rbuels
commented
11 years ago Maybe you are visiting the wrong URL in your browser?
Could you paste some of the messages in the error log?
Closed amitMTCC closed 11 years ago
rbuels
commented
11 years ago Maybe you are visiting the wrong URL in your browser?
Could you paste some of the messages in the error log?
amitMTCC
commented
11 years ago thanks for the reply. I am attaching 6 files:
thanks again....
setup.sh terminal output:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
...$sudo ./setup.sh
Installing Perl prerequisites ... done.
Formatting Volvox example data ... done. To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.
Formatting Yeast example data ... done. To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.
Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.
Building and installing legacy BAM support (bam-to-json.pl, samtools, and Bio::DB::Sam) ... done.
setup.log::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
============== System information ====
Written by John Gilmore and Jay Fenlason. You have /usr/bin/unzip Checking if you have ExtUtils::MakeMaker 6.31 ... Yes (6.68) Checking if you have ExtUtils::Install 1.46 ... Yes (1.54) --> Working on . Entering /var/www/JBrowse-1.9.5 Configuring /var/www/JBrowse-1.9.5 ... Running Makefile.PL
Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] Checking prerequisites... recommends: * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene) * Optional prerequisite Class::AutoClass is not installed (wanted for creating objects, used by Bio::Graph::SimpleGraph, Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) * Optional prerequisite PostScript::TextBlock is not installed (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) * Optional prerequisite XML::DOM::XPath is not installed (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) * Optional prerequisite XML::SAX::Writer is not installed (wanted for writing xml, used by Bio::SeqIO::tigrxml) * Optional prerequisite XML::Writer is not installed (wanted for parsing and writing xml, used by Bio::SeqIO::agave, Bio::SeqIO::game::gameWriter, Bio::SeqIO::chadoxml, Bio::SeqIO::tinyseq, Bio::Variation::IO::xml and Bio::SearchIO::Writer::BSMLResultWriter) * Could not connect to test database
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation
Checking features: BioDBSeqFeature_mysql....disabled BioDBGFF.................enabled BioDBSeqFeature_BDB......enabled
Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts
Do you want to run the BioDBGFF live database tests? y/n [n] Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Artistic_1_0' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2] at /var/www/JBrowse-1.9.5/extlib/lib/perl5/Module/Build/Base.pm line 4581.
Could not create MYMETA files
Creating new 'Build' script for 'bioperl' version '1.005002102' Can't parse version 'dev' Can't parse version 'dev' Writing Makefile for JBrowse Writing MYMETA.yml and MYMETA.json OK Checking dependencies from MYMETA.json ... Checking if you have Test::More 0 ... Yes (0.98) Checking if you have Test::Warn 0 ... Yes (0.24) Checking if you have Capture::Tiny 0 ... Yes (0.22) Checking if you have DBD::SQLite 0 ... Yes (1.39) Checking if you have Pod::Usage 0 ... Yes (1.33) Checking if you have Storable 0 ... Yes (2.15) Checking if you have JSON::XS 0 ... Yes (2.34) Checking if you have PerlIO::gzip 0 ... Yes (0.18) Checking if you have List::Util 0 ... Yes (1.27) Checking if you have File::Path 2 ... Yes (2.09) Checking if you have Digest::Crc32 0 ... Yes (0.01) Checking if you have local::lib 0 ... Yes (1.008010) Checking if you have DBI 0 ... Yes (1.601) Checking if you have Bio::FeatureIO 0 ... Yes (undef) Checking if you have warnings 0 ... Yes (1.05) Checking if you have base 0 ... Yes (2.07) Checking if you have Getopt::Long 0 ... Yes (2.35) Checking if you have IO::File 0 ... Yes (1.13) Checking if you have Bio::Index::Fasta 0 ... Yes (undef) Checking if you have Data::Dumper 0 ... Yes (2.121_08) Checking if you have Bio::Root::Version 1.006000 ... Yes (1.006901) Checking if you have vars 0 ... Yes (1.01) Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef) Checking if you have strict 0 ... Yes (1.03) Checking if you have File::Temp 0 ... Yes (0.22) Checking if you have Scalar::Util 0 ... Yes (1.27) Checking if you have FindBin 0 ... Yes (1.47) Checking if you have Fcntl 0 ... Yes (1.05) Checking if you have File::Spec 0 ... Yes (3.40) Checking if you have Heap::Simple 0 ... Yes (0.13) Checking if you have Heap::Simple::XS 0 ... Yes (0.10) Checking if you have POSIX 0 ... Yes (1.09) Checking if you have Devel::Size 0 ... Yes (0.79) Checking if you have File::Spec::Functions 0 ... Yes (3.40) Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef) Checking if you have Bio::GFF3::LowLevel::Parser 1.4 ... Yes (1.5) Checking if you have Hash::Merge 0 ... Yes (0.12) Checking if you have constant 0 ... Yes (1.05) Checking if you have GD::Image 0 ... Yes (2.38) Checking if you have Exporter 0 ... Yes (5.58) Checking if you have Bio::OntologyIO 0 ... Yes (undef) Checking if you have Carp 0 ... Yes (1.26) Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (undef) Checking if you have File::Basename 0 ... Yes (2.74) Checking if you have JSON 2 ... Yes (2.59) Checking if you have Cache::Ref::FIFO 0 ... Yes (0.04) Checking if you have Cwd 0 ... Yes (3.40) <== Installed dependencies for .. Finishing.
Written by John Gilmore and Jay Fenlason. You have /usr/bin/unzip Checking if you have ExtUtils::MakeMaker 6.31 ... Yes (6.68) Checking if you have ExtUtils::Install 1.46 ... Yes (1.54) --> Working on . Entering /var/www/JBrowse-1.9.5 Configuring /var/www/JBrowse-1.9.5 ... Running Makefile.PL
Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] Checking prerequisites... recommends: * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene) * Optional prerequisite Class::AutoClass is not installed (wanted for creating objects, used by Bio::Graph::SimpleGraph, Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) * Optional prerequisite PostScript::TextBlock is not installed (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) * Optional prerequisite XML::DOM::XPath is not installed (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) * Optional prerequisite XML::SAX::Writer is not installed (wanted for writing xml, used by Bio::SeqIO::tigrxml) * Optional prerequisite XML::Writer is not installed (wanted for parsing and writing xml, used by Bio::SeqIO::agave, Bio::SeqIO::game::gameWriter, Bio::SeqIO::chadoxml, Bio::SeqIO::tinyseq, Bio::Variation::IO::xml and Bio::SearchIO::Writer::BSMLResultWriter) * Could not connect to test database
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation
Checking features: BioDBGFF.................enabled BioDBSeqFeature_mysql....disabled BioDBSeqFeature_BDB......enabled
Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts
Do you want to run the BioDBGFF live database tests? y/n [n] Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Artistic_1_0' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2] at /var/www/JBrowse-1.9.5/extlib/lib/perl5/Module/Build/Base.pm line 4581.
Could not create MYMETA files
Creating new 'Build' script for 'bioperl' version '1.005002102' Can't parse version 'dev' Can't parse version 'dev' Writing Makefile for JBrowse Writing MYMETA.yml and MYMETA.json OK Checking dependencies from MYMETA.json ... Checking if you have Test::More 0 ... Yes (0.98) Checking if you have Test::Warn 0 ... Yes (0.24) Checking if you have Capture::Tiny 0 ... Yes (0.22) Checking if you have DBD::SQLite 0 ... Yes (1.39) Checking if you have Pod::Usage 0 ... Yes (1.33) Checking if you have Storable 0 ... Yes (2.15) Checking if you have JSON::XS 0 ... Yes (2.34) Checking if you have PerlIO::gzip 0 ... Yes (0.18) Checking if you have List::Util 0 ... Yes (1.27) Checking if you have File::Path 2 ... Yes (2.09) Checking if you have Digest::Crc32 0 ... Yes (0.01) Checking if you have local::lib 0 ... Yes (1.008010) Checking if you have DBI 0 ... Yes (1.601) Checking if you have Bio::FeatureIO 0 ... Yes (undef) Checking if you have warnings 0 ... Yes (1.05) Checking if you have base 0 ... Yes (2.07) Checking if you have Getopt::Long 0 ... Yes (2.35) Checking if you have IO::File 0 ... Yes (1.13) Checking if you have Bio::Index::Fasta 0 ... Yes (undef) Checking if you have Data::Dumper 0 ... Yes (2.121_08) Checking if you have Bio::Root::Version 1.006000 ... Yes (1.006901) Checking if you have vars 0 ... Yes (1.01) Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef) Checking if you have strict 0 ... Yes (1.03) Checking if you have File::Temp 0 ... Yes (0.22) Checking if you have Scalar::Util 0 ... Yes (1.27) Checking if you have FindBin 0 ... Yes (1.47) Checking if you have Fcntl 0 ... Yes (1.05) Checking if you have File::Spec 0 ... Yes (3.40) Checking if you have Heap::Simple 0 ... Yes (0.13) Checking if you have Heap::Simple::XS 0 ... Yes (0.10) Checking if you have POSIX 0 ... Yes (1.09) Checking if you have Devel::Size 0 ... Yes (0.79) Checking if you have File::Spec::Functions 0 ... Yes (3.40) Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef) Checking if you have Bio::GFF3::LowLevel::Parser 1.4 ... Yes (1.5) Checking if you have Hash::Merge 0 ... Yes (0.12) Checking if you have constant 0 ... Yes (1.05) Checking if you have GD::Image 0 ... Yes (2.38) Checking if you have Exporter 0 ... Yes (5.58) Checking if you have Bio::OntologyIO 0 ... Yes (undef) Checking if you have Carp 0 ... Yes (1.26) Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (undef) Checking if you have File::Basename 0 ... Yes (2.74) Checking if you have JSON 2 ... Yes (2.59) Checking if you have Cache::Ref::FIFO 0 ... Yes (0.04) Checking if you have Cwd 0 ... Yes (3.40) <== Installed dependencies for .. Finishing.
Written by John Gilmore and Jay Fenlason. You have /usr/bin/unzip Checking if you have ExtUtils::MakeMaker 6.31 ... Yes (6.68) Checking if you have ExtUtils::Install 1.46 ... Yes (1.54) --> Working on . Entering /var/www/JBrowse-1.9.5 Configuring /var/www/JBrowse-1.9.5 ... Running Makefile.PL
Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Encountered CODE ref, using dummy placeholder at /usr/lib/perl/5.8.8/Data/Dumper.pm line 179. Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] Checking prerequisites... recommends: * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene) * Optional prerequisite Class::AutoClass is not installed (wanted for creating objects, used by Bio::Graph::SimpleGraph, Bio::Graph::SimpleGraph::Traversal and Bio::Graph::ProteinGraph) * Optional prerequisite PostScript::TextBlock is not installed (wanted for EPS output, used by Bio::Tree::Draw::Cladogram) * Optional prerequisite XML::DOM::XPath is not installed (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) * Optional prerequisite XML::SAX::Writer is not installed (wanted for writing xml, used by Bio::SeqIO::tigrxml) * Optional prerequisite XML::Writer is not installed (wanted for parsing and writing xml, used by Bio::SeqIO::agave, Bio::SeqIO::game::gameWriter, Bio::SeqIO::chadoxml, Bio::SeqIO::tinyseq, Bio::Variation::IO::xml and Bio::SearchIO::Writer::BSMLResultWriter) * Could not connect to test database
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation
Checking features: BioDBSeqFeature_mysql....disabled BioDBGFF.................enabled BioDBSeqFeature_BDB......enabled
Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts
Do you want to run the BioDBGFF live database tests? y/n [n] Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Artistic_1_0' for 'license' does not have a URL scheme (resources -> license) [Validation: 1.2] at /var/www/JBrowse-1.9.5/extlib/lib/perl5/Module/Build/Base.pm line 4581.
Could not create MYMETA files
Creating new 'Build' script for 'bioperl' version '1.005002102' Can't parse version 'dev' Can't parse version 'dev' Writing Makefile for JBrowse Writing MYMETA.yml and MYMETA.json OK Checking dependencies from MYMETA.json ... Checking if you have Test::More 0 ... Yes (0.98) Checking if you have Test::Warn 0 ... Yes (0.24) Checking if you have Capture::Tiny 0 ... Yes (0.22) Checking if you have DBD::SQLite 0 ... Yes (1.39) Checking if you have Pod::Usage 0 ... Yes (1.33) Checking if you have Storable 0 ... Yes (2.15) Checking if you have JSON::XS 0 ... Yes (2.34) Checking if you have PerlIO::gzip 0 ... Yes (0.18) Checking if you have List::Util 0 ... Yes (1.27) Checking if you have File::Path 2 ... Yes (2.09) Checking if you have Digest::Crc32 0 ... Yes (0.01) Checking if you have local::lib 0 ... Yes (1.008010) Checking if you have DBI 0 ... Yes (1.601) Checking if you have Bio::FeatureIO 0 ... Yes (undef) Checking if you have warnings 0 ... Yes (1.05) Checking if you have base 0 ... Yes (2.07) Checking if you have Getopt::Long 0 ... Yes (2.35) Checking if you have IO::File 0 ... Yes (1.13) Checking if you have Bio::Index::Fasta 0 ... Yes (undef) Checking if you have Data::Dumper 0 ... Yes (2.121_08) Checking if you have Bio::Root::Version 1.006000 ... Yes (1.006901) Checking if you have vars 0 ... Yes (1.01) Checking if you have Bio::Annotation::SimpleValue 0 ... Yes (undef) Checking if you have strict 0 ... Yes (1.03) Checking if you have File::Temp 0 ... Yes (0.22) Checking if you have Scalar::Util 0 ... Yes (1.27) Checking if you have FindBin 0 ... Yes (1.47) Checking if you have Fcntl 0 ... Yes (1.05) Checking if you have File::Spec 0 ... Yes (3.40) Checking if you have Heap::Simple 0 ... Yes (0.13) Checking if you have Heap::Simple::XS 0 ... Yes (0.10) Checking if you have POSIX 0 ... Yes (1.09) Checking if you have Devel::Size 0 ... Yes (0.79) Checking if you have File::Spec::Functions 0 ... Yes (3.40) Checking if you have Bio::SeqFeature::Lite 0 ... Yes (undef) Checking if you have Bio::GFF3::LowLevel::Parser 1.4 ... Yes (1.5) Checking if you have Hash::Merge 0 ... Yes (0.12) Checking if you have constant 0 ... Yes (1.05) Checking if you have GD::Image 0 ... Yes (2.38) Checking if you have Exporter 0 ... Yes (5.58) Checking if you have Bio::OntologyIO 0 ... Yes (undef) Checking if you have Carp 0 ... Yes (1.26) Checking if you have Bio::SeqFeature::Annotated 0 ... Yes (undef) Checking if you have File::Basename 0 ... Yes (2.74) Checking if you have JSON 2 ... Yes (2.59) Checking if you have Cache::Ref::FIFO 0 ... Yes (0.04) Checking if you have Cwd 0 ... Yes (3.40) <== Installed dependencies for .. Finishing.
working on refseq ctgA working on track ExampleFeatures mergedTrackCfg: $VAR1 = { 'feature' => [ 'remark' ], 'autocomplete' => 'all', 'track' => 'ExampleFeatures', 'style' => { 'className' => 'feature2' }, 'compress' => 0, 'key' => 'Example Features' }; searching for features of type: remark working on track NameTest mergedTrackCfg: $VAR1 = { 'feature' => [ 'protein_coding_primary_transcript', 'polypeptide' ], 'autocomplete' => 'all', 'track' => 'NameTest', 'style' => { 'className' => 'feature2' }, 'compress' => 0, 'key' => 'Name test track has a really long track label' }; searching for features of type: protein_coding_primary_transcript, polypeptide working on track snps mergedTrackCfg: $VAR1 = { 'feature' => [ 'SNP' ], 'autocomplete' => 'all', 'track' => 'snps', 'style' => { 'className' => 'triangle hgred' }, 'compress' => 0, 'key' => 'Test SNPs' }; searching for features of type: SNP working on track Motifs mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'Motifs', 'style' => { 'className' => 'feature3', 'label' => 'function(feature) { return feature.get(\'Name\')+\' (via JS callback)\' }', 'description' => 'function(feature) { return feature.get(\'Name\')+\': \'+feature.get(\'Note\'); }' }, 'description' => 1, 'key' => 'Example motifs', 'feature' => [ 'polypeptide_domain' ], 'compress' => 0 }; searching for features of type: polypeptide_domain working on track malformed_alignments mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'malformed_alignments', 'style' => { 'className' => 'feature4' }, 'menuTemplate' => [ { 'children' => [ { 'children' => [ { 'iconClass' => 'dijitIconBookmark', 'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}', 'action' => 'newWindow', 'label' => 'Query trin for {name}' }, { 'iconClass' => 'dijitIconSearch', 'url' => 'http://example.com/{name}-{start}-{end}', 'label' => 'Query example.com for {name}' } ], 'label' => 'Check gene on databases' }, { 'label' => '2nd child of demo' }, { 'label' => '3rd child: this is a track' } ], 'label' => 'Item with submenu' }, { 'iconClass' => 'dijitIconDatabase', 'url' => 'http://www.example.com?featurename={name}', 'action' => 'iframeDialog', 'title' => 'The magnificent example.com (feature {name})', 'label' => 'Open example.com in an iframe popup' }, { 'iconClass' => 'dijitIconDatabase', 'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}', 'action' => 'xhrDialog', 'title' => 'function(track,feature,div) { return \'Random XHR HTML \'+Math.random()+\' title!\'; }', 'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'content' => 'function(track,feature,div) { return \'
This is some test content!
This message brought to you by the number \'+Math.round(Math.random()100)+\'.
\';} ', 'action' => 'contentDialog', 'title' => 'function(track,feature,div) { return \'Random content snippet \'+Math.random()+\' title!\'; }', 'label' => 'Popup with content snippet from a function (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'content' => 'This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.
', 'action' => 'contentDialog', 'title' => 'function(track,feature,div) { return \'Random content snippet \'+Math.random()+\' title!\'; }', 'label' => 'Popup with content snippet from string (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'action' => 'function( evt ){ alert(\'Hi there! Ran the callback on feature \'+this.feature.get(\'name\')); }', 'label' => 'function(track,feature,div) { return \'Run a JS callback \'+Math.random()+\' title!\'; }' } ], 'hooks' => { 'modify' => 'function( track, feature, div ) { div.style.backgroundColor = [\'green\',\'blue\',\'red\',\'orange\',\'purple\'][Math.round(Math.random()5)];}' }, 'key' => 'Example Features with Menus', 'feature' => [ 'match' ], 'compress' => 0, 'metadata' => { 'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.' } }; searching for features of type: match working on track Genes mergedTrackCfg: $VAR1 = { 'feature' => [ 'gene' ], 'autocomplete' => 'all', 'track' => 'Genes', 'style' => { 'className' => 'feature5' }, 'compress' => 0, 'key' => 'Protein-coding genes', 'onClick' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}' }; searching for features of type: gene working on track ReadingFrame mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'ReadingFrame', 'style' => { 'className' => 'dblhelix' }, 'key' => 'Frame usage', 'onClick' => { 'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}', 'label' => 'search at NCBI' }, 'feature' => [ 'mRNA' ], 'compress' => 0, 'category' => 'Genes' }; searching for features of type: mRNA working on track CDS mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'CDS', 'style' => { 'className' => 'cds', 'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}' }, 'key' => 'Predicted genes', 'feature' => [ 'CDS:predicted', 'mRNA:exonerate', 'mRNA:predicted' ], 'phase' => 1, 'compress' => 0, 'category' => 'Genes' }; searching for features of type: CDS:predicted, mRNA:exonerate, mRNA:predicted working on track Transcript mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'Transcript', 'style' => { 'className' => 'transcript', 'subfeatureClasses' => { 'CDS' => 'transcript-CDS', 'UTR' => 'transcript-UTR' }, 'arrowheadClass' => 'transcript-arrowhead' }, 'description' => 1, 'key' => 'Exonerate predictions', 'onClick' => 'function() { alert(\'This is a user-configurable JavaScript action!\'); };', 'feature' => [ 'mRNA:exonerate' ], 'compress' => 0, 'category' => 'Genes', 'subfeatures' => bless( do{(my $o = 1)}, 'JSON::XS::Boolean' ) }; searching for features of type: mRNA:exonerate working on track Clones mergedTrackCfg: $VAR1 = { 'feature' => [ 'BAC' ], 'autocomplete' => 'all', 'track' => 'Clones', 'style' => { 'className' => 'exon' }, 'compress' => 0, 'description' => 1, 'key' => 'Fingerprinted BACs' }; searching for features of type: BAC working on track EST mergedTrackCfg: $VAR1 = { 'feature' => [ 'EST_match:est' ], 'autocomplete' => 'all', 'track' => 'EST', 'style' => { 'className' => 'est' }, 'compress' => 0, 'key' => 'ESTs' }; searching for features of type: EST_match:estworking on refseq ctgB working on track ExampleFeatures mergedTrackCfg: $VAR1 = { 'feature' => [ 'remark' ], 'autocomplete' => 'all', 'track' => 'ExampleFeatures', 'style' => { 'className' => 'feature2' }, 'compress' => 0, 'key' => 'Example Features' }; searching for features of type: remark working on track NameTest mergedTrackCfg: $VAR1 = { 'feature' => [ 'protein_coding_primary_transcript', 'polypeptide' ], 'autocomplete' => 'all', 'track' => 'NameTest', 'style' => { 'className' => 'feature2' }, 'compress' => 0, 'key' => 'Name test track has a really long track label' }; searching for features of type: protein_coding_primary_transcript, polypeptide working on track snps mergedTrackCfg: $VAR1 = { 'feature' => [ 'SNP' ], 'autocomplete' => 'all', 'track' => 'snps', 'style' => { 'className' => 'triangle hgred' }, 'compress' => 0, 'key' => 'Test SNPs' }; searching for features of type: SNP working on track Motifs mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'Motifs', 'style' => { 'className' => 'feature3', 'label' => 'function(feature) { return feature.get(\'Name\')+\' (via JS callback)\' }', 'description' => 'function(feature) { return feature.get(\'Name\')+\': \'+feature.get(\'Note\'); }' }, 'description' => 1, 'key' => 'Example motifs', 'feature' => [ 'polypeptide_domain' ], 'compress' => 0 }; searching for features of type: polypeptide_domain working on track malformed_alignments mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'malformed_alignments', 'style' => { 'className' => 'feature4' }, 'menuTemplate' => [ { 'children' => [ { 'children' => [ { 'iconClass' => 'dijitIconBookmark', 'url' => 'http://wiki.trin.org.au/{name}-{start}-{end}', 'action' => 'newWindow', 'label' => 'Query trin for {name}' }, { 'iconClass' => 'dijitIconSearch', 'url' => 'http://example.com/{name}-{start}-{end}', 'label' => 'Query example.com for {name}' } ], 'label' => 'Check gene on databases' }, { 'label' => '2nd child of demo' }, { 'label' => '3rd child: this is a track' } ], 'label' => 'Item with submenu' }, { 'iconClass' => 'dijitIconDatabase', 'url' => 'http://www.example.com?featurename={name}', 'action' => 'iframeDialog', 'title' => 'The magnificent example.com (feature {name})', 'label' => 'Open example.com in an iframe popup' }, { 'iconClass' => 'dijitIconDatabase', 'url' => 'sample_data/test_snippet.html?featurename={name}:{start}-{end}', 'action' => 'xhrDialog', 'title' => 'function(track,feature,div) { return \'Random XHR HTML \'+Math.random()+\' title!\'; }', 'label' => 'Open popup with XHR HTML snippet (btw this is feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'content' => 'function(track,feature,div) { return \'
This is some test content!
This message brought to you by the number \'+Math.round(Math.random()100)+\'.
\';} ', 'action' => 'contentDialog', 'title' => 'function(track,feature,div) { return \'Random content snippet \'+Math.random()+\' title!\'; }', 'label' => 'Popup with content snippet from a function (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'content' => 'This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.
', 'action' => 'contentDialog', 'title' => 'function(track,feature,div) { return \'Random content snippet \'+Math.random()+\' title!\'; }', 'label' => 'Popup with content snippet from string (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'action' => 'function( evt ){ alert(\'Hi there! Ran the callback on feature \'+this.feature.get(\'name\')); }', 'label' => 'function(track,feature,div) { return \'Run a JS callback \'+Math.random()+\' title!\'; }' } ], 'hooks' => { 'modify' => 'function( track, feature, div ) { div.style.backgroundColor = [\'green\',\'blue\',\'red\',\'orange\',\'purple\'][Math.round(Math.random()5)];}' }, 'key' => 'Example Features with Menus', 'feature' => [ 'match' ], 'compress' => 0, 'metadata' => { 'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.' } }; searching for features of type: match working on track Genes mergedTrackCfg: $VAR1 = { 'feature' => [ 'gene' ], 'autocomplete' => 'all', 'track' => 'Genes', 'style' => { 'className' => 'feature5' }, 'compress' => 0, 'key' => 'Protein-coding genes', 'onClick' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}' }; searching for features of type: gene working on track ReadingFrame mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'ReadingFrame', 'style' => { 'className' => 'dblhelix' }, 'key' => 'Frame usage', 'onClick' => { 'url' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}', 'label' => 'search at NCBI' }, 'feature' => [ 'mRNA' ], 'compress' => 0, 'category' => 'Genes' }; searching for features of type: mRNA working on track CDS mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'CDS', 'style' => { 'className' => 'cds', 'linkTemplate' => 'http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}' }, 'key' => 'Predicted genes', 'feature' => [ 'CDS:predicted', 'mRNA:exonerate', 'mRNA:predicted' ], 'phase' => 1, 'compress' => 0, 'category' => 'Genes' }; searching for features of type: CDS:predicted, mRNA:exonerate, mRNA:predicted working on track Transcript mergedTrackCfg: $VAR1 = { 'autocomplete' => 'all', 'track' => 'Transcript', 'style' => { 'className' => 'transcript', 'subfeatureClasses' => { 'CDS' => 'transcript-CDS', 'UTR' => 'transcript-UTR' }, 'arrowheadClass' => 'transcript-arrowhead' }, 'description' => 1, 'key' => 'Exonerate predictions', 'onClick' => 'function() { alert(\'This is a user-configurable JavaScript action!\'); };', 'feature' => [ 'mRNA:exonerate' ], 'compress' => 0, 'category' => 'Genes', 'subfeatures' => bless( do{(my $o = 1)}, 'JSON::XS::Boolean' ) }; searching for features of type: mRNA:exonerate working on track Clones mergedTrackCfg: $VAR1 = { 'feature' => [ 'BAC' ], 'autocomplete' => 'all', 'track' => 'Clones', 'style' => { 'className' => 'exon' }, 'compress' => 0, 'description' => 1, 'key' => 'Fingerprinted BACs' }; searching for features of type: BAC working on track EST mergedTrackCfg: $VAR1 = { 'feature' => [ 'EST_match:est' ], 'autocomplete' => 'all', 'track' => 'EST', 'style' => { 'className' => 'est' }, 'compress' => 0, 'key' => 'ESTs' }; searching for features of type: EST_match:estworking on refseq chrI working on track Genes working on track transcript_with_no_features
working on refseq chrII working on track Genes working on track transcript_with_no_features
amitMTCC
commented
11 years ago Pardon me for this repeat message, but i was eager to know if i am making any major mistakes. Do the files provided show any errors or incomplete procedures/steps? thanx
rbuels
commented
11 years ago I don't have any ideas from the error dumps above.
Is your malfunctioning JBrowse instance available at a public URL so I can look at it directly to find out what's going on?
amitMTCC
commented
11 years ago No the malfunctioning JBrowse is not available publicly.. i am just testing it out for out near future genomics requirements. There is one thing that i did that may be of some importance. Initially i was getting errors in this when doing ./setup.sh: Building and installing legacy BAM support (bam-to-json.pl, samtools, and Bio::DB::Sam) ... ERROR.
i then manually ran the code from setup.sh .. line by line... after installing the samtools... (for that module).
do u feel some conflicts would have remained in BioPerl, samtools, etc?
thanx..
rbuels
commented
11 years ago Really, everything you have pasted looks fairly normal, except for the fact that it's not working in your browser.
Maybe try clearing Firefox's cache before reloading?
Also, when you look at the firefox error console, ignore the warnings. Hit the 'error' button at the top of the window to show only errors.
amitMTCC
commented
11 years ago The only error that it produces is at line 16:
require is not defined.. line 16
Here is the page source::::::
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content = "text/html; charset=utf-8">
<title>JBrowse</title>
<link rel="stylesheet" type="text/css" href="genome.css">
<script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="async: 1"></script>
<script type="text/javascript">
window.onerror=function(msg){
if( document.body )
document.body.setAttribute("JSError",msg);
}
var JBrowse;
require( { baseUrl: 'src',
packages: [ 'dojo', 'dijit', 'dojox', 'jszlib',
{ name: 'lazyload', main: 'lazyload' },
'dgrid', 'xstyle', 'put-selector',
{ name: 'jDataView', location: 'jDataView/src', main: 'jdataview' },
'JBrowse'
]
},
[ 'JBrowse/Browser', 'dojo/io-query' ],
function (Browser,ioQuery) {
var queryParams = ioQuery.queryToObject( window.location.search.slice(1) );
var dataRoot = queryParams.data || 'data';
JBrowse = new Browser({
containerID: "GenomeBrowser",
refSeqs: dataRoot + "/seq/refSeqs.json",
baseUrl: dataRoot+'/',
include: [
'jbrowse_conf.json',
dataRoot + "/trackList.json"
],
nameUrl: dataRoot + "/names/root.json",
defaultTracks: "DNA,Annotations,RefSeq",
queryParams: queryParams,
location: queryParams.loc,
forceTracks: queryParams.tracks,
initialHighlight: queryParams.highlight,
show_nav: queryParams.nav,
show_tracklist: queryParams.tracklist,
show_overview: queryParams.overview,
makeFullViewURL: function( browser ) {
// the URL for the 'Full view' link
// in embedded mode should be the current
// view URL, except with 'nav', 'tracklist',
// and 'overview' parameters forced to 1.
return browser.makeCurrentViewURL({ nav: 1, tracklist: 1, overview: 1 });
},
updateBrowserURL: true
});
});
</script>
</head>
<body>
<div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0; border: 0;"></div>
<div style="display: none">JBrowseDefaultMainPage</div>
</body>
</html>Well, require is defined by dojo.js. Does your web browser not fetch src/dojo/dojo.js? Or is there some kind of parse error with it?
amitMTCC
commented
11 years ago dojo.js is located at "/var/www/JBrowse-1.9.5/src/dojo". When i view the source code of the blank JBrowse local host page, the link is present. Clicking on the "src/dojo/dojo.js" shows a html code that says "
you dont have permission to access JBrowse-1.9.5/src/dojo/dojo.js on this server
"Some problem with the permissions? What went wrong?
Thanks.....
rbuels
commented
11 years ago It sounds like a web server configuration issue, which is not controlled by JBrowse. Check your web server configuration.
rbuels
commented
11 years ago No further activity on this issue in a month, closing.
I have a new installation of JBrowse and the ./setup.sh did not give any errors. The links: http://localhost/JBrowse-1.9.5, http://localhost/JBrowse-1.9.5/index.html and http://localhost/JBrowse-1.9.5/index.html?data=sample_data/json/volvox do not display anything in the browser (Ubuntu using Firefox).
The link from the example (http://jbrowse.org/code/JBrowse-1.9.6/index.html?data=sample_data/json/volvox) does show a working JBrowser in the same browser.
All the above links do produce multiple JavaScript warnings of ".... declaration dropped". Also the localhost JBrowse is showing an error "require is not defined".
The page source of both the localhost JBrowse as well as online example show identical code.
Why is the localhost JBrowse now visible? Please help...