Organisms missing Jbrowse links

CaseyRichards92 commented 4 years ago

These organism either do not have a link to Jbrowse or need Jbrowse done for them.

[x] Acer saccharum - Transcriptome Assembly
[x] Alnus rhombifolia - Transcriptome Assembly
[x] Alnus rubra - Transcriptome Assembly
[ ] Carya cathayensis - Patrick
[ ] Carya illinoinensis - Error see below (Patrick)
[x] Castenea crenata - Pretty sure this a transcriptome
[x] Castanea dentata - Transcriptome
[x] Castanea sativa - Transcriptome
[x] Cornus florida - Transcriptome Assembly
[x] Fagus grandifolia - Transcriptome Assembly
[x] Gleditsia triacanthas - Transcriptome Assembly
[x] Hydrangea macrophylla - Transcriptome Assembly
[x] Juglans regia - This organism already had a JBrowse instance (Patrick)
[x] Lagerstroemia indica - Transcriptome Assembly
[x] Liquidambar styraciflua - Transcriptome Assembly
[x] Liriodendron tulipifera - Transcriptome Assembly
[ ] Morus notabilis - Need to edit gff (Patrick)
[x] Nyssa sylvatica - Transcriptome
[ ] Olea europaea - gff track isn't showing up, probably need to edit gff (Patrick)
[x] Persea borbonia - No .gff (Casey)
[x] Pistacia vera - Transcriptome
[x] Populus deltoides - Patrick
[x] Prunus serotina - Transcriptome
[x] Quercus robur - Casey
[x] Quercus rubra - Transcriptome
[x] Quercus alba - Transcriptome

CaseyRichards92 commented 4 years ago

@patricksis @RaymondS1 I added a list of all the organisms missing Jbrowse. I will start on mine and then move on to the others but if yall want to help with this just put your name next to the one you are doing and check the box when done.

patricksis commented 4 years ago

Loading the gff track for Carya illinoinensis resulted in this error:

/var/www/html/sites/default/files/sequences/Carya_illinoinensis/raw_data/Cil.gff3:449: type mRNA is not the same as previous type gene for ID 'CIL1277S0025' at /var/www/html/tools/jbrowse/bin/../src/perl5/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm line 15.
 at /var/www/html/tools/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7, <$f> line 449.
    Bio::JBrowse::ConfigurationManager::__ANON__('/var/www/html/sites/default/files/sequences/Carya_illinoinens...') called at /usr/share/perl5/vendor_perl/Carp.pm line 100
    Carp::croak('/var/www/html/sites/default/files/sequences/Carya_illinoinens...') called at /var/www/html/tools/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/GFF3/LowLevel/Parser.pm line 173
    Bio::GFF3::LowLevel::Parser::_parse_error('Bio::GFF3::LowLevel::Parser=HASH(0x1988e50)', 'type mRNA is not the same as previous type gene for ID \'CIL1...') called at /var/www/html/tools/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/GFF3/LowLevel/Parser.pm line 306
    Bio::GFF3::LowLevel::Parser::_buffer_feature('Bio::GFF3::LowLevel::Parser=HASH(0x1988e50)', 'HASH(0x1a6e588)') called at /var/www/html/tools/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/GFF3/LowLevel/Parser.pm line 104
    Bio::GFF3::LowLevel::Parser::_buffer_items('Bio::GFF3::LowLevel::Parser=HASH(0x1988e50)') called at /var/www/html/tools/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/Bio/GFF3/LowLevel/Parser.pm line 73
    Bio::GFF3::LowLevel::Parser::next_item('Bio::GFF3::LowLevel::Parser=HASH(0x1988e50)') called at /var/www/html/tools/jbrowse/bin/../src/perl5/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm line 15
    Bio::JBrowse::FeatureStream::GFF3_LowLevel::next_items('Bio::JBrowse::FeatureStream::GFF3_LowLevel=HASH(0x19ad808)') called at /var/www/html/tools/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm line 52
    Bio::JBrowse::Cmd::NCFormatter::_format('Bio::JBrowse::Cmd::FlatFileToJson=HASH(0x10a2b90)', 'trackConfig', 'HASH(0x186e9b8)', 'featureStream', 'Bio::JBrowse::FeatureStream::GFF3_LowLevel=HASH(0x19ad808)', 'featureFilter', 'CODE(0x187af20)', 'trackLabel', 'pecan', ...) called at /var/www/html/tools/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm line 128
    Bio::JBrowse::Cmd::FlatFileToJson::run('Bio::JBrowse::Cmd::FlatFileToJson=HASH(0x10a2b90)') called at /var/www/html/tools/jbrowse/bin/flatfile-to-json.pl line 9
Job execution failed: Unable to add track. See errors above.             [error]

mestato commented 4 years ago

@patricksis lets try to get this fixed (calling on @MattHuff to help look at formatting, @almasaeed2010 if formatting isn't the problem). Would be nice to finish this up especially since there are some other fixes for Carya

almasaeed2010 commented 4 years ago

As far as I can tell, this is a GFF file issue. But we can try to update the jbrowse scripts to see if a newer version fixes this.

mestato commented 4 years ago

For both Carya, need to add IDs to mRNA,CDS and exon features

statonlab / hardwoods_site

Organisms missing Jbrowse links #534