gmod-ajax — JBrowse list

Re: [Gmod-ajax] [apollo] InterProScan loading into JBrowse

[Lbl <nat...@lb...>]

Cross posting to jbrowse list 

> On Jul 23, 2019, at 12:17 AM, Michał T. Lorenc <m.t...@gm...> wrote:
> 
> Hi
> Our annotation is based on BRAKER2 additionally I ran InterProScan and I got GFF3, TSV and XML. I tried to load the GFF3 file using  
> 
> > perl /apollo/jbrowse/bin/flatfile-to-json.pl --gff /apollo/braker-soft_utr-interproscan.gff3 --compress --trackType HTMLFeatures --trackLabel "interproscan" --out /apollo/
> 
> It appears that no InterProScan results has been loaded. I assume that the InterProScan's GFF3 file does not contain any chromosome names:
> 
> ##gff-version 3
> ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
> ##interproscan-version 5.36-75.0
> ##sequence-region g109343.t1 1 1358
> g109343.t1      .       polypeptide     1       1358    .       +       .       ID=g109343.t1;md5=3e908dc966fefe367e64dc9d98b0d3ab
> g109343.t1      ProSiteProfiles protein_match   628     724     18.261  +       .       date=20-07-2019;Target=g109343.t1 628 724;Ontology_term="GO:0015074";ID=match$1_628_724;signature_desc=Integrase c
> atalytic domain profile.;Name=PS50994;status=T;Dbxref="InterPro:IPR001584"
> g109343.t1      SUPERFAMILY     protein_match   586     624     4.19E-5 +       .       date=20-07-2019;Target=g109343.t1 586 624;Ontology_term="GO:0003676","GO:0008270";ID=match$2_586_624;Name=SSF57756
> ;status=T;Dbxref="InterPro:IPR036875"
> g109343.t1      SUPERFAMILY     protein_match   622     725     4.93E-29        +       .       date=20-07-2019;Target=g109343.t1 622 725;ID=match$3_622_725;Name=SSF53098;status=T;Dbxref="InterPro:IPR01
> 2337"
> g109343.t1      ProSiteProfiles protein_match   278     294     9.636   +       .       date=20-07-2019;Target=g109343.t1 278 294;Ontology_term="GO:0003676","GO:0008270";ID=match$4_278_294;signature_des
> c=Zinc finger CCHC-type profile.;Name=PS50158;status=T;Dbxref="InterPro:IPR001878"
> g109343.t1      SMART   protein_match   600     616     0.36    +       .       date=20-07-2019;Target=g109343.t1 600 616;Ontology_term="GO:0003676","GO:0008270";ID=match$5_600_616;Name=SM00343;status=T
> ;Dbxref="InterPro:IPR001878"
> g109343.t1      SMART   protein_match   278     294     6.3E-4  +       .       date=20-07-2019;Target=g109343.t1 278 294;Ontology_term="GO:0003676","GO:0008270";ID=match$5_278_294;Name=SM00343;status=T
> ;Dbxref="InterPro:IPR001878"
> g109343.t1      Pfam    protein_match   82      216     1.2E-24 +       .       date=20-07-2019;Target=g109343.t1 82 216;ID=match$6_82_216;signature_desc=gag-polypeptide of LTR copia-type;Name=PF14223;s
> tatus=T
> 
> Is there a solution how to load InterProScan results as a track into JBrowse or are there any scripts which combine InterProScan with BRAKER2?
> 
> Thank you in advance,
> 
> Michal

Re: [Gmod-ajax] two seetings about JBrowse

[<li...@ma...>]

  Ok, thanks for your kind reminding. Close the translation defalut is what I want because too much tracks makes me confused.

Thank you, Ke Jiang.
Wei  Liu


li...@ma...  
From: Ke Jiang
Date: 2019-07-20 21:46
To: li...@ma...
CC: gmod-ajax
Subject: Re: Re: [Gmod-ajax] two seetings about JBrowse
As Colin suggested, you don’t have to change the settings at the source level. These could be modified for each genome or track.

On Sat, Jul 20, 2019 at 8:28 AM li...@ma... <li...@ma...> wrote:
Hi, Ke Jiang!
    Thanks for your kind response. I have follow  the suggestion of another member of GMOD and solve it successfully.
   I have change the "showTranslation: true," to  "showTranslation: false,"  in  src/JBrowse/View/Track/Sequence.js and  then  rebuid the jbrowse with "./setup.sh ". 

Thanks again!
Wei Liu


li...@ma... 
Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
State Key Laboratory of Genetic Resources and Evolution 
Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
#21,QingsongLu, Ciba, Kunming 650203
 
From: Ke Jiang
Date: 2019-07-19 23:58
To: li...@ma...
CC: gmod-ajax
Subject: Re: [Gmod-ajax] two seetings about JBrowse
For the translation setting, have you tried clearing the browser history and caches before opening the genome browser? 

On Fri, Jul 19, 2019 at 10:55 AM li...@ma... <li...@ma...> wrote:
Hi, member of GMOD;
    Rencently, I am using JBrowse to show our genomes. But  I have encountered two questions.
    1, how to close the translation function when showing the genome?  I have change the "showTranslation: true," to  "showTranslation: false,"  in  src/JBrowse/View/Track/Sequence.js. but it stiil show the translation track once I used the genome track.
    2, I have noticed that  Users can disable usage statistics by setting suppressUsageStatistics: true in the JBrowse configuration.  but which file I shoud change?
    Could you offer some help? Thanks!

Best wishes!
Wei Liu



li...@ma... 
Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
State Key Laboratory of Genetic Resources and Evolution 
Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
#21,QingsongLu, Ciba, Kunming 650203
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] two seetings about JBrowse

[Ke J. <bio...@gm...>]

As Colin suggested, you don’t have to change the settings at the source
level. These could be modified for each genome or track.

On Sat, Jul 20, 2019 at 8:28 AM li...@ma... <li...@ma...>
wrote:

> Hi, Ke Jiang!
>     Thanks for your kind response. I have follow  the suggestion of
> another member of GMOD and solve it successfully.
>    I have change the *"**showTranslation: true,*" to  "*showTranslation:
> false,*"  in  src/JBrowse/View/Track/Sequence.js and  then  rebuid the
> jbrowse with "./setup.sh ".
>
> Thanks again!
> Wei Liu
> ------------------------------
> li...@ma...
> Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
> State Key Laboratory of Genetic Resources and Evolution
> Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
> #21,QingsongLu, Ciba, Kunming 650203
>
>
> *From:* Ke Jiang <bio...@gm...>
> *Date:* 2019-07-19 23:58
> *To:* li...@ma...
> *CC:* gmod-ajax <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] two seetings about JBrowse
> For the translation setting, have you tried clearing the browser history
> and caches before opening the genome browser?
>
> On Fri, Jul 19, 2019 at 10:55 AM li...@ma... <
> li...@ma...> wrote:
>
>> Hi, member of GMOD;
>>     Rencently, I am using JBrowse to show our genomes. But  I have
>> encountered two questions.
>>     1, how to close the translation function when showing the genome?  I
>> have change the *"**showTranslation: true,*" to  "*showTranslation:
>> false,*"  in  src/JBrowse/View/Track/Sequence.js. but it stiil show the
>> translation track once I used the genome track.
>>     2, I have noticed that  Users can disable usage statistics by
>> setting suppressUsageStatistics: true in the JBrowse configuration.  but
>> which file I shoud change?
>>     Could you offer some help? Thanks!
>>
>> Best wishes!
>> Wei Liu
>>
>> ------------------------------
>> li...@ma...
>> Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
>> State Key Laboratory of Genetic Resources and Evolution
>> Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
>> #21,QingsongLu, Ciba, Kunming 650203
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] two seetings about JBrowse

[<li...@ma...>]

Thanks for you kind help. I followed your suggestions and solved the translocation problem successfully.
 I have change the "showTranslation: true," to  "showTranslation: false,"  in  src/JBrowse/View/Track/Sequence.js and  then  rebuid the jbrowse with "./setup.sh ". 

Thanks for your help agian!
Wei Liu


li...@ma... 
Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
State Key Laboratory of Genetic Resources and Evolution 
Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
#21,QingsongLu, Ciba, Kunming 650203
 
From: Colin
Date: 2019-07-19 23:59
To: li...@ma...
CC: gmod-ajax
Subject: Re: [Gmod-ajax] two seetings about JBrowse
Hi there

These settings are enabled via the configuration file generally.

You mention directly modifying the source code, but to see updates from modifying the source code, you have to perform a rebuild of jbrowse, and you also have to be using a "dev" version of jbrowse or a github clone of the repo.

See here about how to modify the source code https://jbrowse.org/docs/faq.html#how-do-i-modify-jbrowse-source-code

But as I mentioned above, you can update these settings by modifying your config files

Look at the file data/trackList.json, and there will be a "Reference sequence" track, you can add "showTranslation": false in this JSON block (note: don't quote the value false)

Also, you can add

suppressUsageStatistics=true

To the bottom of jbrowse.conf

-Colin

On Fri, Jul 19, 2019 at 11:55 AM li...@ma... <li...@ma...> wrote:
Hi, member of GMOD;
    Rencently, I am using JBrowse to show our genomes. But  I have encountered two questions.
    1, how to close the translation function when showing the genome?  I have change the "showTranslation: true," to  "showTranslation: false,"  in  src/JBrowse/View/Track/Sequence.js. but it stiil show the translation track once I used the genome track.
    2, I have noticed that  Users can disable usage statistics by setting suppressUsageStatistics: true in the JBrowse configuration.  but which file I shoud change?
    Could you offer some help? Thanks!

Best wishes!
Wei Liu



li...@ma... 
Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
State Key Laboratory of Genetic Resources and Evolution 
Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
#21,QingsongLu, Ciba, Kunming 650203
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] two seetings about JBrowse

[<li...@ma...>]

Hi, Ke Jiang!
    Thanks for your kind response. I have follow  the suggestion of another member of GMOD and solve it successfully.
   I have change the "showTranslation: true," to  "showTranslation: false,"  in  src/JBrowse/View/Track/Sequence.js and  then  rebuid the jbrowse with "./setup.sh ". 

Thanks again!
Wei Liu


li...@ma... 
Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
State Key Laboratory of Genetic Resources and Evolution 
Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
#21,QingsongLu, Ciba, Kunming 650203
 
From: Ke Jiang
Date: 2019-07-19 23:58
To: li...@ma...
CC: gmod-ajax
Subject: Re: [Gmod-ajax] two seetings about JBrowse
For the translation setting, have you tried clearing the browser history and caches before opening the genome browser? 

On Fri, Jul 19, 2019 at 10:55 AM li...@ma... <li...@ma...> wrote:
Hi, member of GMOD;
    Rencently, I am using JBrowse to show our genomes. But  I have encountered two questions.
    1, how to close the translation function when showing the genome?  I have change the "showTranslation: true," to  "showTranslation: false,"  in  src/JBrowse/View/Track/Sequence.js. but it stiil show the translation track once I used the genome track.
    2, I have noticed that  Users can disable usage statistics by setting suppressUsageStatistics: true in the JBrowse configuration.  but which file I shoud change?
    Could you offer some help? Thanks!

Best wishes!
Wei Liu



li...@ma... 
Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
State Key Laboratory of Genetic Resources and Evolution 
Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
#21,QingsongLu, Ciba, Kunming 650203
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] two seetings about JBrowse

[Colin <col...@gm...>]

Hi there

These settings are enabled via the configuration file generally.

You mention directly modifying the source code, but to see updates from
modifying the source code, you have to perform a rebuild of jbrowse, and
you also have to be using a "dev" version of jbrowse or a github clone of
the repo.

See here about how to modify the source code
https://jbrowse.org/docs/faq.html#how-do-i-modify-jbrowse-source-code

But as I mentioned above, you can update these settings by modifying your
config files

Look at the file data/trackList.json, and there will be a "Reference
sequence" track, you can add "showTranslation": false in this JSON block
(note: don't quote the value false)

Also, you can add

suppressUsageStatistics=true

To the bottom of jbrowse.conf

-Colin

On Fri, Jul 19, 2019 at 11:55 AM li...@ma... <
li...@ma...> wrote:

> Hi, member of GMOD;
>     Rencently, I am using JBrowse to show our genomes. But  I have
> encountered two questions.
>     1, how to close the translation function when showing the genome?  I
> have change the *"**showTranslation: true,*" to  "*showTranslation:
> false,*"  in  src/JBrowse/View/Track/Sequence.js. but it stiil show the
> translation track once I used the genome track.
>     2, I have noticed that  Users can disable usage statistics by setting suppressUsageStatistics:
> true in the JBrowse configuration.  but which file I shoud change?
>     Could you offer some help? Thanks!
>
> Best wishes!
> Wei Liu
>
> ------------------------------
> li...@ma...
> Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
> State Key Laboratory of Genetic Resources and Evolution
> Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
> #21,QingsongLu, Ciba, Kunming 650203
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] two seetings about JBrowse

[Ke J. <bio...@gm...>]

For the translation setting, have you tried clearing the browser history
and caches before opening the genome browser?

On Fri, Jul 19, 2019 at 10:55 AM li...@ma... <
li...@ma...> wrote:

> Hi, member of GMOD;
>     Rencently, I am using JBrowse to show our genomes. But  I have
> encountered two questions.
>     1, how to close the translation function when showing the genome?  I
> have change the *"**showTranslation: true,*" to  "*showTranslation:
> false,*"  in  src/JBrowse/View/Track/Sequence.js. but it stiil show the
> translation track once I used the genome track.
>     2, I have noticed that  Users can disable usage statistics by setting suppressUsageStatistics:
> true in the JBrowse configuration.  but which file I shoud change?
>     Could you offer some help? Thanks!
>
> Best wishes!
> Wei Liu
>
> ------------------------------
> li...@ma...
> Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
> State Key Laboratory of Genetic Resources and Evolution
> Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
> #21,QingsongLu, Ciba, Kunming 650203
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] two seetings about JBrowse

[<li...@ma...>]

Hi, member of GMOD;
    Rencently, I am using JBrowse to show our genomes. But  I have encountered two questions.
    1, how to close the translation function when showing the genome?  I have change the "showTranslation: true," to  "showTranslation: false,"  in  src/JBrowse/View/Track/Sequence.js. but it stiil show the translation track once I used the genome track.
    2, I have noticed that  Users can disable usage statistics by setting suppressUsageStatistics: true in the JBrowse configuration.  but which file I shoud change?
    Could you offer some help? Thanks!

Best wishes!
Wei Liu



li...@ma... 
Group of Evolutionary Genomics and Origin of New Genes (Wen Wang's Group)
State Key Laboratory of Genetic Resources and Evolution 
Kunming Institute of Zoology (KIZ), Chinese Academy of Science (CAS)
#21,QingsongLu, Ciba, Kunming 650203

[Gmod-ajax] Apollo 2.4.2 minor release

[Nathan D. <nat...@lb...>]

https://github.com/GMOD/Apollo/releases/tag/2.4.1 <https://github.com/GMOD/Apollo/releases/tag/2.4.1>

This is a small release to fix a small JBrowse error where dragging Apollo / JBrowse on a Mac would result in going to the previous or next page in history. 

Fixes Mac Drag Error by upgrading JBrowse default to 1.16.6 GMOD/jbrowse#1397 <https://github.com/GMOD/jbrowse/issues/1397>
Makes organisms and groups searchable. 2081 <https://github.com/GMOD/Apollo/pull/2081>


Cheers,

Nathan

[Gmod-ajax] JBrowse 1.16.6 released

[Colin <col...@gm...>]

Hi all,
JBrowse version 1.16.6 is released. The main thing that this release
contains is a fix for a bug with side-scrolling on Macs. Please see the
release notes.



   - JBrowse-1.16.6.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.6-release/JBrowse-1.16.6.zip>
-
   minified release
   - JBrowse-1.16.6-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.6-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.6-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.6-release/JBrowse-1.16.6-desktop-win32-x64.zip>
   - JBrowse-1.16.6-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.6-release/JBrowse-1.16.6-desktop-linux-x64.zip>
   - JBrowse-1.16.6-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.6-release/JBrowse-1.16.6-desktop-darwin-x64.zip>

Blog post http://jbrowse.org/blog/2019/07/11/jbrowse-1-16-6.html

Minor improvements

   -

   Add name regularization for drosophila style chromsome naming so that 2L
   maps to chr2L and vice versa (@scottcain <https://github.com/scottcain>)
   -

   Add ability to index names in a BEDTabix file, enabled by default.
   Thanks to @billzt <https://github.com/billzt> for the idea and
   implementation (issue #1393 <https://github.com/gmod/jbrowse/pull/1393>)

<http://jbrowse.org/blog/2019/07/11/jbrowse-1-16-6.html#bug-fixes>Bug fixes

   - Fix the side scrolling on Mac misbehaving and triggering the browser's
   back action (a bug that existed only in 1.16.5). Thanks to @nathandunn
   <https://github.com/nathandunn> for debugging (issue #1397
   <https://github.com/gmod/jbrowse/issues/1397>)

Re: [Gmod-ajax] [apollo] change the width of yellow highlighted frame by BLAST

[Nathan D. <nat...@lb...>]

Not that I am aware of, but the folks at JBrowse might know of a way. 

What is the reason for adjusting the highlighted region? 

Nathan


> On Jul 8, 2019, at 9:51 PM, Michał T. Lorenc <m.t...@gm...> wrote:
> 
> Hi,
> We are using the build in Apollo's BLAST. How is it possible to extend (change the width) of yellow highlighted sequence e.g. with the mouse?
> 
> Thank you in advance,
> 
> Michal

Re: [Gmod-ajax] Jbrowse error

[Colin <col...@gm...>]

A previous thread suggests simply force installing this dependency

http://gmod.827538.n3.nabble.com/Gmod-ajax-JBrowse-Dependencies-Unable-to-install-Heap-Simple-Perl-and-Heap-Simple-XS-td4053362.html

-Colin

On Thu, Jun 27, 2019 at 2:12 PM Beppu, Lan W <lb...@fr...> wrote:

> Hi Colin,
>
>
>
> I’m getting this error below. Do you have any suggestions to what I should
> try?
>
>
>
> Thanks,
>
> Lan
>
>
>
> Can't locate Heap::Simple::XS(0.10) nor Heap::Simple::Perl(0.13) in @INC.
> This probably means you didn't install any of them. (@INC contains:
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/5.18.4/darwin-thread-multi-2level
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/5.18.4
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/5.18.4/darwin-thread-multi-2level
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/5.18.4
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/../../extlib/lib/perl5
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5
> /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18
> /Network/Library/Perl/5.18/darwin-thread-multi-2level
> /Network/Library/Perl/5.18
> /Library/Perl/Updates/5.18.4/darwin-thread-multi-2level
> /Library/Perl/Updates/5.18.4
> /System/Library/Perl/5.18/darwin-thread-multi-2level
> /System/Library/Perl/5.18
> /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.18 .) at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm
> line 41.
>
> Compilation failed in require at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm
> line 41.
>
> BEGIN failed--compilation aborted at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm
> line 41.
>
> Compilation failed in require at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm
> line 8.
>
> BEGIN failed--compilation aborted at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/NCFormatter.pm
> line 8.
>
> Compilation failed in require at (eval 7) line 2.
>
>        ...propagated at /System/Library/Perl/5.18/base.pm line 84.
>
> BEGIN failed--compilation aborted at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
> line 7.
>
>  at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm
> line 7.
>
>        Bio::JBrowse::ConfigurationManager::__ANON__('Can\'t locate
> Heap::Simple::XS(0.10) nor Heap::Simple::Perl(0...') called at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
> line 7
>
>        require Bio/JBrowse/Cmd/BioDBToJson.pm called at bin/
> biodb-to-json.pl line 7
>
>        main::BEGIN() called at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
> line 7
>
>        eval {...} called at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm
> line 7
>
> Compilation failed in require at bin/biodb-to-json.pl line 7.
>
>  at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm
> line 7.
>
>        Bio::JBrowse::ConfigurationManager::__ANON__('Can\'t locate
> Heap::Simple::XS(0.10) nor Heap::Simple::Perl(0...') called at bin/
> biodb-to-json.pl line 7
>
>        main::BEGIN() called at bin/biodb-to-json.pl line 7
>
>        eval {...} called at bin/biodb-to-json.pl line 7
>
> BEGIN failed--compilation aborted at bin/biodb-to-json.pl line 7.
>
>  at
> /Users/lbeppu/Downloads/JBrowse-1.16.4/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm
> line 7.
>
>        Bio::JBrowse::ConfigurationManager::__ANON__('Can\'t locate
> Heap::Simple::XS(0.10) nor Heap::Simple::Perl(0...') called at bin/
> biodb-to-json.pl line 7
>
>
>
>
>
> *From: *Colin <col...@gm...>
> *Date: *Tuesday, June 25, 2019 at 1:53 PM
> *To: *"Beppu, Lan W" <lb...@fr...>, gmod-ajax <
> gmo...@li...>
> *Subject: *Re: [Gmod-ajax] Jbrowse error
>
>
>
> Hi there,
>
>
>
> The JBrowse root directory is the same directory that the setup.sh file is
> in, so you can simply "cd" into this directory and then run ./setup.sh
>
>
>
> -Colin
>
>
>
> On Tue, Jun 25, 2019 at 4:29 PM Beppu, Lan W <lb...@fr...> wrote:
>
> Hello,
>
>
>
> How do I get into the jbrowse root directory? Would that be on my local
> directory?
>
>
>
> Thanks,
>
> Lan
>
>
>
> *From: *Colin <col...@gm...>
> *Date: *Friday, June 14, 2019 at 8:59 AM
> *To: *"Spencer, Kaolu L" <ksp...@fr...>
> *Cc: *"gmo...@li..." <gmo...@li...>,
> "Beppu, Lan W" <lb...@fr...>
> *Subject: *Re: [Gmod-ajax] Jbrowse error
>
>
>
> Hi there,
>
>
>
> I think from looking at the setup.log that you didn't run the setup.sh
> while inside the jbrowse root directory
>
>
>
> You have to be inside the jbrowse directory and then run ./setup.sh
>
>
>
> Hope that helps
>
>
>
> -Colin
>
>
>
> On Fri, Jun 14, 2019 at 11:55 AM Spencer, Kaolu L <ksp...@fr...>
> wrote:
>
>
> * Kaolu Spencer*
>
> Service Desk Engineer II
> 206-667-2431
> ksp...@fr...
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=5Q3pdOsuHwhWZuGW442xs8pm3CinFqJwR4J_vipi41U&m=NOaDnU1JmuxDslc25J19FOnk4Aq_M8jq8VaXlLot9Zk&s=Ut0GJ5oBvAwAHYNeigDCHiOghWHyrFWfzfvR2bYs-tA&e=>
>
>

[Gmod-ajax] Apollo 2.4.0 has been released

[Nathan D. <nat...@lb...>]

Apollo 2.4.0 has been officially released

https://github.com/GMOD/Apollo/releases/tag/2.4.0 <https://github.com/GMOD/Apollo/releases/tag/2.4.0>


Major features include:

GO Annotations with GPAD2 export
Upload file to server to create genome annotations and tracked
UI support for manual variant effect prediction
All bug fixes and features detailed here:

https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md#240 <https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md#240>
Docker builds are on quay and docker hub <https://genomearchitect.readthedocs.io/en/latest/Docker.html>:

https://quay.io/repository/gmod/apollo?tab=builds <https://quay.io/repository/gmod/apollo?tab=builds>
https://hub.docker.com/r/gmod/apollo <https://hub.docker.com/r/gmod/apollo>
Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/ <http://genomearchitect.readthedocs.io/en/latest/>
Note: You can find a guide upgrading existing Apollo installations here:
https://genomearchitect.readthedocs.io/en/latest/Migration.html <https://genomearchitect.readthedocs.io/en/latest/Migration.html>
Please open a GitHub issue if you find any problems: https://github.com/GMOD/Apollo/issues/ <https://github.com/GMOD/Apollo/issues/>
Active mailing list (ap...@li... <mailto:ap...@li...>) and archive <https://groups.google.com/a/lbl.gov/forum/#!forum/apollo>.


Cheers,

Apollo / JBrowse Teams

Re: [Gmod-ajax] Jbrowse error

[Colin <col...@gm...>]

Hi there,

The JBrowse root directory is the same directory that the setup.sh file is
in, so you can simply "cd" into this directory and then run ./setup.sh

-Colin

On Tue, Jun 25, 2019 at 4:29 PM Beppu, Lan W <lb...@fr...> wrote:

> Hello,
>
>
>
> How do I get into the jbrowse root directory? Would that be on my local
> directory?
>
>
>
> Thanks,
>
> Lan
>
>
>
> *From: *Colin <col...@gm...>
> *Date: *Friday, June 14, 2019 at 8:59 AM
> *To: *"Spencer, Kaolu L" <ksp...@fr...>
> *Cc: *"gmo...@li..." <gmo...@li...>,
> "Beppu, Lan W" <lb...@fr...>
> *Subject: *Re: [Gmod-ajax] Jbrowse error
>
>
>
> Hi there,
>
>
>
> I think from looking at the setup.log that you didn't run the setup.sh
> while inside the jbrowse root directory
>
>
>
> You have to be inside the jbrowse directory and then run ./setup.sh
>
>
>
> Hope that helps
>
>
>
> -Colin
>
>
>
> On Fri, Jun 14, 2019 at 11:55 AM Spencer, Kaolu L <ksp...@fr...>
> wrote:
>
>
> * Kaolu Spencer*
>
> Service Desk Engineer II
> 206-667-2431
> ksp...@fr...
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=5Q3pdOsuHwhWZuGW442xs8pm3CinFqJwR4J_vipi41U&m=NOaDnU1JmuxDslc25J19FOnk4Aq_M8jq8VaXlLot9Zk&s=Ut0GJ5oBvAwAHYNeigDCHiOghWHyrFWfzfvR2bYs-tA&e=>
>
>

Re: [Gmod-ajax] Jbrowse error

[Colin <col...@gm...>]

Hi there,

I think from looking at the setup.log that you didn't run the setup.sh
while inside the jbrowse root directory

You have to be inside the jbrowse directory and then run ./setup.sh

Hope that helps

-Colin

On Fri, Jun 14, 2019 at 11:55 AM Spencer, Kaolu L <ksp...@fr...>
wrote:

>
> * Kaolu Spencer*
>
> Service Desk Engineer II
> 206-667-2431
> ksp...@fr...
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Jbrowse error

[Spencer, K. L <ksp...@fr...>]

Kaolu Spencer
Service Desk Engineer II
206-667-2431
ksp...@fr...<mailto:ksp...@fr...>

[Gmod-ajax] JBrowse 1.16.5 released

[Colin <col...@gm...>]

Hello all,
This is the real release announcement for the latest jbrowse version, 1.16.5

It contains a number of nice bugfixes contributed by the community. Please
see the release notes below

Enjoy browsing!


   - JBrowse-1.16.5.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5.zip>
-
   minified release
   - JBrowse-1.16.5-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.5-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.5-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5-desktop-win32-x64.zip>
   - JBrowse-1.16.5-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5-desktop-linux-x64.zip>
   - JBrowse-1.16.5-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5-desktop-darwin-x64.zip>

<http://jbrowse.org/blog/#minor-improvements>Minor improvements

   -

   Added better error reporting if there is a BAI file for a genome that is
   longer than 2^29 and requires a CSI index
   -

   Added default dontRedispatch=chromosome,region which avoids long
   GFF3Tabix redispatching for common gff3 types that don't need it.
   -

   Added a hideIframeDialogUrl option to hide the iframe url in a
   iframeDialog popup. Thanks to @mictadlo <https://github.com/mictadlo> for
   the suggestion (issue #1365)
   -

   Updated @gmod <https://github.com/gmod>/tabix and @gmod
   <https://github.com/gmod>/bam to unzip bgzf chunks as they are received
   instead of performing chunk merges. This also allows actual fileOffset to
   be used as a feature ID instead of CRC32 hash (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added regularization of chromosome names using roman numerals, common in
   both S. cerevisiae and C. elegans genome communities. Thanks to
   @scottcain <https://github.com/scottcain> for assistance (issue #1376
   <https://github.com/gmod/jbrowse/pull/1376>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added ability for vertical scroll events to bubble out of the jbrowse
   div or iframe, which can be more intuitive in embedded jbrowse's.
   Otherwise, the GenomeView stopped all vertical scroll events in it's area.
   If you need the old behavior use alwaysStopScrollBubble. (@cmdcolin
   <https://github.com/cmdcolin>, issue #1373
   <https://github.com/gmod/jbrowse/pull/1373>)

<http://jbrowse.org/blog/#bug-fixes>Bug fixes

   -

   Fixed a long standing issue with BigWig files not accessing the lowest
   summary zoom level (e.g. the first one after unzoomed). (@cmdcolin
   <https://github.com/cmdcolin>, issue #1359
   <https://github.com/gmod/jbrowse/issues/1359>)
   -

   Fixed a bug with using the scoreType: maxScore configuration on Wiggle
   tracks failing at non-summary zoom levels. Thanks to @patrickcng90
   <https://github.com/patrickcng90> for reporting
   -

   Fixed a bug with name regularizing that particularly affected CRAM on
   mitochondrial chromosomes. Thanks to @sachalau
   <https://github.com/sachalau> for patience and sample data for debugging
   this issue! (issue #1367 <https://github.com/gmod/jbrowse/issues/1367>,
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Fixed issue with GFF3/Tabix types colliding their attribute names with
   the field e.g. if start=0 was in column 9. Thanks to @loraine-gueguen
   <https://github.com/loraine-gueguen> for reporting (issue #1364
   <https://github.com/gmod/jbrowse/issues/1364>).
   -

   Fixed an issue with NeatHTMLFeatures when zoomed out. Thanks to @abretaud
   <https://github.com/abretaud> for the implementation and fix (issue #1368
   <https://github.com/gmod/jbrowse/pull/1368>).
   -

   Restored ability to access widest zoom level from bigwig. Thanks to
   @lukaw3d <https://github.com/lukaw3d> for noticing and debugging (issue
   #1375 <https://github.com/gmod/jbrowse/issues/1375>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed some minor parsing of 'b' type data series in CRAM files, which
   happens when CRAM is not using reference based compression so it is
   uncommon (@cmdcolin <https://github.com/cmdcolin>)
   -

   Added some more checks for track types for combination tracks (issue
   #1361)

[Gmod-ajax] JBrowse 1.16.4 released

[Colin <col...@gm...>]

Hello all,
This is late after the fact, but I missed sending out the JBrowse 1.16.4
announcement, so I wanted to send one out. JBrowse 1.16.5 was also released
today, and you will receive that announcement too.

Here are the notes


   - JBrowse-1.16.4.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.4-release/JBrowse-1.16.4.zip>
-
   minified release
   - JBrowse-1.16.4-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.4-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.4-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.4-release/JBrowse-1.16.4-desktop-win32-x64.zip>
   - JBrowse-1.16.4-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.4-release/JBrowse-1.16.4-desktop-linux-x64.zip>
   - JBrowse-1.16.4-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.4-release/JBrowse-1.16.4-desktop-darwin-x64.zip>

<http://jbrowse.org/blog/#minor-improvements>Minor improvements

   -

   Added indexedFeatures tracklist attribute for GFF3Tabix track types
   which controls the feature types from a GFF3Tabix file that are indexed.
   Thanks to @loraine-gueguen <https://github.com/loraine-gueguen> for the
   idea and implementation! (issue #1337
   <https://github.com/gmod/jbrowse/pull/1337>, @loraine-guegen
   <https://github.com/loraine-guegen>)
   -

   Added inferHTMLSubfeatures which automatically creates multiple mRNA
   transcripts from a single gene parent feature. Thanks to @abretaud
   <https://github.com/abretaud> for the idea and implementation! Note that
   this is enabled by default now (issue #1343
   <https://github.com/gmod/jbrowse/pull/1343>, issue #1340
   <https://github.com/gmod/jbrowse/pull/1340>)
   -

   Updated jbrowse.org website to run entirely off amazon S3 (issue #1347
   <https://github.com/gmod/jbrowse/pull/1347>, issue #1348
   <https://github.com/gmod/jbrowse/pull/1348>)

<http://jbrowse.org/blog/#bug-fixes>Bug fixes

   -

   Added better error reporting to GFF3Tabix tracks for if a parsing error
   occured. Thanks to @nathanhaigh <https://github.com/nathanhaigh>for
   reporting (@cmdcolin <https://github.com/cmdcolin>)
   -

   Added fix for VCF that don't contain alternative alleles (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added better error handling if there is a case where a tabix file is
   loaded that is on a genome longer than 2^29. CSI indexes are needed for
   this. Old versions of tabix which hadn't invented CSI would generate
   invalid tabix indexes in this case. Thanks to Hans Vasquez-Gross for
   reporting (@cmdcolin <https://github.com/cmdcolin>)
   -

   Fixed link in documentation. Thanks @agarciamontoro
   <https://github.com/agarciamontoro> (issue #1341
   <https://github.com/gmod/jbrowse/pull/1341>)
   -

   Fixed issue with ucsc-to-json.pl creating subfeatures with the wrong
   strand. Thanks to @sachalau <https://github.com/sachalau> for finding
   and fixing (issue #1346 <https://github.com/gmod/jbrowse/pull/1346>)

Re: [Gmod-ajax] Error: Cannot read property slice of null for VCF + CSI

[Hans Vasquez-G. <hav...@uc...>]

Thanks, that was problem.

Re: [Gmod-ajax] Error: Cannot read property slice of null for VCF + CSI

[Colin <col...@gm...>]

I think the line

##CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO

Should just be

#CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO

And I think it should be the last line before the data lines

On Wed, Jun 5, 2019 at 6:30 PM Hans Vasquez-Gross <
hav...@uc...> wrote:

> Hi all,
>
> I am trying to load a new VCF+CSI file to my jbrowse.  However, I am
> getting the following error: Cannot read property slice of null
>
> [image: Screen Shot 2019-06-05 at 2.56.38 PM.png]
>
> You can view at this link here
> <https://dubcovskylab.ucdavis.edu/ecotilling/?loc=chr1A%3A189961459..189962859&tracks=DNA%2CHighConfGenes%2Ccombinedmaps2019&addFeatures=%5B%7B%22seq_id%22%3A%22chr7A%22%2C%20%22start%22%3A%20674082831%2C%20%22end%22%3A%20674082918%2C%20%22name%22%3A%20%22MyBLASTHit_1%22%2C%20%22description%22%20%3A%20%22evalue%205.74e-37%22%7D%5D&addTracks=%5B%7B%22label%22%3A%22blast%22%2C%22store%22%3A%22url%22%2C%22type%22%3A%22JBrowse%2FView%2FTrack%2FHTMLFeatures%22%2C%20%22key%22%3A%22BlastHSP%20Results%22%7D%5D%0A&highlight=>.
> And here is a small sample of the VCF. It seems like maybe the CSI is
> invalid? However, it looks like there is data in the file. Any advice would
> be greatly appreciated.
>
> ##fileformat=VCFv4.0
> ##fileDate=201964
> ##source=Kronos
> ##referece=IWGSC
> ##phasing=full
> ##CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO
> ##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
> ##SnpEffCmd="SnpEff  iwgsc1 ./combined_maps.vcf "
> ##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations:
> 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID |
> Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p |
> cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length |
> Distance | ERRORS / WARNINGS / INFO' ">
> ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of
> function effects for this variant. Format: 'Gene_Name | Gene_ID |
> Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
> ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense
> mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID |
> Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
> chr1A   1145762 Kronos2392:G1145762A    G       A       40.0    Pass
>  seed_avail=Kronos2392;hethom=hom;ANN=A|downstream_gene_variant|MODIFIER|TraesCS1A01G001800|TraesCS1A01G001800|transcript|TraesCS1A01G001800.1|protein_coding||c.*164G>A|||||164|,A|intergenic_region|MODIFIER|TraesCS1A01G001800-TraesCS1A01G001900|TraesCS1A01G001800-TraesCS1A01G001900|intergenic_region|TraesCS1A01G001800-TraesCS1A01G001900|||n.1145762G>A||||||
> chr1A   1159612 Kronos473:G1159612A     G       A       40.0    Pass
>  seed_avail=Kronos473;hethom=het;ANN=A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.10|protein_coding|9/9|c.1436C>T|p.Ser479Phe|1436/1527|1436/1527|479/508||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.1|protein_coding|10/10|c.1331C>T|p.Ser444Phe|1331/1422|1331/1422|444/473||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.2|protein_coding|10/10|c.1328C>T|p.Ser443Phe|1328/1419|1328/1419|443/472||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.3|protein_coding|9/9|c.1430C>T|p.Ser477Phe|1430/1521|1430/1521|477/506||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.4|protein_coding|10/10|c.1331C>T|p.Ser444Phe|1331/1422|1331/1422|444/473||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.5|protein_coding|9/9|c.1157C>T|p.Ser386Phe|1157/1248|1157/1248|386/415||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.6|protein_coding|10/10|c.1340C>T|p.Ser447Phe|1340/1431|1340/1431|447/476||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.7|protein_coding|10/10|c.1337C>T|p.Ser446Phe|1337/1428|1337/1428|446/475||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.8|protein_coding|10/10|c.1340C>T|p.Ser447Phe|1340/1431|1340/1431|447/476||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.9|protein_coding|10/10|c.1343C>T|p.Ser448Phe|1343/1434|1343/1434|448/477||,A|downstream_gene_variant|MODIFIER|TraesCS1A01G002000|TraesCS1A01G002000|transcript|TraesCS1A01G002000.1|protein_coding||c.*4356C>T|||||4356|
> chr1A   1159898 Kronos2566:C1159898T    C       T       40.0    Pass
>  seed_avail=Kronos2566;hethom=het;ANN=T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.10|protein_coding|9/9|c.1150G>A|p.Asp384Asn|1150/1527|1150/1527|384/508||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.1|protein_coding|10/10|c.1045G>A|p.Asp349Asn|1045/1422|1045/1422|349/473||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.2|protein_coding|10/10|c.1042G>A|p.Asp348Asn|1042/1419|1042/1419|348/472||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.3|protein_coding|9/9|c.1144G>A|p.Asp382Asn|1144/1521|1144/1521|382/506||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.4|protein_coding|10/10|c.1045G>A|p.Asp349Asn|1045/1422|1045/1422|349/473||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.5|protein_coding|9/9|c.871G>A|p.Asp291Asn|871/1248|871/1248|291/415||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.6|protein_coding|10/10|c.1054G>A|p.Asp352Asn|1054/1431|1054/1431|352/476||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.7|protein_coding|10/10|c.1051G>A|p.Asp351Asn|1051/1428|1051/1428|351/475||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.8|protein_coding|10/10|c.1054G>A|p.Asp352Asn|1054/1431|1054/1431|352/476||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.9|protein_coding|10/10|c.1057G>A|p.Asp353Asn|1057/1434|1057/1434|353/477||,T|downstream_gene_variant|MODIFIER|TraesCS1A01G002000|TraesCS1A01G002000|transcript|TraesCS1A01G002000.1|protein_coding||c.*4070G>A|||||4070|
>
>
> Cheers,
> -Hans
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Error: Cannot read property slice of null for VCF + CSI

[Hans Vasquez-G. <hav...@uc...>]

Hi all,

I am trying to load a new VCF+CSI file to my jbrowse.  However, I am
getting the following error: Cannot read property slice of null

[image: Screen Shot 2019-06-05 at 2.56.38 PM.png]

You can view at this link here
<https://dubcovskylab.ucdavis.edu/ecotilling/?loc=chr1A%3A189961459..189962859&tracks=DNA%2CHighConfGenes%2Ccombinedmaps2019&addFeatures=%5B%7B%22seq_id%22%3A%22chr7A%22%2C%20%22start%22%3A%20674082831%2C%20%22end%22%3A%20674082918%2C%20%22name%22%3A%20%22MyBLASTHit_1%22%2C%20%22description%22%20%3A%20%22evalue%205.74e-37%22%7D%5D&addTracks=%5B%7B%22label%22%3A%22blast%22%2C%22store%22%3A%22url%22%2C%22type%22%3A%22JBrowse%2FView%2FTrack%2FHTMLFeatures%22%2C%20%22key%22%3A%22BlastHSP%20Results%22%7D%5D%0A&highlight=>.
And here is a small sample of the VCF. It seems like maybe the CSI is
invalid? However, it looks like there is data in the file. Any advice would
be greatly appreciated.

##fileformat=VCFv4.0
##fileDate=201964
##source=Kronos
##referece=IWGSC
##phasing=full
##CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO
##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
##SnpEffCmd="SnpEff  iwgsc1 ./combined_maps.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations:
'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID |
Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p |
cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length |
Distance | ERRORS / WARNINGS / INFO' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function
effects for this variant. Format: 'Gene_Name | Gene_ID |
Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense
mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID |
Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
chr1A   1145762 Kronos2392:G1145762A    G       A       40.0    Pass
 seed_avail=Kronos2392;hethom=hom;ANN=A|downstream_gene_variant|MODIFIER|TraesCS1A01G001800|TraesCS1A01G001800|transcript|TraesCS1A01G001800.1|protein_coding||c.*164G>A|||||164|,A|intergenic_region|MODIFIER|TraesCS1A01G001800-TraesCS1A01G001900|TraesCS1A01G001800-TraesCS1A01G001900|intergenic_region|TraesCS1A01G001800-TraesCS1A01G001900|||n.1145762G>A||||||
chr1A   1159612 Kronos473:G1159612A     G       A       40.0    Pass
 seed_avail=Kronos473;hethom=het;ANN=A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.10|protein_coding|9/9|c.1436C>T|p.Ser479Phe|1436/1527|1436/1527|479/508||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.1|protein_coding|10/10|c.1331C>T|p.Ser444Phe|1331/1422|1331/1422|444/473||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.2|protein_coding|10/10|c.1328C>T|p.Ser443Phe|1328/1419|1328/1419|443/472||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.3|protein_coding|9/9|c.1430C>T|p.Ser477Phe|1430/1521|1430/1521|477/506||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.4|protein_coding|10/10|c.1331C>T|p.Ser444Phe|1331/1422|1331/1422|444/473||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.5|protein_coding|9/9|c.1157C>T|p.Ser386Phe|1157/1248|1157/1248|386/415||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.6|protein_coding|10/10|c.1340C>T|p.Ser447Phe|1340/1431|1340/1431|447/476||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.7|protein_coding|10/10|c.1337C>T|p.Ser446Phe|1337/1428|1337/1428|446/475||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.8|protein_coding|10/10|c.1340C>T|p.Ser447Phe|1340/1431|1340/1431|447/476||,A|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.9|protein_coding|10/10|c.1343C>T|p.Ser448Phe|1343/1434|1343/1434|448/477||,A|downstream_gene_variant|MODIFIER|TraesCS1A01G002000|TraesCS1A01G002000|transcript|TraesCS1A01G002000.1|protein_coding||c.*4356C>T|||||4356|
chr1A   1159898 Kronos2566:C1159898T    C       T       40.0    Pass
 seed_avail=Kronos2566;hethom=het;ANN=T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.10|protein_coding|9/9|c.1150G>A|p.Asp384Asn|1150/1527|1150/1527|384/508||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.1|protein_coding|10/10|c.1045G>A|p.Asp349Asn|1045/1422|1045/1422|349/473||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.2|protein_coding|10/10|c.1042G>A|p.Asp348Asn|1042/1419|1042/1419|348/472||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.3|protein_coding|9/9|c.1144G>A|p.Asp382Asn|1144/1521|1144/1521|382/506||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.4|protein_coding|10/10|c.1045G>A|p.Asp349Asn|1045/1422|1045/1422|349/473||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.5|protein_coding|9/9|c.871G>A|p.Asp291Asn|871/1248|871/1248|291/415||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.6|protein_coding|10/10|c.1054G>A|p.Asp352Asn|1054/1431|1054/1431|352/476||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.7|protein_coding|10/10|c.1051G>A|p.Asp351Asn|1051/1428|1051/1428|351/475||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.8|protein_coding|10/10|c.1054G>A|p.Asp352Asn|1054/1431|1054/1431|352/476||,T|missense_variant|MODERATE|TraesCS1A01G001900|TraesCS1A01G001900|transcript|TraesCS1A01G001900.9|protein_coding|10/10|c.1057G>A|p.Asp353Asn|1057/1434|1057/1434|353/477||,T|downstream_gene_variant|MODIFIER|TraesCS1A01G002000|TraesCS1A01G002000|transcript|TraesCS1A01G002000.1|protein_coding||c.*4070G>A|||||4070|


Cheers,
-Hans

Re: [Gmod-ajax] fasta setup

[Zhihao D. <zhi...@gm...>]

Sorry for the delayed reply, but thanks Ke and Scott.
Your feedback is very helpful. I cleared the browser catching and it seems
to have fixed it. The server side is fine.

Best wishes,
Zhihao



On Fri, 3 May 2019 at 20:11, Scott Cain <sc...@sc...> wrote:

> Hello Zhihao,
>
> There are a few things I would check:
>
> * Did the browser reload/refresh really work? With javascript and json
> files, browsers can be very conservative about caching.  There are a few
> ways to get around this: open the browser's dev tools and turn off caching
> explicitly, or open the URL in a incognito/private window.
> * In the data/seq directory, do you see entries in the refSeqs.json file
> for both chromosomes?
> * Also in the data/seq directory, do you see two directories, one for each
> chromosome?
>
> Scott
>
>
> On Fri, May 3, 2019 at 8:10 AM Zhihao Ding <zhi...@gm...> wrote:
>
>> Dear Jbrowse developers,
>>
>> Thanks for developing Jbrowse. I've been trying to setup an instance
>> following the instructions. I am able to see the browser page, but haven't
>> managed to get the reference sequence right.
>>
>> I've downloaded a couple of fasta files just for testing from the
>> following link
>> ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
>>
>> I then run the following two commands:
>> bin/prepare-refseqs.pl --fasta
>> Homo_sapiens.GRCh38.dna_rm.chromosome.1.fa.gz
>> bin/prepare-refseqs.pl --fasta
>> Homo_sapiens.GRCh38.dna_rm.chromosome.2.fa.gz
>>
>> This is  trackList.json generated:
>> {
>>    "formatVersion" : 1,
>>    "tracks" : [
>>       {
>>          "category" : "Reference sequence",
>>          "chunkSize" : 20000,
>>          "key" : "Reference sequence",
>>          "label" : "DNA",
>>          "seqType" : "dna",
>>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>>          "type" : "SequenceTrack",
>>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
>>       }
>>    ]
>> }
>>
>> On the browser page, I have only contig 1 in the dropdown list.
>>
>> Could anyone point me to the right directions here?
>>
>> Thank you,
>> Zhihao
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


-- 
Regards,
Zhihao Ding

Re: [Gmod-ajax] JBrowse setup problems

[Nathan D. <nat...@lb...>]

That’s not memory, that’s disk-space. 

df -h

Just delete the JBrowse directory and try to recover the space for re-installing.  

Nathan



> On May 7, 2019, at 3:13 PM, Inderski, Blake - ARS via Gmod-ajax <gmo...@li...> wrote:
> 
> Hello,
>  
> I’ve encountered difficulties with the setup of JQuery. Running ./setup.sh multiple times resulted in the same output (setup.log attached):
>  
> Gathering system information ...done.
> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier.
> Installing node.js dependencies and building with webpack ...done.
> Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.
>  
> Formatting Volvox example data ... failed.  See setup.log file for error messages.
>  
> Formatting Yeast example data ...done.
> To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast <http://your.jbrowse.root/index.html?data=sample_data/json/yeast>.
>  
> Each time, I attempted to download additional dependencies, but it seems I’m still missing some. Recently, I encountered memory issues:
>  
> Gathering system information ...done.
> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier.
> Installing node.js dependencies and building with webpack ...done.
> Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.
>  
> ./setup.sh: line 25: echo: write error: No space left on device
> ./setup.sh: line 26: echo: write error: No space left on device
> ./setup.sh: line 27: echo: write error: No space left on device
> Formatting Volvox example data ..../setup.sh: line 25: echo: write error: No space left on device
> ./setup.sh: line 26: echo: write error: No space left on device
> ./setup.sh: line 27: echo: write error: No space left on device
>  failed.  See setup.log file for error messages.
>  
> Formatting Yeast example data ...done.
> To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast <http://your.jbrowse.root/index.html?data=sample_data/json/yeast>.
>  
> It seems that every time I ran the setup script there was redundant buildup that ultimately resulted in my memory getting capped:
>  
> Filesystem      Size  Used Avail Use% Mounted on
> udev            488M     0  488M   0% /dev
> tmpfs           100M  3.4M   96M   4% /run
> /dev/xvda1      7.7G  7.7G   23M 100% /
> tmpfs           496M  4.0K  496M   1% /dev/shm
> tmpfs           5.0M     0  5.0M   0% /run/lock
> tmpfs           496M     0  496M   0% /sys/fs/cgroup
> tmpfs           100M     0  100M   0% /run/user/1000
>  
> Is there an uninstall script available? Alternatively I would have to revert to a backup to specifically address the memory problems. Any advice on how I should proceed?
>  
> Thanks,
> Blake
> 
> 
> 
> 
> 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. <jbrowse_setup.log>_______________________________________________
> Gmod-ajax mailing list
> Gmo...@li... <mailto:Gmo...@li...>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax>

[Gmod-ajax] JBrowse setup problems

[Inderski, B. - A. <Bla...@AR...>]

Hello,

I’ve encountered difficulties with the setup of JQuery. Running ./setup.sh multiple times resulted in the same output (setup.log attached):


Gathering system information ...done.

NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier.

Installing node.js dependencies and building with webpack ...done.

Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.



Formatting Volvox example data ... failed.  See setup.log file for error messages.



Formatting Yeast example data ...done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Each time, I attempted to download additional dependencies, but it seems I’m still missing some. Recently, I encountered memory issues:


Gathering system information ...done.

NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier.

Installing node.js dependencies and building with webpack ...done.

Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.



./setup.sh: line 25: echo: write error: No space left on device

./setup.sh: line 26: echo: write error: No space left on device

./setup.sh: line 27: echo: write error: No space left on device

Formatting Volvox example data ..../setup.sh: line 25: echo: write error: No space left on device

./setup.sh: line 26: echo: write error: No space left on device

./setup.sh: line 27: echo: write error: No space left on device

 failed.  See setup.log file for error messages.



Formatting Yeast example data ...done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

It seems that every time I ran the setup script there was redundant buildup that ultimately resulted in my memory getting capped:


Filesystem      Size  Used Avail Use% Mounted on

udev            488M     0  488M   0% /dev

tmpfs           100M  3.4M   96M   4% /run

/dev/xvda1      7.7G  7.7G   23M 100% /

tmpfs           496M  4.0K  496M   1% /dev/shm

tmpfs           5.0M     0  5.0M   0% /run/lock

tmpfs           496M     0  496M   0% /sys/fs/cgroup

tmpfs           100M     0  100M   0% /run/user/1000

Is there an uninstall script available? Alternatively I would have to revert to a backup to specifically address the memory problems. Any advice on how I should proceed?

Thanks,
Blake




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.

Re: [Gmod-ajax] Setting up the directory in Mac

[Colin <col...@gm...>]

This FAQ entry might help with setting up multiple reference. Each one gets
it's own "data directory" and then you can use the URL bar to select
between them
https://jbrowse.org/docs/faq.html#how-do-i-set-up-multiple-genomes-in-a-single-jbrowse-instance


-Colin

On Mon, May 6, 2019 at 2:10 PM Rahnama, Mostafa <Mos...@uk...>
wrote:

> Thanks Nathan. Its working now.
>
>
> Another question:
>
> If I want to have multiple references, could you please give me an example
> that show how my track.conf file should looks like? or should I have
> multiple track.conf files?
>
>
> Thanks,
>
> Mostafa
>
>
>
>
>
> *Mostafa Rahnama, PhD*
> *Postdoctoral Scholar*
> *Department of Plant Pathology *
> *University of Kentucky*
> *Lexington, KY 40546 USA*
> *Tel:  (859) 218-0728 *
>
> ------------------------------
> *From:* Lbl <nat...@lb...>
> *Sent:* Sunday, May 5, 2019 10:14:53 PM
> *To:* Rahnama, Mostafa
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Setting up the directory in Mac
>
> That should work unless the server is not on.
>
> Nathan
>
> On May 5, 2019, at 8:13 AM, Rahnama, Mostafa <Mos...@uk...>
> wrote:
>
> Dear Sir/Madam,
>
>
> I'm trying to setup Jbrowse in my iMac (Retina 5K) and I followed all the
> steps as mentioned in your page. Every commands run properly but I have a
> problem for loading the website.
>
> I think the problem is finding /var/www/html/ directory.
>
> I think mac doesn't have that so I put the jbrowse in
> /Library/WebServer/Documents/.
>
>
> Could you please let me know how I can solve this problem?
>
>
> Best regards,
>
> Mostafa
>
>
>
> *Mostafa Rahnama, PhD*
> *Postdoctoral Scholar*
> *Department of Plant Pathology *
> *University of Kentucky*
> *Lexington, KY 40546 USA*
> *Tel:  (859) 218-0728 *
>
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