib/gbrowse2 userdata_base = /var/lib/gbrowse2/userdata db_base = /var/www/cgi-bin/gb2/gbrowse However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? David Jeang This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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In reply to this post by Jeang, David - ARS
Hi David,
This typically happens if in one of two situations: 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. Is there anything in the error_log? Scott On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: > I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. > > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo > psql=# ALTER USER tripaldemo SET search_path TO chado; > config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF > htdocs_base = /var/www/html/gbrowse2 > url_base = /gbrowse2 > tmp_base = /var/tmp/gbrowse2 > persistent_base = /var/lib/gbrowse2 > userdata_base = /var/lib/gbrowse2/userdata > db_base = /var/www/cgi-bin/gb2/gbrowse > > However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? > > David Jeang > > > > > This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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This is from the error log.
[Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of uninitialized val ue in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /Bio/Graphics/Browser2/DataSource.pm line 1048. [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of uninitialized val ue in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi o/Graphics/Browser2/RegionSearch.pm line 392. [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC (@INC contains : /opt/ActivePerl-5.12 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per l5/5.8.8 .) at (eval 164) line 3. [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at /usr/lib64/perl5/sit e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . Also, I tried to make a conf for the file I wanted called Dmelanogaster.conf And amended Gbrowse conf for it. ############################################################################################### # # DATASOURCE DEFINITIONS # One stanza for each configured data source # ############################################################################################### [Dmelanogaster] description = Fruitfly path = Dmelanogaster.conf And Dmelanogaster.conf: ################################# # database definitions ################################# [scaffolds:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo [annotations:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? David -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Tuesday, July 03, 2012 12:44 PM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, This typically happens if in one of two situations: 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. Is there anything in the error_log? Scott On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: > I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. > > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo psql=# ALTER USER tripaldemo > SET search_path TO chado; > config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF > htdocs_base = /var/www/html/gbrowse2 > url_base = /gbrowse2 > tmp_base = /var/tmp/gbrowse2 > persistent_base = /var/lib/gbrowse2 > userdata_base = /var/lib/gbrowse2/userdata > db_base = /var/www/cgi-bin/gb2/gbrowse > > However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? > > David Jeang > > > > > This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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Hi David,
A few things: 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. Scott On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: > This is from the error log. > > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of uninitialized val > ue in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi > /Bio/Graphics/Browser2/DataSource.pm line 1048. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of uninitialized val > ue in string eq at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi > o/Graphics/Browser2/RegionSearch.pm line 392. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: > Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC (@INC contains > : /opt/ActivePerl-5.12 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult > i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendo > r_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib > /perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per > l5/5.8.8 .) at (eval 164) line 3. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at /usr/lib64/perl5/sit > e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 > . > > Also, I tried to make a conf for the file I wanted called Dmelanogaster.conf > And amended Gbrowse conf for it. > ############################################################################################### > # > # DATASOURCE DEFINITIONS > # One stanza for each configured data source > # > ############################################################################################### > > [Dmelanogaster] > description = Fruitfly > path = Dmelanogaster.conf > > And Dmelanogaster.conf: > ################################# > # database definitions > ################################# > > [scaffolds:database] > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo > [annotations:database] > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo > > But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? > > David > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Tuesday, July 03, 2012 12:44 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > This typically happens if in one of two situations: > > 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. > > 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. > > Is there anything in the error_log? > > Scott > > > On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >> >> db_adaptor = Bio::DB::Das::Chado >> db_args = -adaptor Bio::DB::Das::Chado >> -dsn dbi:Pg:dbname=tripal;host=localhost >> -user tripaldemo >> -pass tripal2demo psql=# ALTER USER tripaldemo >> SET search_path TO chado; >> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >> htdocs_base = /var/www/html/gbrowse2 >> url_base = /gbrowse2 >> tmp_base = /var/tmp/gbrowse2 >> persistent_base = /var/lib/gbrowse2 >> userdata_base = /var/lib/gbrowse2/userdata >> db_base = /var/www/cgi-bin/gb2/gbrowse >> >> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >> >> David Jeang >> >> >> >> >> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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I made a chado conf for the Gbrowse, this is it.
description = Chado database database = scaffolds initial landmark = chrI:143000..180000 plugins = FilterTest RestrictionAnnotator TrackDumper FastaDumper autocomplete = 1 default tracks = Genes ORFs tRNAs CDS Transp Centro:overview GC:region # examples to show in the introduction examples = chrI chrII chrI:80,000..120,000 "membrane trafficking" NUT21 YAL063C # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone ################################# # database definitions ################################# [scaffolds:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo [annotations:database] db_adaptor = Bio::DB::Das::Chado db_args = -adaptor Bio::DB::Das::Chado -dsn dbi:Pg:dbname=tripal;host=localhost -user tripaldemo -pass tripal2demo # Default glyph settings [TRACK DEFAULTS] glyph = generic database = annotations height = 8 bgcolor = cyan fgcolor = black label density = 25 bump density = 100 show summary = 99999 # go into summary mode when zoomed out to 100k ### TRACK CONFIGURATION #### # the remainder of the sections configure individual tracks [Centro:overview] feature = centromere bgcolor = blue glyph = dot fgcolor = black height = 8 point = 1 show summary = 0 # no summary of this one key = Centromeres [tRNA:overview] feature = tRNA glyph = generic bgcolor = lightgray fgcolor = black height = 4 stranded = 1 description = 1 show summary = 0 # no summary of this one key = tRNAs [GC:region] glyph = dna global feature = 1 database = scaffolds height = 40 gc_window = auto do_gc = 1 strand = both fgcolor = red axis_color = blue show summary = 0 # no summary of this one key = GC Content [Genes] feature = gene glyph = gene bgcolor = yellow forwardcolor = yellow reversecolor = turquoise label = sub { my $f = shift; my $name = $f->display_name; my @aliases = sort $f->attributes('Alias'); $name .= " (@aliases)" if @aliases; $name; } height = 6 description = 0 key = Named gene [CDS] feature = gene glyph = cds description = 0 height = 26 sixframe = 1 label = sub {shift->name . " reading frame"} key = CDS citation = This track shows CDS reading frames. [tRNAs] feature = tRNA glyph = generic bgcolor = lightgray fgcolor = black height = 4 stranded = 1 description = 1 key = tRNAs [Transp] feature = LTR_retrotransposon glyph = segments bgcolor = yellow fgcolor = black height = 5 stranded = 1 key = Transposons [LTRs] feature = long_terminal_repeat fgcolor = black glyph = anchored_arrow height = 6 key = Long Terminal Repeats [Translation] glyph = translation global feature = 1 database = scaffolds height = 40 fgcolor = purple strand = +1 translation = 6frame key = 6-frame translation [TranslationF] glyph = translation global feature = 1 database = scaffolds height = 20 fgcolor = purple strand = +1 translation = 3frame key = 3-frame translation (forward) [DNA/GC Content] glyph = dna global feature = 1 database = scaffolds height = 40 do_gc = 1 gc_window = auto strand = both fgcolor = red axis_color = blue [TranslationR] glyph = translation global feature = 1 database = scaffolds height = 20 fgcolor = blue strand = -1 translation = 3frame key = 3-frame translation (reverse) [ncRNA] feature = RNAd rRNA:sgd snRNA:sgd snoRNA:sgd fgcolor = orange glyph = generic description = 1 key = Noncoding RNAs And this is the latest error log when I try to connect to http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/chado/: [Mon Jul 09 09:43:56 2012] [error] [client 10.12.20.67] Use of uninitialized val ue in join or string at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mul ti/Bio/Graphics/Browser2/DataSource.pm line 921., referer: http://i5k.nal.usda.g ov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 09:43:56 2012] [error] [client 10.12.20.67] Unknown database defined for general at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/G raphics/Browser2/DataSource.pm line 927., referer: http://i5k.nal.usda.gov/cgi-b in/gb2/gbrowse/yeast/ [Mon Jul 09 09:43:56 2012] [error] [client 10.12.20.67] Could not open database: Can't call method "new" on an undefined value at /usr/lib64/perl5/site_perl/5.8 .8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44., referer : http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 09:43:56 2012] [error] [client 10.12.20.67] Use of uninitialized val ue in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /Bio/Graphics/Browser2/DataSource.pm line 1048., referer: http://i5k.nal.usda.go v/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 09:43:56 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ Did I do something wrong with the conf for chado? David Jeang -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Tuesday, July 03, 2012 1:18 PM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, A few things: 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. Scott On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: > This is from the error log. > > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of > uninitialized val ue in hash element at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi > /Bio/Graphics/Browser2/DataSource.pm line 1048. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of > uninitialized val ue in string eq at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi > o/Graphics/Browser2/RegionSearch.pm line 392. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: > Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC > (@INC contains > : /opt/ActivePerl-5.12 > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult > i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl > /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl > /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per > l5/5.8.8 .) at (eval 164) line 3. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at > /usr/lib64/perl5/sit > e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . > > Also, I tried to make a conf for the file I wanted called > Dmelanogaster.conf And amended Gbrowse conf for it. > ###################################################################### > ######################### > # > # DATASOURCE DEFINITIONS > # One stanza for each configured data source # > ###################################################################### > ######################### > > [Dmelanogaster] > description = Fruitfly > path = Dmelanogaster.conf > > And Dmelanogaster.conf: > ################################# > # database definitions > ################################# > > [scaffolds:database] > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo [annotations:database] > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo > > But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? > > David > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Tuesday, July 03, 2012 12:44 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > This typically happens if in one of two situations: > > 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. > > 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. > > Is there anything in the error_log? > > Scott > > > On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >> >> db_adaptor = Bio::DB::Das::Chado >> db_args = -adaptor Bio::DB::Das::Chado >> -dsn dbi:Pg:dbname=tripal;host=localhost >> -user tripaldemo >> -pass tripal2demo psql=# ALTER USER >> tripaldemo SET search_path TO chado; >> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >> htdocs_base = /var/www/html/gbrowse2 >> url_base = /gbrowse2 >> tmp_base = /var/tmp/gbrowse2 >> persistent_base = /var/lib/gbrowse2 >> userdata_base = /var/lib/gbrowse2/userdata >> db_base = /var/www/cgi-bin/gb2/gbrowse >> >> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >> >> David Jeang >> >> >> >> >> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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In reply to this post by Scott Cain
We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using.
However there are still some problems with establishing a link to the chado. I got this message when I tried again: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. And the error log has these. [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisati on of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p m line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisati on of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p m line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. David Jeang -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Tuesday, July 03, 2012 1:18 PM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, A few things: 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. Scott On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: > This is from the error log. > > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of > uninitialized val ue in hash element at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi > /Bio/Graphics/Browser2/DataSource.pm line 1048. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of > uninitialized val ue in string eq at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi > o/Graphics/Browser2/RegionSearch.pm line 392. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: > Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC > (@INC contains > : /opt/ActivePerl-5.12 > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult > i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl > /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl > /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per > l5/5.8.8 .) at (eval 164) line 3. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at > /usr/lib64/perl5/sit > e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . > > Also, I tried to make a conf for the file I wanted called > Dmelanogaster.conf And amended Gbrowse conf for it. > ###################################################################### > ######################### > # > # DATASOURCE DEFINITIONS > # One stanza for each configured data source # > ###################################################################### > ######################### > > [Dmelanogaster] > description = Fruitfly > path = Dmelanogaster.conf > > And Dmelanogaster.conf: > ################################# > # database definitions > ################################# > > [scaffolds:database] > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo [annotations:database] > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo > > But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? > > David > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Tuesday, July 03, 2012 12:44 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > This typically happens if in one of two situations: > > 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. > > 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. > > Is there anything in the error_log? > > Scott > > > On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >> >> db_adaptor = Bio::DB::Das::Chado >> db_args = -adaptor Bio::DB::Das::Chado >> -dsn dbi:Pg:dbname=tripal;host=localhost >> -user tripaldemo >> -pass tripal2demo psql=# ALTER USER >> tripaldemo SET search_path TO chado; >> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >> htdocs_base = /var/www/html/gbrowse2 >> url_base = /gbrowse2 >> tmp_base = /var/tmp/gbrowse2 >> persistent_base = /var/lib/gbrowse2 >> userdata_base = /var/lib/gbrowse2/userdata >> db_base = /var/www/cgi-bin/gb2/gbrowse >> >> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >> >> David Jeang >> >> >> >> >> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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In reply to this post by Scott Cain
-----Original Message----- From: Jeang, David - ARS Sent: Monday, July 09, 2012 11:26 AM To: 'Scott Cain' Cc: [hidden email] Subject: RE: Gbrowse keeps rerouting to the demo We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. However there are still some problems with establishing a link to the chado. I got this message when I tried again: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. And the error log has these. [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisati on of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p m line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisati on of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p m line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. David Jeang -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Tuesday, July 03, 2012 1:18 PM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, A few things: 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. Scott On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: > This is from the error log. > > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of > uninitialized val ue in hash element at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi > /Bio/Graphics/Browser2/DataSource.pm line 1048. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of > uninitialized val ue in string eq at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi > o/Graphics/Browser2/RegionSearch.pm line 392. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: > Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC > (@INC contains > : /opt/ActivePerl-5.12 > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult > i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl > /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl > /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per > l5/5.8.8 .) at (eval 164) line 3. > [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at > /usr/lib64/perl5/sit > e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . > > Also, I tried to make a conf for the file I wanted called > Dmelanogaster.conf And amended Gbrowse conf for it. > ###################################################################### > ######################### > # > # DATASOURCE DEFINITIONS > # One stanza for each configured data source # > ###################################################################### > ######################### > > [Dmelanogaster] > description = Fruitfly > path = Dmelanogaster.conf > > And Dmelanogaster.conf: > ################################# > # database definitions > ################################# > > [scaffolds:database] > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo [annotations:database] > db_adaptor = Bio::DB::Das::Chado > db_args = -adaptor Bio::DB::Das::Chado > -dsn dbi:Pg:dbname=tripal;host=localhost > -user tripaldemo > -pass tripal2demo > > But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? > > David > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Tuesday, July 03, 2012 12:44 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > This typically happens if in one of two situations: > > 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. > > 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. > > Is there anything in the error_log? > > Scott > > > On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >> >> db_adaptor = Bio::DB::Das::Chado >> db_args = -adaptor Bio::DB::Das::Chado >> -dsn dbi:Pg:dbname=tripal;host=localhost >> -user tripaldemo >> -pass tripal2demo psql=# ALTER USER >> tripaldemo SET search_path TO chado; >> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >> htdocs_base = /var/www/html/gbrowse2 >> url_base = /gbrowse2 >> tmp_base = /var/tmp/gbrowse2 >> persistent_base = /var/lib/gbrowse2 >> userdata_base = /var/lib/gbrowse2/userdata >> db_base = /var/www/cgi-bin/gb2/gbrowse >> >> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >> >> David Jeang >> >> >> >> >> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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Hi David,
My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? Scott On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: > > > -----Original Message----- > From: Jeang, David - ARS > Sent: Monday, July 09, 2012 11:26 AM > To: 'Scott Cain' > Cc: [hidden email] > Subject: RE: Gbrowse keeps rerouting to the demo > > We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. > However there are still some problems with establishing a link to the chado. > > I got this message when I tried again: > DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. > > And the error log has these. > > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisati on of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p > m line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: > DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisati on of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p > m line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: > DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg" at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > > FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. > > David Jeang > > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Tuesday, July 03, 2012 1:18 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > A few things: > > 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. > > 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. > > 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. > > Scott > > > On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >> This is from the error log. >> >> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >> uninitialized val ue in hash element at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >> /Bio/Graphics/Browser2/DataSource.pm line 1048. >> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >> uninitialized val ue in string eq at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >> o/Graphics/Browser2/RegionSearch.pm line 392. >> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >> (@INC contains >> : /opt/ActivePerl-5.12 >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >> l5/5.8.8 .) at (eval 164) line 3. >> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >> /usr/lib64/perl5/sit >> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >> >> Also, I tried to make a conf for the file I wanted called >> Dmelanogaster.conf And amended Gbrowse conf for it. >> ###################################################################### >> ######################### >> # >> # DATASOURCE DEFINITIONS >> # One stanza for each configured data source # >> ###################################################################### >> ######################### >> >> [Dmelanogaster] >> description = Fruitfly >> path = Dmelanogaster.conf >> >> And Dmelanogaster.conf: >> ################################# >> # database definitions >> ################################# >> >> [scaffolds:database] >> db_adaptor = Bio::DB::Das::Chado >> db_args = -adaptor Bio::DB::Das::Chado >> -dsn dbi:Pg:dbname=tripal;host=localhost >> -user tripaldemo >> -pass tripal2demo [annotations:database] >> db_adaptor = Bio::DB::Das::Chado >> db_args = -adaptor Bio::DB::Das::Chado >> -dsn dbi:Pg:dbname=tripal;host=localhost >> -user tripaldemo >> -pass tripal2demo >> >> But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? >> >> David >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Tuesday, July 03, 2012 12:44 PM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> This typically happens if in one of two situations: >> >> 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. >> >> 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. >> >> Is there anything in the error_log? >> >> Scott >> >> >> On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >>> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >>> >>> db_adaptor = Bio::DB::Das::Chado >>> db_args = -adaptor Bio::DB::Das::Chado >>> -dsn dbi:Pg:dbname=tripal;host=localhost >>> -user tripaldemo >>> -pass tripal2demo psql=# ALTER USER >>> tripaldemo SET search_path TO chado; >>> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >>> htdocs_base = /var/www/html/gbrowse2 >>> url_base = /gbrowse2 >>> tmp_base = /var/tmp/gbrowse2 >>> persistent_base = /var/lib/gbrowse2 >>> userdata_base = /var/lib/gbrowse2/userdata >>> db_base = /var/www/cgi-bin/gb2/gbrowse >>> >>> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >>> >>> David Jeang >>> >>> >>> >>> >>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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It was installed by untar and unzipping the downloaded file, then using perl Makefile.PL
This is the result when I tried to make test cp testme.tmp.pl blib/lib/DBD/testme.tmp.pl cp lib/Bundle/DBD/Pg.pm blib/lib/Bundle/DBD/Pg.pm cp Pg.pm blib/lib/DBD/Pg.pm /usr/bin/perl5.8.8 -p -e "s/~DRIVER~/Pg/g; s/^do\(/dontdo\(/" /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI/Driver.xst > Pg.xsi /usr/bin/perl5.8.8 /usr/lib/perl5/vendor_perl/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap Pg.xs > Pg.xsc && mv Pg.xsc Pg.c gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Pg.c gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" dbdimp.c dbdimp.c: In function âpg_st_prepare_statementâ: dbdimp.c:2175: warning: comparison is always false due to limited range of data type dbdimp.c: In function âpg_st_executeâ: dbdimp.c:3031: warning: comparison is always false due to limited range of data type dbdimp.c:3041: warning: comparison is always false due to limited range of data type dbdimp.c:3042: warning: comparison is always false due to limited range of data type dbdimp.c:3180: warning: comparison is always false due to limited range of data type dbdimp.c: In function âpg_st_fetchâ: dbdimp.c:3408: warning: comparison is always false due to limited range of data type gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" quote.c Pg.h:65: warning: âdbi_get_stateâ defined but not used gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" types.c Pg.h:65: warning: âdbi_get_stateâ defined but not used Running Mkbootstrap for DBD::Pg () chmod 644 Pg.bs rm -f blib/arch/auto/DBD/Pg/Pg.so LD_RUN_PATH="/usr/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Pg.o dbdimp.o quote.o types.o -o blib/arch/auto/DBD/Pg/Pg.so \ -L/usr/lib64 -lpq -lm \ chmod 755 blib/arch/auto/DBD/Pg/Pg.so cp Pg.bs blib/arch/auto/DBD/Pg/Pg.bs chmod 644 blib/arch/auto/DBD/Pg/Pg.bs PGINITDB="/usr/bin/initdb" PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/00_signature.t .... skipped: Set the environment variable TEST_SIGNATURE to enable this test t/00basic.t ......... 1/3 # Failed test 'use DBD::Pg;' # at t/00basic.t line 14. Bailout called. Further testing stopped: Cannot continue without DBD::Pg # Tried to use 'DBD::Pg'. # Error: Can't load '/home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so' for module DBD::Pg: /home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so: undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. # at (eval 7) line 2. # Compilation failed in require at (eval 7) line 2. # BEGIN failed--compilation aborted at (eval 7) line 2. FAILED--Further testing stopped: Cannot continue without DBD::Pg make: *** [test_dynamic] Error 255 David Jeang -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Tuesday, July 10, 2012 11:09 AM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? Scott On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: > > > -----Original Message----- > From: Jeang, David - ARS > Sent: Monday, July 09, 2012 11:26 AM > To: 'Scott Cain' > Cc: [hidden email] > Subject: RE: Gbrowse keeps rerouting to the demo > > We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. > However there are still some problems with establishing a link to the chado. > > I got this message when I tried again: > DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. > > And the error log has these. > > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: > http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the > capitalisati on of DBD 'Pg' isn't right. at > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p > m line 234., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: > DBD::Pg initialisation failed: Can't locate object method "driver" > via package "DBD::Pg" at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l > ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: > http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the > capitalisati on of DBD 'Pg' isn't right. at > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p > m line 234., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: > DBD::Pg initialisation failed: Can't locate object method "driver" > via package "DBD::Pg" at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l > ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the > capitalisation of DBD 'Pg' isn't right. at > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open > database: DBD::Pg initialisation failed: Can't locate object method > "driver" via package "DBD::Pg" at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line > 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the > capitalisation of DBD 'Pg' isn't right. at > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open > database: DBD::Pg initialisation failed: Can't locate object method > "driver" via package "DBD::Pg" at > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line > 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the > capitalisation of DBD 'Pg' isn't right. at > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: > http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ > > FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. > > David Jeang > > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Tuesday, July 03, 2012 1:18 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > A few things: > > 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. > > 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. > > 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. > > Scott > > > On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >> This is from the error log. >> >> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >> uninitialized val ue in hash element at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >> /Bio/Graphics/Browser2/DataSource.pm line 1048. >> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >> uninitialized val ue in string eq at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >> o/Graphics/Browser2/RegionSearch.pm line 392. >> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >> (@INC contains >> : /opt/ActivePerl-5.12 >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >> l5/5.8.8 .) at (eval 164) line 3. >> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >> /usr/lib64/perl5/sit >> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >> >> Also, I tried to make a conf for the file I wanted called >> Dmelanogaster.conf And amended Gbrowse conf for it. >> ##################################################################### >> # >> ######################### >> # >> # DATASOURCE DEFINITIONS >> # One stanza for each configured data source # >> ##################################################################### >> # >> ######################### >> >> [Dmelanogaster] >> description = Fruitfly >> path = Dmelanogaster.conf >> >> And Dmelanogaster.conf: >> ################################# >> # database definitions >> ################################# >> >> [scaffolds:database] >> db_adaptor = Bio::DB::Das::Chado >> db_args = -adaptor Bio::DB::Das::Chado >> -dsn dbi:Pg:dbname=tripal;host=localhost >> -user tripaldemo >> -pass tripal2demo [annotations:database] >> db_adaptor = Bio::DB::Das::Chado >> db_args = -adaptor Bio::DB::Das::Chado >> -dsn dbi:Pg:dbname=tripal;host=localhost >> -user tripaldemo >> -pass tripal2demo >> >> But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? >> >> David >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Tuesday, July 03, 2012 12:44 PM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> This typically happens if in one of two situations: >> >> 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. >> >> 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. >> >> Is there anything in the error_log? >> >> Scott >> >> >> On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >>> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >>> >>> db_adaptor = Bio::DB::Das::Chado >>> db_args = -adaptor Bio::DB::Das::Chado >>> -dsn dbi:Pg:dbname=tripal;host=localhost >>> -user tripaldemo >>> -pass tripal2demo psql=# ALTER USER >>> tripaldemo SET search_path TO chado; >>> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >>> htdocs_base = /var/www/html/gbrowse2 >>> url_base = /gbrowse2 >>> tmp_base = /var/tmp/gbrowse2 >>> persistent_base = /var/lib/gbrowse2 >>> userdata_base = /var/lib/gbrowse2/userdata >>> db_base = /var/www/cgi-bin/gb2/gbrowse >>> >>> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >>> >>> David Jeang >>> >>> >>> >>> >>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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Hi David,
I'm not sure why DBD::Pg failed to compile. If I remember correctly, you're using Fedora, right? Why don't you use yum to install prereqs when possible, like this: sudo yum install perl-DBD-Pg (I think that's the command and library name--it's been a while since I've used an RPM-based distribution.) Scott On Wed, Jul 11, 2012 at 2:55 PM, Jeang, David - ARS <[hidden email]> wrote: > It was installed by untar and unzipping the downloaded file, then using perl Makefile.PL > > This is the result when I tried to make test > > cp testme.tmp.pl blib/lib/DBD/testme.tmp.pl > cp lib/Bundle/DBD/Pg.pm blib/lib/Bundle/DBD/Pg.pm > cp Pg.pm blib/lib/DBD/Pg.pm > /usr/bin/perl5.8.8 -p -e "s/~DRIVER~/Pg/g; s/^do\(/dontdo\(/" /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI/Driver.xst > Pg.xsi > /usr/bin/perl5.8.8 /usr/lib/perl5/vendor_perl/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap Pg.xs > Pg.xsc && mv Pg.xsc Pg.c > gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Pg.c > gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" dbdimp.c > dbdimp.c: In function âpg_st_prepare_statementâ: > dbdimp.c:2175: warning: comparison is always false due to limited range of data type > dbdimp.c: In function âpg_st_executeâ: > dbdimp.c:3031: warning: comparison is always false due to limited range of data type > dbdimp.c:3041: warning: comparison is always false due to limited range of data type > dbdimp.c:3042: warning: comparison is always false due to limited range of data type > dbdimp.c:3180: warning: comparison is always false due to limited range of data type > dbdimp.c: In function âpg_st_fetchâ: > dbdimp.c:3408: warning: comparison is always false due to limited range of data type > gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" quote.c > Pg.h:65: warning: âdbi_get_stateâ defined but not used > gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" types.c > Pg.h:65: warning: âdbi_get_stateâ defined but not used > Running Mkbootstrap for DBD::Pg () > chmod 644 Pg.bs > rm -f blib/arch/auto/DBD/Pg/Pg.so > LD_RUN_PATH="/usr/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Pg.o dbdimp.o quote.o types.o -o blib/arch/auto/DBD/Pg/Pg.so \ > -L/usr/lib64 -lpq -lm \ > > chmod 755 blib/arch/auto/DBD/Pg/Pg.so > cp Pg.bs blib/arch/auto/DBD/Pg/Pg.bs > chmod 644 blib/arch/auto/DBD/Pg/Pg.bs > PGINITDB="/usr/bin/initdb" PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/00_signature.t .... skipped: Set the environment variable TEST_SIGNATURE to enable this test > t/00basic.t ......... 1/3 > # Failed test 'use DBD::Pg;' > # at t/00basic.t line 14. > Bailout called. Further testing stopped: Cannot continue without DBD::Pg > # Tried to use 'DBD::Pg'. > # Error: Can't load '/home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so' for module DBD::Pg: /home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so: undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. > # at (eval 7) line 2. > # Compilation failed in require at (eval 7) line 2. > # BEGIN failed--compilation aborted at (eval 7) line 2. > FAILED--Further testing stopped: Cannot continue without DBD::Pg > make: *** [test_dynamic] Error 255 > > > David Jeang > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Tuesday, July 10, 2012 11:09 AM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? > > Scott > > > On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: >> >> >> -----Original Message----- >> From: Jeang, David - ARS >> Sent: Monday, July 09, 2012 11:26 AM >> To: 'Scott Cain' >> Cc: [hidden email] >> Subject: RE: Gbrowse keeps rerouting to the demo >> >> We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. >> However there are still some problems with establishing a link to the chado. >> >> I got this message when I tried again: >> DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. >> >> And the error log has these. >> >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisati on of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >> m line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >> DBD::Pg initialisation failed: Can't locate object method "driver" >> via package "DBD::Pg" at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >> ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisati on of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >> m line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >> DBD::Pg initialisation failed: Can't locate object method "driver" >> via package "DBD::Pg" at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >> ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisation of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open >> database: DBD::Pg initialisation failed: Can't locate object method >> "driver" via package "DBD::Pg" at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line >> 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisation of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open >> database: DBD::Pg initialisation failed: Can't locate object method >> "driver" via package "DBD::Pg" at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line >> 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisation of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> >> FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. >> >> David Jeang >> >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Tuesday, July 03, 2012 1:18 PM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> A few things: >> >> 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. >> >> 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. >> >> 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. >> >> Scott >> >> >> On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >>> This is from the error log. >>> >>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>> uninitialized val ue in hash element at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >>> /Bio/Graphics/Browser2/DataSource.pm line 1048. >>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>> uninitialized val ue in string eq at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >>> o/Graphics/Browser2/RegionSearch.pm line 392. >>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >>> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >>> (@INC contains >>> : /opt/ActivePerl-5.12 >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >>> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >>> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >>> l5/5.8.8 .) at (eval 164) line 3. >>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >>> /usr/lib64/perl5/sit >>> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >>> >>> Also, I tried to make a conf for the file I wanted called >>> Dmelanogaster.conf And amended Gbrowse conf for it. >>> ##################################################################### >>> # >>> ######################### >>> # >>> # DATASOURCE DEFINITIONS >>> # One stanza for each configured data source # >>> ##################################################################### >>> # >>> ######################### >>> >>> [Dmelanogaster] >>> description = Fruitfly >>> path = Dmelanogaster.conf >>> >>> And Dmelanogaster.conf: >>> ################################# >>> # database definitions >>> ################################# >>> >>> [scaffolds:database] >>> db_adaptor = Bio::DB::Das::Chado >>> db_args = -adaptor Bio::DB::Das::Chado >>> -dsn dbi:Pg:dbname=tripal;host=localhost >>> -user tripaldemo >>> -pass tripal2demo [annotations:database] >>> db_adaptor = Bio::DB::Das::Chado >>> db_args = -adaptor Bio::DB::Das::Chado >>> -dsn dbi:Pg:dbname=tripal;host=localhost >>> -user tripaldemo >>> -pass tripal2demo >>> >>> But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? >>> >>> David >>> -----Original Message----- >>> From: Scott Cain [mailto:[hidden email]] >>> Sent: Tuesday, July 03, 2012 12:44 PM >>> To: Jeang, David - ARS >>> Cc: [hidden email] >>> Subject: Re: Gbrowse keeps rerouting to the demo >>> >>> Hi David, >>> >>> This typically happens if in one of two situations: >>> >>> 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. >>> >>> 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. >>> >>> Is there anything in the error_log? >>> >>> Scott >>> >>> >>> On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >>>> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >>>> >>>> db_adaptor = Bio::DB::Das::Chado >>>> db_args = -adaptor Bio::DB::Das::Chado >>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>> -user tripaldemo >>>> -pass tripal2demo psql=# ALTER USER >>>> tripaldemo SET search_path TO chado; >>>> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >>>> htdocs_base = /var/www/html/gbrowse2 >>>> url_base = /gbrowse2 >>>> tmp_base = /var/tmp/gbrowse2 >>>> persistent_base = /var/lib/gbrowse2 >>>> userdata_base = /var/lib/gbrowse2/userdata >>>> db_base = /var/www/cgi-bin/gb2/gbrowse >>>> >>>> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >>>> >>>> David Jeang >>>> >>>> >>>> >>>> >>>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >>>> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at scottcain dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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All it gave was this message:
Setting up Install Process Package perl-DBD-Pg-1.49-2.el5_3.1.x86_64 already installed and latest version Nothing to do David -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Wednesday, July 11, 2012 3:10 PM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, I'm not sure why DBD::Pg failed to compile. If I remember correctly, you're using Fedora, right? Why don't you use yum to install prereqs when possible, like this: sudo yum install perl-DBD-Pg (I think that's the command and library name--it's been a while since I've used an RPM-based distribution.) Scott On Wed, Jul 11, 2012 at 2:55 PM, Jeang, David - ARS <[hidden email]> wrote: > It was installed by untar and unzipping the downloaded file, then > using perl Makefile.PL > > This is the result when I tried to make test > > cp testme.tmp.pl blib/lib/DBD/testme.tmp.pl cp lib/Bundle/DBD/Pg.pm > blib/lib/Bundle/DBD/Pg.pm cp Pg.pm blib/lib/DBD/Pg.pm > /usr/bin/perl5.8.8 -p -e "s/~DRIVER~/Pg/g; s/^do\(/dontdo\(/" > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI/Dr > iver.xst > Pg.xsi > /usr/bin/perl5.8.8 /usr/lib/perl5/vendor_perl/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap Pg.xs > Pg.xsc && mv Pg.xsc Pg.c > gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Pg.c > gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" dbdimp.c > dbdimp.c: In function âpg_st_prepare_statementâ: > dbdimp.c:2175: warning: comparison is always false due to limited > range of data type > dbdimp.c: In function âpg_st_executeâ: > dbdimp.c:3031: warning: comparison is always false due to limited > range of data type > dbdimp.c:3041: warning: comparison is always false due to limited > range of data type > dbdimp.c:3042: warning: comparison is always false due to limited > range of data type > dbdimp.c:3180: warning: comparison is always false due to limited > range of data type > dbdimp.c: In function âpg_st_fetchâ: > dbdimp.c:3408: warning: comparison is always false due to limited range of data type > gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" quote.c > Pg.h:65: warning: âdbi_get_stateâ defined but not used > gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" types.c > Pg.h:65: warning: âdbi_get_stateâ defined but not used Running > Mkbootstrap for DBD::Pg () chmod 644 Pg.bs rm -f > blib/arch/auto/DBD/Pg/Pg.so > LD_RUN_PATH="/usr/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Pg.o dbdimp.o quote.o types.o -o blib/arch/auto/DBD/Pg/Pg.so \ > -L/usr/lib64 -lpq -lm \ > > chmod 755 blib/arch/auto/DBD/Pg/Pg.so > cp Pg.bs blib/arch/auto/DBD/Pg/Pg.bs > chmod 644 blib/arch/auto/DBD/Pg/Pg.bs > PGINITDB="/usr/bin/initdb" PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 > "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', > 'blib/arch')" t/*.t t/00_signature.t .... skipped: Set the environment variable TEST_SIGNATURE to enable this test t/00basic.t ......... 1/3 > # Failed test 'use DBD::Pg;' > # at t/00basic.t line 14. > Bailout called. Further testing stopped: Cannot continue without DBD::Pg > # Tried to use 'DBD::Pg'. > # Error: Can't load '/home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so' for module DBD::Pg: /home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so: undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. > # at (eval 7) line 2. > # Compilation failed in require at (eval 7) line 2. > # BEGIN failed--compilation aborted at (eval 7) line 2. > FAILED--Further testing stopped: Cannot continue without DBD::Pg > make: *** [test_dynamic] Error 255 > > > David Jeang > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Tuesday, July 10, 2012 11:09 AM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? > > Scott > > > On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: >> >> >> -----Original Message----- >> From: Jeang, David - ARS >> Sent: Monday, July 09, 2012 11:26 AM >> To: 'Scott Cain' >> Cc: [hidden email] >> Subject: RE: Gbrowse keeps rerouting to the demo >> >> We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. >> However there are still some problems with establishing a link to the chado. >> >> I got this message when I tried again: >> DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. >> >> And the error log has these. >> >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisati on of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >> m line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >> DBD::Pg initialisation failed: Can't locate object method "driver" >> via package "DBD::Pg" at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >> ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisati on of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >> m line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >> DBD::Pg initialisation failed: Can't locate object method "driver" >> via package "DBD::Pg" at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >> ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisation of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >> open >> database: DBD::Pg initialisation failed: Can't locate object method >> "driver" via package "DBD::Pg" at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >> line 808., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisation of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >> open >> database: DBD::Pg initialisation failed: Can't locate object method >> "driver" via package "DBD::Pg" at >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >> line 808., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >> capitalisation of DBD 'Pg' isn't right. at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >> >> FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. >> >> David Jeang >> >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Tuesday, July 03, 2012 1:18 PM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> A few things: >> >> 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. >> >> 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. >> >> 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. >> >> Scott >> >> >> On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >>> This is from the error log. >>> >>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>> uninitialized val ue in hash element at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >>> /Bio/Graphics/Browser2/DataSource.pm line 1048. >>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>> uninitialized val ue in string eq at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >>> o/Graphics/Browser2/RegionSearch.pm line 392. >>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >>> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >>> (@INC contains >>> : /opt/ActivePerl-5.12 >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >>> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >>> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >>> l5/5.8.8 .) at (eval 164) line 3. >>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >>> /usr/lib64/perl5/sit >>> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >>> >>> Also, I tried to make a conf for the file I wanted called >>> Dmelanogaster.conf And amended Gbrowse conf for it. >>> #################################################################### >>> # >>> # >>> ######################### >>> # >>> # DATASOURCE DEFINITIONS >>> # One stanza for each configured data source # >>> #################################################################### >>> # >>> # >>> ######################### >>> >>> [Dmelanogaster] >>> description = Fruitfly >>> path = Dmelanogaster.conf >>> >>> And Dmelanogaster.conf: >>> ################################# >>> # database definitions >>> ################################# >>> >>> [scaffolds:database] >>> db_adaptor = Bio::DB::Das::Chado >>> db_args = -adaptor Bio::DB::Das::Chado >>> -dsn dbi:Pg:dbname=tripal;host=localhost >>> -user tripaldemo >>> -pass tripal2demo [annotations:database] >>> db_adaptor = Bio::DB::Das::Chado >>> db_args = -adaptor Bio::DB::Das::Chado >>> -dsn dbi:Pg:dbname=tripal;host=localhost >>> -user tripaldemo >>> -pass tripal2demo >>> >>> But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? >>> >>> David >>> -----Original Message----- >>> From: Scott Cain [mailto:[hidden email]] >>> Sent: Tuesday, July 03, 2012 12:44 PM >>> To: Jeang, David - ARS >>> Cc: [hidden email] >>> Subject: Re: Gbrowse keeps rerouting to the demo >>> >>> Hi David, >>> >>> This typically happens if in one of two situations: >>> >>> 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. >>> >>> 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. >>> >>> Is there anything in the error_log? >>> >>> Scott >>> >>> >>> On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >>>> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >>>> >>>> db_adaptor = Bio::DB::Das::Chado >>>> db_args = -adaptor Bio::DB::Das::Chado >>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>> -user tripaldemo >>>> -pass tripal2demo psql=# ALTER USER >>>> tripaldemo SET search_path TO chado; >>>> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >>>> htdocs_base = /var/www/html/gbrowse2 >>>> url_base = /gbrowse2 >>>> tmp_base = /var/tmp/gbrowse2 >>>> persistent_base = /var/lib/gbrowse2 >>>> userdata_base = /var/lib/gbrowse2/userdata >>>> db_base = /var/www/cgi-bin/gb2/gbrowse >>>> >>>> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >>>> >>>> David Jeang >>>> >>>> >>>> >>>> >>>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >>>> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at scottcain dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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Hi David,
That's a little weird, since that is a really old version of DBD::Pg (the RPM repositories I just looked at have DBD::Pg version 2.18). I'm guessing there is a conflict of some sort between DBD::Pg (really old) and postgres (presumably not as old). Remind me what linux distribution you're using and is it by any chance possible that you could switch to Ubuntu? There are apt packages available for recent Ubuntu releases that allow installing GBrowse with a simple apt-get command. Scott On Wed, Jul 11, 2012 at 3:11 PM, Jeang, David - ARS <[hidden email]> wrote: > All it gave was this message: > > Setting up Install Process > Package perl-DBD-Pg-1.49-2.el5_3.1.x86_64 already installed and latest version > Nothing to do > > David > > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Wednesday, July 11, 2012 3:10 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > I'm not sure why DBD::Pg failed to compile. If I remember correctly, you're using Fedora, right? Why don't you use yum to install prereqs when possible, like this: > > sudo yum install perl-DBD-Pg > > (I think that's the command and library name--it's been a while since I've used an RPM-based distribution.) > > Scott > > > On Wed, Jul 11, 2012 at 2:55 PM, Jeang, David - ARS <[hidden email]> wrote: >> It was installed by untar and unzipping the downloaded file, then >> using perl Makefile.PL >> >> This is the result when I tried to make test >> >> cp testme.tmp.pl blib/lib/DBD/testme.tmp.pl cp lib/Bundle/DBD/Pg.pm >> blib/lib/Bundle/DBD/Pg.pm cp Pg.pm blib/lib/DBD/Pg.pm >> /usr/bin/perl5.8.8 -p -e "s/~DRIVER~/Pg/g; s/^do\(/dontdo\(/" >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI/Dr >> iver.xst > Pg.xsi >> /usr/bin/perl5.8.8 /usr/lib/perl5/vendor_perl/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap Pg.xs > Pg.xsc && mv Pg.xsc Pg.c >> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Pg.c >> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" dbdimp.c >> dbdimp.c: In function âpg_st_prepare_statementâ: >> dbdimp.c:2175: warning: comparison is always false due to limited >> range of data type >> dbdimp.c: In function âpg_st_executeâ: >> dbdimp.c:3031: warning: comparison is always false due to limited >> range of data type >> dbdimp.c:3041: warning: comparison is always false due to limited >> range of data type >> dbdimp.c:3042: warning: comparison is always false due to limited >> range of data type >> dbdimp.c:3180: warning: comparison is always false due to limited >> range of data type >> dbdimp.c: In function âpg_st_fetchâ: >> dbdimp.c:3408: warning: comparison is always false due to limited range of data type >> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" quote.c >> Pg.h:65: warning: âdbi_get_stateâ defined but not used >> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" types.c >> Pg.h:65: warning: âdbi_get_stateâ defined but not used Running >> Mkbootstrap for DBD::Pg () chmod 644 Pg.bs rm -f >> blib/arch/auto/DBD/Pg/Pg.so >> LD_RUN_PATH="/usr/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Pg.o dbdimp.o quote.o types.o -o blib/arch/auto/DBD/Pg/Pg.so \ >> -L/usr/lib64 -lpq -lm \ >> >> chmod 755 blib/arch/auto/DBD/Pg/Pg.so >> cp Pg.bs blib/arch/auto/DBD/Pg/Pg.bs >> chmod 644 blib/arch/auto/DBD/Pg/Pg.bs >> PGINITDB="/usr/bin/initdb" PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 >> "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', >> 'blib/arch')" t/*.t t/00_signature.t .... skipped: Set the environment variable TEST_SIGNATURE to enable this test t/00basic.t ......... 1/3 >> # Failed test 'use DBD::Pg;' >> # at t/00basic.t line 14. >> Bailout called. Further testing stopped: Cannot continue without DBD::Pg >> # Tried to use 'DBD::Pg'. >> # Error: Can't load '/home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so' for module DBD::Pg: /home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so: undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> # at (eval 7) line 2. >> # Compilation failed in require at (eval 7) line 2. >> # BEGIN failed--compilation aborted at (eval 7) line 2. >> FAILED--Further testing stopped: Cannot continue without DBD::Pg >> make: *** [test_dynamic] Error 255 >> >> >> David Jeang >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Tuesday, July 10, 2012 11:09 AM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? >> >> Scott >> >> >> On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: >>> >>> >>> -----Original Message----- >>> From: Jeang, David - ARS >>> Sent: Monday, July 09, 2012 11:26 AM >>> To: 'Scott Cain' >>> Cc: [hidden email] >>> Subject: RE: Gbrowse keeps rerouting to the demo >>> >>> We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. >>> However there are still some problems with establishing a link to the chado. >>> >>> I got this message when I tried again: >>> DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. >>> >>> And the error log has these. >>> >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisati on of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>> m line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>> DBD::Pg initialisation failed: Can't locate object method "driver" >>> via package "DBD::Pg" at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>> ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisati on of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>> m line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>> DBD::Pg initialisation failed: Can't locate object method "driver" >>> via package "DBD::Pg" at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>> ine 808., referer: http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisation of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>> open >>> database: DBD::Pg initialisation failed: Can't locate object method >>> "driver" via package "DBD::Pg" at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>> line 808., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisation of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>> open >>> database: DBD::Pg initialisation failed: Can't locate object method >>> "driver" via package "DBD::Pg" at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>> line 808., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisation of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> >>> FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. >>> >>> David Jeang >>> >>> -----Original Message----- >>> From: Scott Cain [mailto:[hidden email]] >>> Sent: Tuesday, July 03, 2012 1:18 PM >>> To: Jeang, David - ARS >>> Cc: [hidden email] >>> Subject: Re: Gbrowse keeps rerouting to the demo >>> >>> Hi David, >>> >>> A few things: >>> >>> 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. >>> >>> 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. >>> >>> 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. >>> >>> Scott >>> >>> >>> On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >>>> This is from the error log. >>>> >>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>> uninitialized val ue in hash element at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >>>> /Bio/Graphics/Browser2/DataSource.pm line 1048. >>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>> uninitialized val ue in string eq at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >>>> o/Graphics/Browser2/RegionSearch.pm line 392. >>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >>>> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >>>> (@INC contains >>>> : /opt/ActivePerl-5.12 >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >>>> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >>>> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >>>> l5/5.8.8 .) at (eval 164) line 3. >>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >>>> /usr/lib64/perl5/sit >>>> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >>>> >>>> Also, I tried to make a conf for the file I wanted called >>>> Dmelanogaster.conf And amended Gbrowse conf for it. >>>> #################################################################### >>>> # >>>> # >>>> ######################### >>>> # >>>> # DATASOURCE DEFINITIONS >>>> # One stanza for each configured data source # >>>> #################################################################### >>>> # >>>> # >>>> ######################### >>>> >>>> [Dmelanogaster] >>>> description = Fruitfly >>>> path = Dmelanogaster.conf >>>> >>>> And Dmelanogaster.conf: >>>> ################################# >>>> # database definitions >>>> ################################# >>>> >>>> [scaffolds:database] >>>> db_adaptor = Bio::DB::Das::Chado >>>> db_args = -adaptor Bio::DB::Das::Chado >>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>> -user tripaldemo >>>> -pass tripal2demo [annotations:database] >>>> db_adaptor = Bio::DB::Das::Chado >>>> db_args = -adaptor Bio::DB::Das::Chado >>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>> -user tripaldemo >>>> -pass tripal2demo >>>> >>>> But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? >>>> >>>> David >>>> -----Original Message----- >>>> From: Scott Cain [mailto:[hidden email]] >>>> Sent: Tuesday, July 03, 2012 12:44 PM >>>> To: Jeang, David - ARS >>>> Cc: [hidden email] >>>> Subject: Re: Gbrowse keeps rerouting to the demo >>>> >>>> Hi David, >>>> >>>> This typically happens if in one of two situations: >>>> >>>> 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. >>>> >>>> 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. >>>> >>>> Is there anything in the error_log? >>>> >>>> Scott >>>> >>>> >>>> On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >>>>> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >>>>> >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo >>>>> -pass tripal2demo psql=# ALTER USER >>>>> tripaldemo SET search_path TO chado; >>>>> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >>>>> htdocs_base = /var/www/html/gbrowse2 >>>>> url_base = /gbrowse2 >>>>> tmp_base = /var/tmp/gbrowse2 >>>>> persistent_base = /var/lib/gbrowse2 >>>>> userdata_base = /var/lib/gbrowse2/userdata >>>>> db_base = /var/www/cgi-bin/gb2/gbrowse >>>>> >>>>> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >>>>> >>>>> David Jeang >>>>> >>>>> >>>>> >>>>> >>>>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>>> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at scottcain dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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My friend doesn't think the problem lies in the distribution, he's more concerned with the error message
undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. In his opinion, it's some sort of C library problem. Is he right? David -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Wednesday, July 11, 2012 3:23 PM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, That's a little weird, since that is a really old version of DBD::Pg (the RPM repositories I just looked at have DBD::Pg version 2.18). I'm guessing there is a conflict of some sort between DBD::Pg (really old) and postgres (presumably not as old). Remind me what linux distribution you're using and is it by any chance possible that you could switch to Ubuntu? There are apt packages available for recent Ubuntu releases that allow installing GBrowse with a simple apt-get command. Scott On Wed, Jul 11, 2012 at 3:11 PM, Jeang, David - ARS <[hidden email]> wrote: > All it gave was this message: > > Setting up Install Process > Package perl-DBD-Pg-1.49-2.el5_3.1.x86_64 already installed and latest > version Nothing to do > > David > > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Wednesday, July 11, 2012 3:10 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > I'm not sure why DBD::Pg failed to compile. If I remember correctly, you're using Fedora, right? Why don't you use yum to install prereqs when possible, like this: > > sudo yum install perl-DBD-Pg > > (I think that's the command and library name--it's been a while since > I've used an RPM-based distribution.) > > Scott > > > On Wed, Jul 11, 2012 at 2:55 PM, Jeang, David - ARS <[hidden email]> wrote: >> It was installed by untar and unzipping the downloaded file, then >> using perl Makefile.PL >> >> This is the result when I tried to make test >> >> cp testme.tmp.pl blib/lib/DBD/testme.tmp.pl cp lib/Bundle/DBD/Pg.pm >> blib/lib/Bundle/DBD/Pg.pm cp Pg.pm blib/lib/DBD/Pg.pm >> /usr/bin/perl5.8.8 -p -e "s/~DRIVER~/Pg/g; s/^do\(/dontdo\(/" >> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI/D >> r >> iver.xst > Pg.xsi >> /usr/bin/perl5.8.8 /usr/lib/perl5/vendor_perl/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap Pg.xs > Pg.xsc && mv Pg.xsc Pg.c >> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Pg.c >> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" dbdimp.c >> dbdimp.c: In function âpg_st_prepare_statementâ: >> dbdimp.c:2175: warning: comparison is always false due to limited >> range of data type >> dbdimp.c: In function âpg_st_executeâ: >> dbdimp.c:3031: warning: comparison is always false due to limited >> range of data type >> dbdimp.c:3041: warning: comparison is always false due to limited >> range of data type >> dbdimp.c:3042: warning: comparison is always false due to limited >> range of data type >> dbdimp.c:3180: warning: comparison is always false due to limited >> range of data type >> dbdimp.c: In function âpg_st_fetchâ: >> dbdimp.c:3408: warning: comparison is always false due to limited range of data type >> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" quote.c >> Pg.h:65: warning: âdbi_get_stateâ defined but not used >> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" types.c >> Pg.h:65: warning: âdbi_get_stateâ defined but not used Running >> Mkbootstrap for DBD::Pg () chmod 644 Pg.bs rm -f >> blib/arch/auto/DBD/Pg/Pg.so >> LD_RUN_PATH="/usr/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Pg.o dbdimp.o quote.o types.o -o blib/arch/auto/DBD/Pg/Pg.so \ >> -L/usr/lib64 -lpq -lm \ >> >> chmod 755 blib/arch/auto/DBD/Pg/Pg.so cp Pg.bs >> blib/arch/auto/DBD/Pg/Pg.bs chmod 644 blib/arch/auto/DBD/Pg/Pg.bs >> PGINITDB="/usr/bin/initdb" PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 >> "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', >> 'blib/arch')" t/*.t t/00_signature.t .... skipped: Set the environment variable TEST_SIGNATURE to enable this test t/00basic.t ......... 1/3 >> # Failed test 'use DBD::Pg;' >> # at t/00basic.t line 14. >> Bailout called. Further testing stopped: Cannot continue without DBD::Pg >> # Tried to use 'DBD::Pg'. >> # Error: Can't load '/home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so' for module DBD::Pg: /home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so: undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. >> # at (eval 7) line 2. >> # Compilation failed in require at (eval 7) line 2. >> # BEGIN failed--compilation aborted at (eval 7) line 2. >> FAILED--Further testing stopped: Cannot continue without DBD::Pg >> make: *** [test_dynamic] Error 255 >> >> >> David Jeang >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Tuesday, July 10, 2012 11:09 AM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? >> >> Scott >> >> >> On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: >>> >>> >>> -----Original Message----- >>> From: Jeang, David - ARS >>> Sent: Monday, July 09, 2012 11:26 AM >>> To: 'Scott Cain' >>> Cc: [hidden email] >>> Subject: RE: Gbrowse keeps rerouting to the demo >>> >>> We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. >>> However there are still some problems with establishing a link to the chado. >>> >>> I got this message when I tried again: >>> DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. >>> >>> And the error log has these. >>> >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisati on of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>> m line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>> DBD::Pg initialisation failed: Can't locate object method "driver" >>> via package "DBD::Pg" at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>> ine 808., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisati on of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>> m line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>> DBD::Pg initialisation failed: Can't locate object method "driver" >>> via package "DBD::Pg" at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>> ine 808., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisation of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>> open >>> database: DBD::Pg initialisation failed: Can't locate object method >>> "driver" via package "DBD::Pg" at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>> line 808., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisation of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>> open >>> database: DBD::Pg initialisation failed: Can't locate object method >>> "driver" via package "DBD::Pg" at >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>> line 808., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>> capitalisation of DBD 'Pg' isn't right. at >>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>> >>> FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. >>> >>> David Jeang >>> >>> -----Original Message----- >>> From: Scott Cain [mailto:[hidden email]] >>> Sent: Tuesday, July 03, 2012 1:18 PM >>> To: Jeang, David - ARS >>> Cc: [hidden email] >>> Subject: Re: Gbrowse keeps rerouting to the demo >>> >>> Hi David, >>> >>> A few things: >>> >>> 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. >>> >>> 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. >>> >>> 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. >>> >>> Scott >>> >>> >>> On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >>>> This is from the error log. >>>> >>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>> uninitialized val ue in hash element at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >>>> /Bio/Graphics/Browser2/DataSource.pm line 1048. >>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>> uninitialized val ue in string eq at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >>>> o/Graphics/Browser2/RegionSearch.pm line 392. >>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >>>> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >>>> (@INC contains >>>> : /opt/ActivePerl-5.12 >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >>>> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >>>> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >>>> l5/5.8.8 .) at (eval 164) line 3. >>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >>>> /usr/lib64/perl5/sit >>>> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >>>> >>>> Also, I tried to make a conf for the file I wanted called >>>> Dmelanogaster.conf And amended Gbrowse conf for it. >>>> ################################################################### >>>> # >>>> # >>>> # >>>> ######################### >>>> # >>>> # DATASOURCE DEFINITIONS >>>> # One stanza for each configured data source # >>>> ################################################################### >>>> # >>>> # >>>> # >>>> ######################### >>>> >>>> [Dmelanogaster] >>>> description = Fruitfly >>>> path = Dmelanogaster.conf >>>> >>>> And Dmelanogaster.conf: >>>> ################################# >>>> # database definitions >>>> ################################# >>>> >>>> [scaffolds:database] >>>> db_adaptor = Bio::DB::Das::Chado >>>> db_args = -adaptor Bio::DB::Das::Chado >>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>> -user tripaldemo >>>> -pass tripal2demo [annotations:database] >>>> db_adaptor = Bio::DB::Das::Chado >>>> db_args = -adaptor Bio::DB::Das::Chado >>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>> -user tripaldemo >>>> -pass tripal2demo >>>> >>>> But that didn't work either. After looking at some other things, on the forums, I'm thinking, am I doing this wrong? Do I just need a conf for the chado database and not the info it contains? >>>> >>>> David >>>> -----Original Message----- >>>> From: Scott Cain [mailto:[hidden email]] >>>> Sent: Tuesday, July 03, 2012 12:44 PM >>>> To: Jeang, David - ARS >>>> Cc: [hidden email] >>>> Subject: Re: Gbrowse keeps rerouting to the demo >>>> >>>> Hi David, >>>> >>>> This typically happens if in one of two situations: >>>> >>>> 1. The GBrowse.conf (assuming GBrowse2) file wasn't updated with the path to the new configuration file; when GBrowse fails to find the conf file, it falls back on the default. >>>> >>>> 2. There is a syntax error in the conf file (GBrowse 1) and it goes to the "next" configuration it can find (which one it uses I think might not be well defined). It's possible that a syntax error would cause this behavior in GBrowse 2, but more frequently it would cause a 500 server error. >>>> >>>> Is there anything in the error_log? >>>> >>>> Scott >>>> >>>> >>>> On Mon, Jul 2, 2012 at 9:48 AM, Jeang, David - ARS <[hidden email]> wrote: >>>>> I've managed to get Gbrowse up and running now, these are the configurations I put in the conf file in order for it to link to the chado database on the same server. >>>>> >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo >>>>> -pass tripal2demo psql=# ALTER USER >>>>> tripaldemo SET search_path TO chado; >>>>> config_base = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF >>>>> htdocs_base = /var/www/html/gbrowse2 >>>>> url_base = /gbrowse2 >>>>> tmp_base = /var/tmp/gbrowse2 >>>>> persistent_base = /var/lib/gbrowse2 >>>>> userdata_base = /var/lib/gbrowse2/userdata >>>>> db_base = /var/www/cgi-bin/gb2/gbrowse >>>>> >>>>> However, every time I try to link, it keeps going back to the yeast example. Is there something missing that keeps it falling back on the demo? >>>>> >>>>> David Jeang >>>>> >>>>> >>>>> >>>>> >>>>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>>> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at scottcain dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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Hi David,
Certainly, any distro should work, but some are more user friendly than others. Ubuntu is great for that. You have an old DBD::Pg installed by the system and so you have to sort out how to upgrade it. Do you have any sysadmin support? Yes, there is clearly a library incompatibility, but debugging that remotely is difficult. Scott Sent from my iPhone On Jul 12, 2012, at 8:46 AM, "Jeang, David - ARS" <[hidden email]> wrote: > My friend doesn't think the problem lies in the distribution, he's more concerned with the error message > > undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. > > In his opinion, it's some sort of C library problem. Is he right? > > David > > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Wednesday, July 11, 2012 3:23 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > That's a little weird, since that is a really old version of DBD::Pg (the RPM repositories I just looked at have DBD::Pg version 2.18). > I'm guessing there is a conflict of some sort between DBD::Pg (really > old) and postgres (presumably not as old). Remind me what linux distribution you're using and is it by any chance possible that you could switch to Ubuntu? There are apt packages available for recent Ubuntu releases that allow installing GBrowse with a simple apt-get command. > > Scott > > > On Wed, Jul 11, 2012 at 3:11 PM, Jeang, David - ARS <[hidden email]> wrote: >> All it gave was this message: >> >> Setting up Install Process >> Package perl-DBD-Pg-1.49-2.el5_3.1.x86_64 already installed and latest >> version Nothing to do >> >> David >> >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Wednesday, July 11, 2012 3:10 PM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> I'm not sure why DBD::Pg failed to compile. If I remember correctly, you're using Fedora, right? Why don't you use yum to install prereqs when possible, like this: >> >> sudo yum install perl-DBD-Pg >> >> (I think that's the command and library name--it's been a while since >> I've used an RPM-based distribution.) >> >> Scott >> >> >> On Wed, Jul 11, 2012 at 2:55 PM, Jeang, David - ARS <[hidden email]> wrote: >>> It was installed by untar and unzipping the downloaded file, then >>> using perl Makefile.PL >>> >>> This is the result when I tried to make test >>> >>> cp testme.tmp.pl blib/lib/DBD/testme.tmp.pl cp lib/Bundle/DBD/Pg.pm >>> blib/lib/Bundle/DBD/Pg.pm cp Pg.pm blib/lib/DBD/Pg.pm >>> /usr/bin/perl5.8.8 -p -e "s/~DRIVER~/Pg/g; s/^do\(/dontdo\(/" >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI/D >>> r >>> iver.xst > Pg.xsi >>> /usr/bin/perl5.8.8 /usr/lib/perl5/vendor_perl/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap Pg.xs > Pg.xsc && mv Pg.xsc Pg.c >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Pg.c >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" dbdimp.c >>> dbdimp.c: In function âpg_st_prepare_statementâ: >>> dbdimp.c:2175: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c: In function âpg_st_executeâ: >>> dbdimp.c:3031: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3041: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3042: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3180: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c: In function âpg_st_fetchâ: >>> dbdimp.c:3408: warning: comparison is always false due to limited range of data type >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" quote.c >>> Pg.h:65: warning: âdbi_get_stateâ defined but not used >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" types.c >>> Pg.h:65: warning: âdbi_get_stateâ defined but not used Running >>> Mkbootstrap for DBD::Pg () chmod 644 Pg.bs rm -f >>> blib/arch/auto/DBD/Pg/Pg.so >>> LD_RUN_PATH="/usr/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Pg.o dbdimp.o quote.o types.o -o blib/arch/auto/DBD/Pg/Pg.so \ >>> -L/usr/lib64 -lpq -lm \ >>> >>> chmod 755 blib/arch/auto/DBD/Pg/Pg.so cp Pg.bs >>> blib/arch/auto/DBD/Pg/Pg.bs chmod 644 blib/arch/auto/DBD/Pg/Pg.bs >>> PGINITDB="/usr/bin/initdb" PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 >>> "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', >>> 'blib/arch')" t/*.t t/00_signature.t .... skipped: Set the environment variable TEST_SIGNATURE to enable this test t/00basic.t ......... 1/3 >>> # Failed test 'use DBD::Pg;' >>> # at t/00basic.t line 14. >>> Bailout called. Further testing stopped: Cannot continue without DBD::Pg >>> # Tried to use 'DBD::Pg'. >>> # Error: Can't load '/home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so' for module DBD::Pg: /home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so: undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. >>> # at (eval 7) line 2. >>> # Compilation failed in require at (eval 7) line 2. >>> # BEGIN failed--compilation aborted at (eval 7) line 2. >>> FAILED--Further testing stopped: Cannot continue without DBD::Pg >>> make: *** [test_dynamic] Error 255 >>> >>> >>> David Jeang >>> -----Original Message----- >>> From: Scott Cain [mailto:[hidden email]] >>> Sent: Tuesday, July 10, 2012 11:09 AM >>> To: Jeang, David - ARS >>> Cc: [hidden email] >>> Subject: Re: Gbrowse keeps rerouting to the demo >>> >>> Hi David, >>> >>> My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? >>> >>> Scott >>> >>> >>> On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: >>>> >>>> >>>> -----Original Message----- >>>> From: Jeang, David - ARS >>>> Sent: Monday, July 09, 2012 11:26 AM >>>> To: 'Scott Cain' >>>> Cc: [hidden email] >>>> Subject: RE: Gbrowse keeps rerouting to the demo >>>> >>>> We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. >>>> However there are still some problems with establishing a link to the chado. >>>> >>>> I got this message when I tried again: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. >>>> >>>> And the error log has these. >>>> >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisati on of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>>> m line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" >>>> via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>>> ine 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisati on of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>>> m line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" >>>> via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>>> ine 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>>> open >>>> database: DBD::Pg initialisation failed: Can't locate object method >>>> "driver" via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>>> line 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>>> open >>>> database: DBD::Pg initialisation failed: Can't locate object method >>>> "driver" via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>>> line 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> >>>> FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. >>>> >>>> David Jeang >>>> >>>> -----Original Message----- >>>> From: Scott Cain [mailto:[hidden email]] >>>> Sent: Tuesday, July 03, 2012 1:18 PM >>>> To: Jeang, David - ARS >>>> Cc: [hidden email] >>>> Subject: Re: Gbrowse keeps rerouting to the demo >>>> >>>> Hi David, >>>> >>>> A few things: >>>> >>>> 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. >>>> >>>> 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. >>>> >>>> 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. >>>> >>>> Scott >>>> >>>> >>>> On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >>>>> This is from the error log. >>>>> >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>>> uninitialized val ue in hash element at >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >>>>> /Bio/Graphics/Browser2/DataSource.pm line 1048. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>>> uninitialized val ue in string eq at >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >>>>> o/Graphics/Browser2/RegionSearch.pm line 392. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >>>>> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >>>>> (@INC contains >>>>> : /opt/ActivePerl-5.12 >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >>>>> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >>>>> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >>>>> l5/5.8.8 .) at (eval 164) line 3. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >>>>> /usr/lib64/perl5/sit >>>>> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >>>>> >>>>> Also, I tried to make a conf for the file I wanted called >>>>> Dmelanogaster.conf And amended Gbrowse conf for it. >>>>> ################################################################### >>>>> # >>>>> # >>>>> # >>>>> ######################### >>>>> # >>>>> # DATASOURCE DEFINITIONS >>>>> # One stanza for each configured data source # >>>>> ################################################################### >>>>> # >>>>> # >>>>> # >>>>> ######################### >>>>> >>>>> [Dmelanogaster] >>>>> description = Fruitfly >>>>> path = Dmelanogaster.conf >>>>> >>>>> And Dmelanogaster.conf: >>>>> ################################# >>>>> # database definitions >>>>> ################################# >>>>> >>>>> [scaffolds:database] >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo >>>>> -pass tripal2demo [annotations:database] >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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We worked to uninstall and update the versions, the DBD::Pg version should be 2.19.2 now, but we're still getting that undefined symbol: GSS_C_NT_HOSTBASED_SERVICE failure. We don't think any of the libraries are missing either.
David -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Thursday, July 12, 2012 11:47 AM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, Certainly, any distro should work, but some are more user friendly than others. Ubuntu is great for that. You have an old DBD::Pg installed by the system and so you have to sort out how to upgrade it. Do you have any sysadmin support? Yes, there is clearly a library incompatibility, but debugging that remotely is difficult. Scott Sent from my iPhone On Jul 12, 2012, at 8:46 AM, "Jeang, David - ARS" <[hidden email]> wrote: > My friend doesn't think the problem lies in the distribution, he's > more concerned with the error message > > undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. > > In his opinion, it's some sort of C library problem. Is he right? > > David > > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Wednesday, July 11, 2012 3:23 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > That's a little weird, since that is a really old version of DBD::Pg (the RPM repositories I just looked at have DBD::Pg version 2.18). > I'm guessing there is a conflict of some sort between DBD::Pg (really > old) and postgres (presumably not as old). Remind me what linux distribution you're using and is it by any chance possible that you could switch to Ubuntu? There are apt packages available for recent Ubuntu releases that allow installing GBrowse with a simple apt-get command. > > Scott > > > On Wed, Jul 11, 2012 at 3:11 PM, Jeang, David - ARS <[hidden email]> wrote: >> All it gave was this message: >> >> Setting up Install Process >> Package perl-DBD-Pg-1.49-2.el5_3.1.x86_64 already installed and >> latest version Nothing to do >> >> David >> >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Wednesday, July 11, 2012 3:10 PM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> I'm not sure why DBD::Pg failed to compile. If I remember correctly, you're using Fedora, right? Why don't you use yum to install prereqs when possible, like this: >> >> sudo yum install perl-DBD-Pg >> >> (I think that's the command and library name--it's been a while since >> I've used an RPM-based distribution.) >> >> Scott >> >> >> On Wed, Jul 11, 2012 at 2:55 PM, Jeang, David - ARS <[hidden email]> wrote: >>> It was installed by untar and unzipping the downloaded file, then >>> using perl Makefile.PL >>> >>> This is the result when I tried to make test >>> >>> cp testme.tmp.pl blib/lib/DBD/testme.tmp.pl cp lib/Bundle/DBD/Pg.pm >>> blib/lib/Bundle/DBD/Pg.pm cp Pg.pm blib/lib/DBD/Pg.pm >>> /usr/bin/perl5.8.8 -p -e "s/~DRIVER~/Pg/g; s/^do\(/dontdo\(/" >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI/ >>> D >>> r >>> iver.xst > Pg.xsi >>> /usr/bin/perl5.8.8 /usr/lib/perl5/vendor_perl/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap Pg.xs > Pg.xsc && mv Pg.xsc Pg.c >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Pg.c >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" dbdimp.c >>> dbdimp.c: In function âpg_st_prepare_statementâ: >>> dbdimp.c:2175: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c: In function âpg_st_executeâ: >>> dbdimp.c:3031: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3041: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3042: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3180: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c: In function âpg_st_fetchâ: >>> dbdimp.c:3408: warning: comparison is always false due to limited range of data type >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" quote.c >>> Pg.h:65: warning: âdbi_get_stateâ defined but not used >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" types.c >>> Pg.h:65: warning: âdbi_get_stateâ defined but not used Running >>> Mkbootstrap for DBD::Pg () chmod 644 Pg.bs rm -f >>> blib/arch/auto/DBD/Pg/Pg.so >>> LD_RUN_PATH="/usr/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Pg.o dbdimp.o quote.o types.o -o blib/arch/auto/DBD/Pg/Pg.so \ >>> -L/usr/lib64 -lpq -lm \ >>> >>> chmod 755 blib/arch/auto/DBD/Pg/Pg.so cp Pg.bs >>> blib/arch/auto/DBD/Pg/Pg.bs chmod 644 blib/arch/auto/DBD/Pg/Pg.bs >>> PGINITDB="/usr/bin/initdb" PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 >>> "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', >>> 'blib/arch')" t/*.t t/00_signature.t .... skipped: Set the environment variable TEST_SIGNATURE to enable this test t/00basic.t ......... 1/3 >>> # Failed test 'use DBD::Pg;' >>> # at t/00basic.t line 14. >>> Bailout called. Further testing stopped: Cannot continue without DBD::Pg >>> # Tried to use 'DBD::Pg'. >>> # Error: Can't load '/home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so' for module DBD::Pg: /home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so: undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. >>> # at (eval 7) line 2. >>> # Compilation failed in require at (eval 7) line 2. >>> # BEGIN failed--compilation aborted at (eval 7) line 2. >>> FAILED--Further testing stopped: Cannot continue without DBD::Pg >>> make: *** [test_dynamic] Error 255 >>> >>> >>> David Jeang >>> -----Original Message----- >>> From: Scott Cain [mailto:[hidden email]] >>> Sent: Tuesday, July 10, 2012 11:09 AM >>> To: Jeang, David - ARS >>> Cc: [hidden email] >>> Subject: Re: Gbrowse keeps rerouting to the demo >>> >>> Hi David, >>> >>> My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? >>> >>> Scott >>> >>> >>> On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: >>>> >>>> >>>> -----Original Message----- >>>> From: Jeang, David - ARS >>>> Sent: Monday, July 09, 2012 11:26 AM >>>> To: 'Scott Cain' >>>> Cc: [hidden email] >>>> Subject: RE: Gbrowse keeps rerouting to the demo >>>> >>>> We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. >>>> However there are still some problems with establishing a link to the chado. >>>> >>>> I got this message when I tried again: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. >>>> >>>> And the error log has these. >>>> >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisati on of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>>> m line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" >>>> via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>>> ine 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisati on of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>>> m line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" >>>> via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>>> ine 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>>> open >>>> database: DBD::Pg initialisation failed: Can't locate object method >>>> "driver" via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>>> line 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>>> open >>>> database: DBD::Pg initialisation failed: Can't locate object method >>>> "driver" via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>>> line 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> >>>> FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. >>>> >>>> David Jeang >>>> >>>> -----Original Message----- >>>> From: Scott Cain [mailto:[hidden email]] >>>> Sent: Tuesday, July 03, 2012 1:18 PM >>>> To: Jeang, David - ARS >>>> Cc: [hidden email] >>>> Subject: Re: Gbrowse keeps rerouting to the demo >>>> >>>> Hi David, >>>> >>>> A few things: >>>> >>>> 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. >>>> >>>> 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. >>>> >>>> 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. >>>> >>>> Scott >>>> >>>> >>>> On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >>>>> This is from the error log. >>>>> >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>>> uninitialized val ue in hash element at >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >>>>> /Bio/Graphics/Browser2/DataSource.pm line 1048. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>>> uninitialized val ue in string eq at >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >>>>> o/Graphics/Browser2/RegionSearch.pm line 392. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >>>>> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >>>>> (@INC contains >>>>> : /opt/ActivePerl-5.12 >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >>>>> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >>>>> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >>>>> l5/5.8.8 .) at (eval 164) line 3. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >>>>> /usr/lib64/perl5/sit >>>>> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >>>>> >>>>> Also, I tried to make a conf for the file I wanted called >>>>> Dmelanogaster.conf And amended Gbrowse conf for it. >>>>> ################################################################## >>>>> # >>>>> # >>>>> # >>>>> # >>>>> ######################### >>>>> # >>>>> # DATASOURCE DEFINITIONS >>>>> # One stanza for each configured data source # >>>>> ################################################################## >>>>> # >>>>> # >>>>> # >>>>> # >>>>> ######################### >>>>> >>>>> [Dmelanogaster] >>>>> description = Fruitfly >>>>> path = Dmelanogaster.conf >>>>> >>>>> And Dmelanogaster.conf: >>>>> ################################# >>>>> # database definitions >>>>> ################################# >>>>> >>>>> [scaffolds:database] >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo >>>>> -pass tripal2demo [annotations:database] >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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In reply to this post by Scott Cain
-----Original Message----- From: Jeang, David - ARS Sent: Thursday, July 12, 2012 11:55 AM To: 'Scott Cain' Cc: [hidden email] Subject: RE: Gbrowse keeps rerouting to the demo We worked to uninstall and update the versions, the DBD::Pg version should be 2.19.2 now, but we're still getting that undefined symbol: GSS_C_NT_HOSTBASED_SERVICE failure. We don't think any of the libraries are missing either. David -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Thursday, July 12, 2012 11:47 AM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, Certainly, any distro should work, but some are more user friendly than others. Ubuntu is great for that. You have an old DBD::Pg installed by the system and so you have to sort out how to upgrade it. Do you have any sysadmin support? Yes, there is clearly a library incompatibility, but debugging that remotely is difficult. Scott Sent from my iPhone On Jul 12, 2012, at 8:46 AM, "Jeang, David - ARS" <[hidden email]> wrote: > My friend doesn't think the problem lies in the distribution, he's > more concerned with the error message > > undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. > > In his opinion, it's some sort of C library problem. Is he right? > > David > > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Wednesday, July 11, 2012 3:23 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > That's a little weird, since that is a really old version of DBD::Pg (the RPM repositories I just looked at have DBD::Pg version 2.18). > I'm guessing there is a conflict of some sort between DBD::Pg (really > old) and postgres (presumably not as old). Remind me what linux distribution you're using and is it by any chance possible that you could switch to Ubuntu? There are apt packages available for recent Ubuntu releases that allow installing GBrowse with a simple apt-get command. > > Scott > > > On Wed, Jul 11, 2012 at 3:11 PM, Jeang, David - ARS <[hidden email]> wrote: >> All it gave was this message: >> >> Setting up Install Process >> Package perl-DBD-Pg-1.49-2.el5_3.1.x86_64 already installed and >> latest version Nothing to do >> >> David >> >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Wednesday, July 11, 2012 3:10 PM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> I'm not sure why DBD::Pg failed to compile. If I remember correctly, you're using Fedora, right? Why don't you use yum to install prereqs when possible, like this: >> >> sudo yum install perl-DBD-Pg >> >> (I think that's the command and library name--it's been a while since >> I've used an RPM-based distribution.) >> >> Scott >> >> >> On Wed, Jul 11, 2012 at 2:55 PM, Jeang, David - ARS <[hidden email]> wrote: >>> It was installed by untar and unzipping the downloaded file, then >>> using perl Makefile.PL >>> >>> This is the result when I tried to make test >>> >>> cp testme.tmp.pl blib/lib/DBD/testme.tmp.pl cp lib/Bundle/DBD/Pg.pm >>> blib/lib/Bundle/DBD/Pg.pm cp Pg.pm blib/lib/DBD/Pg.pm >>> /usr/bin/perl5.8.8 -p -e "s/~DRIVER~/Pg/g; s/^do\(/dontdo\(/" >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI/ >>> D >>> r >>> iver.xst > Pg.xsi >>> /usr/bin/perl5.8.8 /usr/lib/perl5/vendor_perl/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap Pg.xs > Pg.xsc && mv Pg.xsc Pg.c >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Pg.c >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" dbdimp.c >>> dbdimp.c: In function âpg_st_prepare_statementâ: >>> dbdimp.c:2175: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c: In function âpg_st_executeâ: >>> dbdimp.c:3031: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3041: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3042: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3180: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c: In function âpg_st_fetchâ: >>> dbdimp.c:3408: warning: comparison is always false due to limited range of data type >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" quote.c >>> Pg.h:65: warning: âdbi_get_stateâ defined but not used >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" types.c >>> Pg.h:65: warning: âdbi_get_stateâ defined but not used Running >>> Mkbootstrap for DBD::Pg () chmod 644 Pg.bs rm -f >>> blib/arch/auto/DBD/Pg/Pg.so >>> LD_RUN_PATH="/usr/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Pg.o dbdimp.o quote.o types.o -o blib/arch/auto/DBD/Pg/Pg.so \ >>> -L/usr/lib64 -lpq -lm \ >>> >>> chmod 755 blib/arch/auto/DBD/Pg/Pg.so cp Pg.bs >>> blib/arch/auto/DBD/Pg/Pg.bs chmod 644 blib/arch/auto/DBD/Pg/Pg.bs >>> PGINITDB="/usr/bin/initdb" PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 >>> "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', >>> 'blib/arch')" t/*.t t/00_signature.t .... skipped: Set the environment variable TEST_SIGNATURE to enable this test t/00basic.t ......... 1/3 >>> # Failed test 'use DBD::Pg;' >>> # at t/00basic.t line 14. >>> Bailout called. Further testing stopped: Cannot continue without DBD::Pg >>> # Tried to use 'DBD::Pg'. >>> # Error: Can't load '/home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so' for module DBD::Pg: /home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so: undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. >>> # at (eval 7) line 2. >>> # Compilation failed in require at (eval 7) line 2. >>> # BEGIN failed--compilation aborted at (eval 7) line 2. >>> FAILED--Further testing stopped: Cannot continue without DBD::Pg >>> make: *** [test_dynamic] Error 255 >>> >>> >>> David Jeang >>> -----Original Message----- >>> From: Scott Cain [mailto:[hidden email]] >>> Sent: Tuesday, July 10, 2012 11:09 AM >>> To: Jeang, David - ARS >>> Cc: [hidden email] >>> Subject: Re: Gbrowse keeps rerouting to the demo >>> >>> Hi David, >>> >>> My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? >>> >>> Scott >>> >>> >>> On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: >>>> >>>> >>>> -----Original Message----- >>>> From: Jeang, David - ARS >>>> Sent: Monday, July 09, 2012 11:26 AM >>>> To: 'Scott Cain' >>>> Cc: [hidden email] >>>> Subject: RE: Gbrowse keeps rerouting to the demo >>>> >>>> We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. >>>> However there are still some problems with establishing a link to the chado. >>>> >>>> I got this message when I tried again: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. >>>> >>>> And the error log has these. >>>> >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisati on of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>>> m line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" >>>> via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>>> ine 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisati on of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>>> m line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" >>>> via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>>> ine 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>>> open >>>> database: DBD::Pg initialisation failed: Can't locate object method >>>> "driver" via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>>> line 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>>> open >>>> database: DBD::Pg initialisation failed: Can't locate object method >>>> "driver" via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>>> line 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> >>>> FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. >>>> >>>> David Jeang >>>> >>>> -----Original Message----- >>>> From: Scott Cain [mailto:[hidden email]] >>>> Sent: Tuesday, July 03, 2012 1:18 PM >>>> To: Jeang, David - ARS >>>> Cc: [hidden email] >>>> Subject: Re: Gbrowse keeps rerouting to the demo >>>> >>>> Hi David, >>>> >>>> A few things: >>>> >>>> 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. >>>> >>>> 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. >>>> >>>> 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. >>>> >>>> Scott >>>> >>>> >>>> On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >>>>> This is from the error log. >>>>> >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>>> uninitialized val ue in hash element at >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >>>>> /Bio/Graphics/Browser2/DataSource.pm line 1048. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>>> uninitialized val ue in string eq at >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >>>>> o/Graphics/Browser2/RegionSearch.pm line 392. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >>>>> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >>>>> (@INC contains >>>>> : /opt/ActivePerl-5.12 >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >>>>> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >>>>> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >>>>> l5/5.8.8 .) at (eval 164) line 3. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >>>>> /usr/lib64/perl5/sit >>>>> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >>>>> >>>>> Also, I tried to make a conf for the file I wanted called >>>>> Dmelanogaster.conf And amended Gbrowse conf for it. >>>>> ################################################################## >>>>> # >>>>> # >>>>> # >>>>> # >>>>> ######################### >>>>> # >>>>> # DATASOURCE DEFINITIONS >>>>> # One stanza for each configured data source # >>>>> ################################################################## >>>>> # >>>>> # >>>>> # >>>>> # >>>>> ######################### >>>>> >>>>> [Dmelanogaster] >>>>> description = Fruitfly >>>>> path = Dmelanogaster.conf >>>>> >>>>> And Dmelanogaster.conf: >>>>> ################################# >>>>> # database definitions >>>>> ################################# >>>>> >>>>> [scaffolds:database] >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo >>>>> -pass tripal2demo [annotations:database] >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Gbrowse keeps rerouting to the demo
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In reply to this post by Scott Cain
I've been working with the DBD:PG for a while now, and think it's ok, but I'm getting internal server errors when I go to http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/Chado again.
Here's the error log [Mon Jul 16 09:42:27 2012] [error] [client 66.249.72.81] Couldn't get session at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser/PageSettings.pm line 19. [Mon Jul 16 09:42:27 2012] [error] [client 66.249.72.81] Premature end of script headers: gbrowse [Mon Jul 16 09:42:39 2012] [error] [client 66.249.72.81] Couldn't get session at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser/PageSettings.pm line 19. [Mon Jul 16 09:42:39 2012] [error] [client 66.249.72.81] Premature end of script headers: gbrowse David Jeang -----Original Message----- From: Scott Cain [mailto:[hidden email]] Sent: Thursday, July 12, 2012 11:47 AM To: Jeang, David - ARS Cc: [hidden email] Subject: Re: Gbrowse keeps rerouting to the demo Hi David, Certainly, any distro should work, but some are more user friendly than others. Ubuntu is great for that. You have an old DBD::Pg installed by the system and so you have to sort out how to upgrade it. Do you have any sysadmin support? Yes, there is clearly a library incompatibility, but debugging that remotely is difficult. Scott Sent from my iPhone On Jul 12, 2012, at 8:46 AM, "Jeang, David - ARS" <[hidden email]> wrote: > My friend doesn't think the problem lies in the distribution, he's > more concerned with the error message > > undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. > > In his opinion, it's some sort of C library problem. Is he right? > > David > > -----Original Message----- > From: Scott Cain [mailto:[hidden email]] > Sent: Wednesday, July 11, 2012 3:23 PM > To: Jeang, David - ARS > Cc: [hidden email] > Subject: Re: Gbrowse keeps rerouting to the demo > > Hi David, > > That's a little weird, since that is a really old version of DBD::Pg (the RPM repositories I just looked at have DBD::Pg version 2.18). > I'm guessing there is a conflict of some sort between DBD::Pg (really > old) and postgres (presumably not as old). Remind me what linux distribution you're using and is it by any chance possible that you could switch to Ubuntu? There are apt packages available for recent Ubuntu releases that allow installing GBrowse with a simple apt-get command. > > Scott > > > On Wed, Jul 11, 2012 at 3:11 PM, Jeang, David - ARS <[hidden email]> wrote: >> All it gave was this message: >> >> Setting up Install Process >> Package perl-DBD-Pg-1.49-2.el5_3.1.x86_64 already installed and >> latest version Nothing to do >> >> David >> >> -----Original Message----- >> From: Scott Cain [mailto:[hidden email]] >> Sent: Wednesday, July 11, 2012 3:10 PM >> To: Jeang, David - ARS >> Cc: [hidden email] >> Subject: Re: Gbrowse keeps rerouting to the demo >> >> Hi David, >> >> I'm not sure why DBD::Pg failed to compile. If I remember correctly, you're using Fedora, right? Why don't you use yum to install prereqs when possible, like this: >> >> sudo yum install perl-DBD-Pg >> >> (I think that's the command and library name--it's been a while since >> I've used an RPM-based distribution.) >> >> Scott >> >> >> On Wed, Jul 11, 2012 at 2:55 PM, Jeang, David - ARS <[hidden email]> wrote: >>> It was installed by untar and unzipping the downloaded file, then >>> using perl Makefile.PL >>> >>> This is the result when I tried to make test >>> >>> cp testme.tmp.pl blib/lib/DBD/testme.tmp.pl cp lib/Bundle/DBD/Pg.pm >>> blib/lib/Bundle/DBD/Pg.pm cp Pg.pm blib/lib/DBD/Pg.pm >>> /usr/bin/perl5.8.8 -p -e "s/~DRIVER~/Pg/g; s/^do\(/dontdo\(/" >>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI/ >>> D >>> r >>> iver.xst > Pg.xsi >>> /usr/bin/perl5.8.8 /usr/lib/perl5/vendor_perl/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap Pg.xs > Pg.xsc && mv Pg.xsc Pg.c >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" Pg.c >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" dbdimp.c >>> dbdimp.c: In function âpg_st_prepare_statementâ: >>> dbdimp.c:2175: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c: In function âpg_st_executeâ: >>> dbdimp.c:3031: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3041: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3042: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c:3180: warning: comparison is always false due to limited >>> range of data type >>> dbdimp.c: In function âpg_st_fetchâ: >>> dbdimp.c:3408: warning: comparison is always false due to limited range of data type >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" quote.c >>> Pg.h:65: warning: âdbi_get_stateâ defined but not used >>> gcc -c -I/usr/include -I/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/DBI -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -DPGLIBVERSION=80412 -DPGDEFPORT=5432 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc -DVERSION=\"2.19.2\" -DXS_VERSION=\"2.19.2\" -fPIC "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" types.c >>> Pg.h:65: warning: âdbi_get_stateâ defined but not used Running >>> Mkbootstrap for DBD::Pg () chmod 644 Pg.bs rm -f >>> blib/arch/auto/DBD/Pg/Pg.so >>> LD_RUN_PATH="/usr/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Pg.o dbdimp.o quote.o types.o -o blib/arch/auto/DBD/Pg/Pg.so \ >>> -L/usr/lib64 -lpq -lm \ >>> >>> chmod 755 blib/arch/auto/DBD/Pg/Pg.so cp Pg.bs >>> blib/arch/auto/DBD/Pg/Pg.bs chmod 644 blib/arch/auto/DBD/Pg/Pg.bs >>> PGINITDB="/usr/bin/initdb" PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 >>> "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', >>> 'blib/arch')" t/*.t t/00_signature.t .... skipped: Set the environment variable TEST_SIGNATURE to enable this test t/00basic.t ......... 1/3 >>> # Failed test 'use DBD::Pg;' >>> # at t/00basic.t line 14. >>> Bailout called. Further testing stopped: Cannot continue without DBD::Pg >>> # Tried to use 'DBD::Pg'. >>> # Error: Can't load '/home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so' for module DBD::Pg: /home/djeang/DBD-Pg-2.19.2/blib/arch/auto/DBD/Pg/Pg.so: undefined symbol: GSS_C_NT_HOSTBASED_SERVICE at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230. >>> # at (eval 7) line 2. >>> # Compilation failed in require at (eval 7) line 2. >>> # BEGIN failed--compilation aborted at (eval 7) line 2. >>> FAILED--Further testing stopped: Cannot continue without DBD::Pg >>> make: *** [test_dynamic] Error 255 >>> >>> >>> David Jeang >>> -----Original Message----- >>> From: Scott Cain [mailto:[hidden email]] >>> Sent: Tuesday, July 10, 2012 11:09 AM >>> To: Jeang, David - ARS >>> Cc: [hidden email] >>> Subject: Re: Gbrowse keeps rerouting to the demo >>> >>> Hi David, >>> >>> My guess is that something went wrong with the DBD::Pg installation; how did you install it and where there any errors? Did it pass all of the tests? Did you "force" the installation? >>> >>> Scott >>> >>> >>> On Tue, Jul 10, 2012 at 10:54 AM, Jeang, David - ARS <[hidden email]> wrote: >>>> >>>> >>>> -----Original Message----- >>>> From: Jeang, David - ARS >>>> Sent: Monday, July 09, 2012 11:26 AM >>>> To: 'Scott Cain' >>>> Cc: [hidden email] >>>> Subject: RE: Gbrowse keeps rerouting to the demo >>>> >>>> We've managed to work through the perl libraries mix up, apparently the stuff was being installed on the one the Apache wasn't using. >>>> However there are still some problems with establishing a link to the chado. >>>> >>>> I got this message when I tried again: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" via package "DBD::Pg". Perhaps the capitalisation of DBD 'Pg' isn't right. at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234. >>>> >>>> And the error log has these. >>>> >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisati on of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>>> m line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" >>>> via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>>> ine 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.na l.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisati on of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.p >>>> m line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not open database: >>>> DBD::Pg initialisation failed: Can't locate object method "driver" >>>> via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm l >>>> ine 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>>> open >>>> database: DBD::Pg initialisation failed: Can't locate object method >>>> "driver" via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>>> line 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Could not >>>> open >>>> database: DBD::Pg initialisation failed: Can't locate object method >>>> "driver" via package "DBD::Pg" at >>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm >>>> line 808., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] , referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> [Mon Jul 09 11:22:57 2012] [error] [client 10.12.20.67] Perhaps the >>>> capitalisation of DBD 'Pg' isn't right. at >>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234., referer: >>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse/yeast/ >>>> >>>> FYI, the DBD it's asking for was installed when it asked for it, but still got the message afterwards. >>>> >>>> David Jeang >>>> >>>> -----Original Message----- >>>> From: Scott Cain [mailto:[hidden email]] >>>> Sent: Tuesday, July 03, 2012 1:18 PM >>>> To: Jeang, David - ARS >>>> Cc: [hidden email] >>>> Subject: Re: Gbrowse keeps rerouting to the demo >>>> >>>> Hi David, >>>> >>>> A few things: >>>> >>>> 1. Jason's message from a few days ago about mixing perl libraries was spot on and I should have thought of that first. You need to pick one perl and use it exclusively. >>>> >>>> 2. Which ever perl is executing the GBrowse script can't find Bio::DB::Das::Chado. It's not going to work without it. BDDChado is a separate install that you can get from cpan. >>>> >>>> 3. As you correctly surmised, you only need one database connection stanza per database. The example yeast file has two stanzas (pointing to two different locations) to provide an example of how to do it. >>>> >>>> Scott >>>> >>>> >>>> On Tue, Jul 3, 2012 at 12:57 PM, Jeang, David - ARS <[hidden email]> wrote: >>>>> This is from the error log. >>>>> >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>>> uninitialized val ue in hash element at >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi >>>>> /Bio/Graphics/Browser2/DataSource.pm line 1048. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Use of >>>>> uninitialized val ue in string eq at >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi >>>>> o/Graphics/Browser2/RegionSearch.pm line 392. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] Could not open database: >>>>> Can't locate Bio/DB/SeqFeature/Store/Bio/DB/Das/Chado.pm in @INC >>>>> (@INC contains >>>>> : /opt/ActivePerl-5.12 >>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult >>>>> i /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl >>>>> /usr/lib64/perl5/vendo r_perl/5.8.8/x86_64-linux-thread-multi >>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib /perl5/vendor_perl >>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/per >>>>> l5/5.8.8 .) at (eval 164) line 3. >>>>> [Mon Jul 02 16:06:10 2012] [error] [client 10.12.20.15] at >>>>> /usr/lib64/perl5/sit >>>>> e_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataBase.pm line 44 . >>>>> >>>>> Also, I tried to make a conf for the file I wanted called >>>>> Dmelanogaster.conf And amended Gbrowse conf for it. >>>>> ################################################################## >>>>> # >>>>> # >>>>> # >>>>> # >>>>> ######################### >>>>> # >>>>> # DATASOURCE DEFINITIONS >>>>> # One stanza for each configured data source # >>>>> ################################################################## >>>>> # >>>>> # >>>>> # >>>>> # >>>>> ######################### >>>>> >>>>> [Dmelanogaster] >>>>> description = Fruitfly >>>>> path = Dmelanogaster.conf >>>>> >>>>> And Dmelanogaster.conf: >>>>> ################################# >>>>> # database definitions >>>>> ################################# >>>>> >>>>> [scaffolds:database] >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo >>>>> -pass tripal2demo [annotations:database] >>>>> db_adaptor = Bio::DB::Das::Chado >>>>> db_args = -adaptor Bio::DB::Das::Chado >>>>> -dsn dbi:Pg:dbname=tripal;host=localhost >>>>> -user tripaldemo This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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