Re: [Gmod-ajax] [apollo] Find annotation in tracks

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I would download and install JBrowse 1 and generate the names with that perl script and then point your Apollo organism directory there.

That’s been more reliable for me in general. 

Nathan	

> On Jun 1, 2022, at 9:20 PM, Johannes Debler <joh...@gm...> wrote:
> 
> Thanks Nathan,
> 
> I can't really figure out how to run it, or what the input is meant to be. 
> I have a file called 'trackList.json' which contains all the tracks.
> 
> But when I run this command:
> generate-names.pl <http://generate-names.pl/> --tracks trackList.json
> 
> I get a bunch of errors:
> syntax error in /home/data/apollo_data/36-AlKewell/data/trackList.json: malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "(end of string)") at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 32.
>  at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7.
>         Bio::JBrowse::ConfigurationManager::__ANON__("malformed JSON string, neither tag, array, object, number, st"...) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 32
>         eval {...} called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 32
>         Bio::JBrowse::ConfigurationManager::slurpJSON("/home/data/apollo_data/36-AlKewell/data/trackList.json") called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 145
>         Bio::JBrowse::ConfigurationManager::_load_include(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900), HASH(0x55984670af60), "data") called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 71
>         Bio::JBrowse::ConfigurationManager::_load_includes(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900), HASH(0x559845add2c8)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 41
>         Bio::JBrowse::ConfigurationManager::get_final_config(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/GenomeDB.pm line 261
>         GenomeDB::refSeqs(GenomeDB=HASH(0x55984670b518)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/IndexNames.pm line 77
>         Bio::JBrowse::Cmd::IndexNames::run(Bio::JBrowse::Cmd::IndexNames=HASH(0x559845b08060)) called at /opt/Apollo-2.6.5/jbrowse/bin/generate-names.pl <http://generate-names.pl/> line 8
>  at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7.
>         Bio::JBrowse::ConfigurationManager::__ANON__("syntax error in /home/data/apollo_data/36-AlKewell/data/track"...) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 33
>         Bio::JBrowse::ConfigurationManager::slurpJSON("/home/data/apollo_data/36-AlKewell/data/trackList.json") called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 145
>         Bio::JBrowse::ConfigurationManager::_load_include(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900), HASH(0x55984670af60), "data") called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 71
>         Bio::JBrowse::ConfigurationManager::_load_includes(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900), HASH(0x559845add2c8)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 41
>         Bio::JBrowse::ConfigurationManager::get_final_config(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/GenomeDB.pm line 261
>         GenomeDB::refSeqs(GenomeDB=HASH(0x55984670b518)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/IndexNames.pm line 77
>         Bio::JBrowse::Cmd::IndexNames::run(Bio::JBrowse::Cmd::IndexNames=HASH(0x559845b08060)) called at /opt/Apollo-2.6.5/jbrowse/bin/generate-names.pl <http://generate-names.pl/> line 8
> 
> Not sure if this is the correct way to run the script in the first place, but the help doesn't go into much detail unfortunately. 
> 
> Cheers,
> Johannes
> 
> On Thu, 2 Jun 2022 at 11:37, Nathan Dunn <nd...@gm... <mailto:nd...@gm...>> wrote:
> 
> If you use generate-names: https://jbrowse.org/docs/generate-names.pl.html <https://jbrowse.org/docs/generate-names.pl.html>
> 
> You should be able to search for genes, etc. in the location box.  
> 
> e.g., https://jbrowse.org/jbrowse1.html <https://jbrowse.org/jbrowse1.html> use the search box to look for Apple3.  
> 
> Nathan
> 
>> On Jun 1, 2022, at 8:28 PM, Johannes Debler <joh...@gm... <mailto:joh...@gm...>> wrote:
>> 
>> Hi,
>> I was wondering if it is possible to search annotations in tracks other than 'User-created Annotations'.
>> I have finished annotating my genome and would now like to get rid of all the models in the 'User-created Annotations' track and only display my final annotations track. 
>> 
>> Currently if I try to search for a gene name in the 'Annotations' tab, it only finds things in the 'User-created Annotations' track. Is there a way to make the other tracks searchable, or alternatively, remove all annotations from the 'User....' track and upload my final annotations to that track.
>> 
>> Cheers,
>> Johannes
>> 
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> 