gmod-ajax — JBrowse list

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

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

I believe utf8 is fine, there is some sample data for JBrowse that tests
Japanese character set:

See
http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1

If there were any particular concerns about it not working feel free to
open a github issue!

-Colin

On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm...> wrote:

> Hi all:
>
> I am curious about the character encoding of JBrowse and Apollo.
> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
> In gff3 file specification
> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md,
> it recommend usage of Latin-1 or Unicode.
> I didn't find any information in any documentation. I probably missed it,
> though.
>
> Best regards,
> Leo (Yi Hsiao)
> --
> Leo (Yi Hsiao),
> Bioinformatics Internship,
> i5k workspace, National Agricultural Library,
> MD, USA
>
> Personal Website: https://hsiaoyi0504.github.io/
> GitHub: https://github.com/hsiaoyi0504/
> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] About character encoding of JBrowse and Apollo

[蕭毅 <hsi...@gm...>]

Hi all:

I am curious about the character encoding of JBrowse and Apollo.
Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
In gff3 file specification
https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md,
it recommend usage of Latin-1 or Unicode.
I didn't find any information in any documentation. I probably missed it,
though.

Best regards,
Leo (Yi Hsiao)
-- 
Leo (Yi Hsiao),
Bioinformatics Internship,
i5k workspace, National Agricultural Library,
MD, USA

Personal Website: https://hsiaoyi0504.github.io/
GitHub: https://github.com/hsiaoyi0504/
LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/

[Gmod-ajax] JBrowse 1.15.1 released

[Robert B. <rb...@gm...>]

Hi all,

JBrowse 1.15.1 has been released!
Files for download

   - JBrowse-1.15.1.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.1-release/JBrowse-1.15.1.zip>
–
   3.2M
   file SHA1 71284c64391798cb2b6648bac125522af1ba17a2
   - JBrowse-1.15.1-dev.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.1-release/JBrowse-1.15.1-dev.zip>
–
   9.4M
   file SHA1 26ccaf7768209fa18e2706ea050fc3f8349ba18d
   - JBrowse-1.15.1-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.1-release/JBrowse-1.15.1-desktop-win32-x64.zip>
–
   68M
   file SHA1 231934c5813bd02710db42e017a0455652559f45
   - JBrowse-1.15.1-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.1-release/JBrowse-1.15.1-desktop-linux-x64.zip>
–
   66M
   file SHA1 d895966abbbe2c2d623be6bb5150bb20d0bdc16e
   - JBrowse-1.15.1-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.1-release/JBrowse-1.15.1-desktop-darwin-x64.zip>
–
   66M
   file SHA1 bf4429998ae005ff2003e19c461e46d1ebd95a0a

Minor Improvements

   -

   Add a internal code attribute for XHR requests that use byte-range
   headers so that if a
   server does not support it, an error is returned immediately. Thanks to
   @theChinster <https://github.com/theChinster>
   for the motivating example (issue #1131
   <https://github.com/gmod/jbrowse/issues/1131>, issue #1132
   <https://github.com/gmod/jbrowse/issues/1132>, issue #1134
   <https://github.com/gmod/jbrowse/pull/1134>, @cmdcolin
   <https://github.com/cmdcolin>).
   -

   Speed up TwoBit file processing with a robust implementation of the file
   spec. The
   improvements are contained in a new npm module @gmod
   <https://www.npmjs.com/package/%3Ca%20href=>/twobit”>@gmod
   <https://github.com/gmod>/twobit.
   Thanks to @cmdcolin <https://github.com/cmdcolin> for some testing and
   motivating examples. (issue #1116
   <https://github.com/gmod/jbrowse/issues/1116>, issue #1146
   <https://github.com/gmod/jbrowse/pull/1146>,
   @rbuels <https://github.com/rbuels>)
   -

   Added feature.get(‘seq’) to CRAM features which enables detailed
   comparison of the
   read versus the reference with the renderAlignment configuration. (issue
   #1126 <https://github.com/gmod/jbrowse/issues/1126>,
   issue #1149 <https://github.com/gmod/jbrowse/pull/1149>, @rbuels
   <https://github.com/rbuels>)
   -

   Added support for 1000genomes CRAM 2.0 codecs via updates to the @gmod
   <https://github.com/gmod>/cram npm module.
   (@rbuels <https://github.com/rbuels>)
   -

   Add some better formatting for rich metadata in the “About this track”
   dialog boxes for
   tracks. Thanks to Wojtek Bażant for the idea and implementation! (issue
   #1148 <https://github.com/gmod/jbrowse/pull/1148>, @wbazant
   <https://github.com/wbazant>)

Bug fixes

   -

   Fix bug where prepare-refseqs with indexed FASTA would allows scrolling
   past the end of
   the chromosome (@cmdcolin <https://github.com/cmdcolin>).
   -

   Fix long standing bug related to not being able to configure dataRoot in
   the config file.
   Now you can set dataRoot=mydirectory to make JBrowse load mydirectory
   instead of the
   default data by default (issue #627
   <https://github.com/gmod/jbrowse/issues/627>, issue #1144
   <https://github.com/gmod/jbrowse/pull/1144>, @cmdcolin
   <https://github.com/cmdcolin>).
   -

   Added hashing of the BAM feature data to generate unique IDs in order to
   distinguish
   reads that have nearly identical information (same read name, start,
   end, seq, etc).
   If the reads literally have identical information in them JBrowse is
   still unable to
   display but this generally seems to be due to limited use case such as
   secondary
   alignments in RNA-seq (issue #1108
   <https://github.com/gmod/jbrowse/issues/1108>, issue #1145
   <https://github.com/gmod/jbrowse/pull/1145>, @cmdcolin
   <https://github.com/cmdcolin>)

Re: [Gmod-ajax] Gene search coordinates issue

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

Hi Vaneet,

I'm wondering how to reproduce the issue because I am not able to reproduce
it by, for example, switching between the volvox and modENCODE sample
browsers.

I guess it might be helpful to see a sample instance that you are using or
get a minimal reproducible case!

-Colin

On Mon, Jul 30, 2018 at 2:51 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I’m testing to upgrade to the latest JBrowse release 1.15.0-dev, and I
> noticed a peculiar issue. I ran the generate-names.pl script to generate
> name indexes for a specific set of my tracks for a given genome.  The gene
> search works correctly.  I noticed though that when I search for a
> particular gene, in this case ‘hhex’ in Xenopus tropicalis 9.1 and go to
> the gene, it retrieves the correct coordinates which are the following:
>
>
>
> Chr07:17287891..17303653 (15.76 Kb)
>
>
>
> Then if I go to another genome using the dataset selector, then come back
> to this tropicalis 9.1 genome, it should show the last gene I was looking
> at but it pops up with an error message box:
>
>
>
> Not found: Chr07:17287891..1730365315.76 Kb
>
>
>
> This issue happens with any gene searched on any genome as long as I
> follow the steps I outlined above by searching a gene and then flipping
> back and forth to the genome version again.  If you look carefully at the
> error message box (in yellow) it appears it’s missing the space between the
> end coordinate and the size of the displayed window in parentheses compared
> to the original coordinates it found in the original search.  Perhaps in
> the code the space and parentheses are not being put in, or perhaps it
> should be omitting the window size altogether as it’s not needed to find
> the gene.
>
>
>
> Is this a problem on my end, or is it a bug?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary AB T2N 1N4*
>
> *CANADA*
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Gene search coordinates issue

[Vaneet L. <van...@uc...>]

Hello,

I'm testing to upgrade to the latest JBrowse release 1.15.0-dev, and I noticed a peculiar issue. I ran the generate-names.pl script to generate name indexes for a specific set of my tracks for a given genome.  The gene search works correctly.  I noticed though that when I search for a particular gene, in this case 'hhex' in Xenopus tropicalis 9.1 and go to the gene, it retrieves the correct coordinates which are the following:

Chr07:17287891..17303653 (15.76 Kb)

Then if I go to another genome using the dataset selector, then come back to this tropicalis 9.1 genome, it should show the last gene I was looking at but it pops up with an error message box:

Not found: Chr07:17287891..1730365315.76 Kb

This issue happens with any gene searched on any genome as long as I follow the steps I outlined above by searching a gene and then flipping back and forth to the genome version again.  If you look carefully at the error message box (in yellow) it appears it's missing the space between the end coordinate and the size of the displayed window in parentheses compared to the original coordinates it found in the original search.  Perhaps in the code the space and parentheses are not being put in, or perhaps it should be omitting the window size altogether as it's not needed to find the gene.

Is this a problem on my end, or is it a bug?

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

Re: [Gmod-ajax] [apollo] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

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

That’s right.  It installs using npm (against 1.12.5-apollo) and then runs the setup.sh script.  

I’m wondering if either the local cpanm commands are out of sync, or not run, or just missing dependencies.  

I seem to have no issues when running this on a linux de novo system.

I’m going to keep poking around.   I sense a rebuild of home-brew might be part of the issue based on googling around, but I’m unsure.   

Nathan


> On Jul 29, 2018, at 7:39 PM, Robert Buels <rb...@gm...> wrote:
> 
> Sounds like you definitely need to try reinstalling the things in the JBrowse extlib/ directory.  I'm not sure how it's wired in Apollo, but I'd recommend deleting jbrowse-download/extlib and re-running setup.sh or the Apollo equivalent.  Nathan, is setup.sh the right thing to run for a clean install?
> 
> 
> On Sun, Jul 29, 2018 at 6:14 PM Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
> 
> Unfortunately Perl + Mac has become more problematic.  
> 
> I’m assuming you’re using home-brew perl? 
> 
> I’ll look at some better solutions this week and reply here.  
> 
> Some workarounds:
> 
> 1 - use docker or another linux-based system to install apollo with the proper dependencies and run the web services through that.   Seems to be less problematic than the Mac.
> 
> 2 - try installing in the same way that you install JBrowse ( brew install --build-from-source perl).  
> 
> 3 - lots of info online about re-installing perl packages if you are using homebrew on the Mac.  
> 
> Again, I’ll follow-up when I have a better solution for you this week, but possibly someone else has already run into this. 
> 
> Nathan
> 
> 
>> On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <you...@va... <mailto:you...@va...>> wrote:
>> 
>> Hi
>> 
>> I can run Apollo, but got error when I wanna to add annotations:
>> 
>> Here is the error info:
>> 
>> Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl <http://add_features_from_gff3_to_annotations.pl/> -h
>> 
>> Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
>> dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
>>   Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
>>   Expected in: flat namespace
>> 
>> dyld: Symbol not found: _Perl_xs_handshake
>>   Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
>>   Expected in: flat namespace
>> 
>> Abort trap: 6
>> 
>> Best
>> Youhuang Bai
>> 
>> 
>> 
>> 
>> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
>> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li... <mailto:sy...@li...> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________
> 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>

Re: [Gmod-ajax] [apollo] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

[Robert B. <rb...@gm...>]

Sounds like you definitely need to try reinstalling the things in the
JBrowse extlib/ directory.  I'm not sure how it's wired in Apollo, but I'd
recommend deleting jbrowse-download/extlib and re-running setup.sh or the
Apollo equivalent.  Nathan, is setup.sh the right thing to run for a clean
install?


On Sun, Jul 29, 2018 at 6:14 PM Nathan Dunn <nat...@lb...> wrote:

>
> Unfortunately Perl + Mac has become more problematic.
>
> I’m assuming you’re using home-brew perl?
>
> I’ll look at some better solutions this week and reply here.
>
> Some workarounds:
>
> 1 - use docker or another linux-based system to install apollo with the
> proper dependencies and run the web services through that.   Seems to be
> less problematic than the Mac.
>
> 2 - try installing in the same way that you install JBrowse ( brew install
> --build-from-source perl).
>
> 3 - lots of info online about re-installing perl packages if you are using
> homebrew on the Mac.
>
> Again, I’ll follow-up when I have a better solution for you this week, but
> possibly someone else has already run into this.
>
> Nathan
>
>
> On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <you...@va...>
> wrote:
>
> Hi
>
> I can run Apollo, but got error when I wanna to add annotations:
>
> Here is the error info:
>
> Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/
> add_features_from_gff3_to_annotations.pl -h
>
> Attempting to create directory
> /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
> dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
>   Referenced from:
> /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
>   Expected in: flat namespace
>
> dyld: Symbol not found: _Perl_xs_handshake
>   Referenced from:
> /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
>   Expected in: flat namespace
>
> Abort trap: 6
>
> Best
> Youhuang Bai
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at
> http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with
> which you subscribed to the list, send a message to sy...@li... |
> 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
> the message body blank.
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] [apollo] dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake

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

Unfortunately Perl + Mac has become more problematic.  

I’m assuming you’re using home-brew perl? 

I’ll look at some better solutions this week and reply here.  

Some workarounds:

1 - use docker or another linux-based system to install apollo with the proper dependencies and run the web services through that.   Seems to be less problematic than the Mac.

2 - try installing in the same way that you install JBrowse ( brew install --build-from-source perl).  

3 - lots of info online about re-installing perl packages if you are using homebrew on the Mac.  

Again, I’ll follow-up when I have a better solution for you this week, but possibly someone else has already run into this. 

Nathan


> On Jul 27, 2018, at 3:03 PM, Bai, Youhuang <you...@va...> wrote:
> 
> Hi
> 
> I can run Apollo, but got error when I wanna to add annotations:
> 
> Here is the error info:
> 
> Xiaozhuans-MacBook-Pro:Apollo-2.1.0 xiaozhuandai$ tools/data/add_features_from_gff3_to_annotations.pl -h
> 
> Attempting to create directory /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib
> dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
>   Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
>   Expected in: flat namespace
> 
> dyld: Symbol not found: _Perl_xs_handshake
>   Referenced from: /Users/xiaozhuandai/Baiyouhuang/Apollo-2.1.0/tools/data/../../jbrowse-download/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level/auto/List/MoreUtils/XS/XS.bundle
>   Expected in: flat namespace
> 
> Abort trap: 6
> 
> Best
> Youhuang Bai
> 
> 
> 
> 
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li... <mailto:sy...@li...> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 

Re: [Gmod-ajax] JBrowse Configuration/Best Practice

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

Hi Frederic,

The generate-names.pl script does work on GFF3Tabix files actually :)

It is a little more limited than flatfile-to-json.pl name indexing because
flatfile-to-json.pl tracks can index arbitrary column 9 data by using the
--nameAttributes parameter, but the GFF3Tabix tracks automatically index
"Name" and "ID" fields (and probably soon it can be made arbitrary fields
too)

-Colin

On Wed, Jul 25, 2018 at 3:59 AM SAPET, Frederic <fre...@bi...>
wrote:

> Hi,
>
>
>
> 1.15 is great, as well as the desktop version, congratulations Rob and
> Colin.
>
>
>
> I would like to ask a question about the use of Tabix GFF. It’s great to
> reduce disk usage and it takes less time for the admin (you don’t need to
> run flatfile-to-json and you just need to focus about the configuration of
> the track). But what about the index of names ?
>
> If I understand well, generate-names.pl works from tracks that have been
> processed through flatfile-to-json ?
>
> So if I would look at migrating my feature tracks away from
> flatfile-to-json like Rob said, I will lose the search function, right ?
>
>
>
> Fred
>
>
>
> *De :* Hough, Heidi [mailto:hei...@ws...]
> *Envoyé :* mardi 24 juillet 2018 17:24
> *À :* Robert Buels <rb...@gm...>
> *Cc :* gmo...@li...; he...@gm...
> *Objet :* Re: [Gmod-ajax] JBrowse Configuration/Best Practice
>
>
>
> Oh my, I’m behind the game.  Too many balls in the air.  I’ll push for
> 1.15.
>
>
>
> Regards,
>
> Heidi
>
>
>
> *From:* Robert Buels [mailto:rb...@gm... <rb...@gm...>]
> *Sent:* Tuesday, July 24, 2018 8:22 AM
> *To:* Hough, Heidi <hei...@ws...>
> *Cc:* Colin <col...@gm...>; Scott Cain <sc...@sc...>;
> gmo...@li...; he...@gm...
> *Subject:* Re: [Gmod-ajax] JBrowse Configuration/Best Practice
>
>
>
> 1.13.3?  The latest JBrowse release is 1.15.0, any reason you're not
> upgrading all the way to 1.15?
>
>
>
> On Tue, Jul 24, 2018 at 8:21 AM Hough, Heidi <hei...@ws...> wrote:
>
> Thank you for the suggestions.  We’ve got a couple other sites using
> various versions.  My goal is to get them all updated to 1.13.3.  I’ll have
> to double-check, but I think we were having problems getting the
> MultiVariantViewer plugin working properly on the latest version; which is
> why we’re using 1.12.3 for that particular site.
>
>
>
> Regards,
>
> Heidi
>
>
>
> *From:* Colin [mailto:col...@gm...]
> *Sent:* Tuesday, July 24, 2018 6:42 AM
> *To:* Robert Buels <rb...@gm...>
> *Cc:* Scott Cain <sc...@sc...>; gmo...@li...;
> he...@gm...; Hough, Heidi <hei...@ws...>
> *Subject:* Re: [Gmod-ajax] JBrowse Configuration/Best Practice
>
>
>
> One other thing that caused some data directory size inflation in older
> jbrowse versions was this bug in flatfile-to-json.pl
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__flatfile-2Dto-2Djson.pl&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=yz6-QhcZnAgcV6_fgyiob6cQIxBPUaAmfVDBXCQgmb0&e=>
> that is now fixed https://github.com/GMOD/jbrowse/issues/470
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_jbrowse_issues_470&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=T82QlGSRm4NZnS8Nl8bGDHfN9fAtymCg_1r6m6uoTPk&e=>
>
>
>
> The bug occurs when you use a perl 5.18+ on jbrowse 1.12.3 or earlier
>
>
>
> You could fix the issue by moving to 1.12.4 or later (to get the bugfix)
> or, if you are sticking with 1.12.1, you could remove the tracks and
> re-running the flatfile-to-json with an older version of perl, e.g. perl
> 5.14
>
>
>
> The Tabix GFF is a great solution to reduce on disk files too, but unless
> you upgrade fully to the latest versions of jbrowse e.g. 1.15 I probably
> wouldn't use it (it didn't even exist in 1.12.1 anyways)
>
>
>
>
>
> -Colin
>
>
>
> On Mon, Jul 23, 2018 at 4:04 PM Robert Buels <rb...@gm...> wrote:
>
> My main recommendation for reducing startup time is to upgrade to the
> latest version of JBrowse.
>
>
>
> For reducing the disk footprint and number of files in the `data/tracks`
> subdirectory, I'd look at migrating your feature tracks away from
> `flatfile-to-json` NCList format to an indexed format like Tabix-indexed
> GFF3 (using JBrowse's GFF3Tabix driver), or BigBed (using JBrowse's BigBed
> driver).
>
>
>
> For the `data/names` subdirectory, there is an ElasticSearch plugin out
> there that would let you store your name-searching index in ElasticSearch,
> see https://github.com/elsiklab/jbrowse_elasticsearch
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_elsiklab_jbrowse-5Felasticsearch&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=4sEmUanU1VseDP5OJH0X2enzv3YKmzzmRzwtncKu_GY&e=>
>
>
>
> Hope this helps! Always happy to answer any further questions.
>
>
>
> On Mon, Jul 23, 2018 at 12:53 PM Scott Cain <sc...@sc...> wrote:
>
> Hi Heidi,
>
>
>
> I'm cc'ing this to the JBrowse mailing list for more input.
>
>
>
> I can say that 346GB sounds like a lot to me, but nematodes have a lot
> smaller genomes than plants!  Have you looked at the javascript console to
> see what takes a lot of time?  Do you want to post a link to the one that
> performs badly?  Also, I'll point out (before Rob gets a chance to) that
> newer releases of JBrowse use webpack and thus have better startup times.
> Finally, things you might want to think about is converting some of your
> GFF-based tracks to tabix indexed files, which will be much cleaner from a
> storage perspective and probably perform better too, though I don't
> remember if tabix indexed GFF files work with 1.12 (or work well, which I
> suppose is two separate things).
>
>
>
> Scott
>
>
>
>
>
> On Mon, Jul 23, 2018 at 11:52 AM, Hough, Heidi <hei...@ws...>
> wrote:
>
> Hello
>
>
>
> I’d appreciate some JBrowse guidance in regards to information I can’t
> seem to adequately locate in the documentation regarding server hardware
> configuration.
>
>
>
> We’re using JBrowse 1.12.3 on several of our websites.  We’ve got one, in
> particular that seems to be causing poor performance with the website.  The
> JBrowse footprint, on disk is 346G.  How does this compare with other
> users?  Is this considered large?  We also have over 5 million files.  This
> creates I/O issues on disk.  What configuration recommendations do you have
> to help alleviate this problem.
>
>
>
> https://www.rosaceae.org/tools/jbrowse
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rosaceae.org_tools_jbrowse&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=ob7Qitvr9e8MWpxJvxak1roVaqk3Y5oMn19djFU5tp0&e=>
>
> Heidi Hough
> System/Database Administrator
> Main Bioinformatics Lab - Department of Horticulture
> Washington State University
> 48 Johnson Hall
> Pullman, WA 99164-6414
>
> 509-335-7093 <(509)%20335-7093>
> hei...@ws...
>
>
>
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=8oM58hLZs7__X1S9C3bp1l2rbbk9dXF07ECcN0f9OcY&e=>)
>                    216-392-3087 <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=MczgiGElisUAjxkUtZUdoub4x_lZbT2NV1Q8jGmYKa8&e=>
> _______________________________________________
> 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=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=20CO3d0fISjaLFo28bA4S16fUZpo4Buz9ur-2E3uImU&e=>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=MczgiGElisUAjxkUtZUdoub4x_lZbT2NV1Q8jGmYKa8&e=>
> _______________________________________________
> 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=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=20CO3d0fISjaLFo28bA4S16fUZpo4Buz9ur-2E3uImU&e=>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse Configuration/Best Practice

[SAPET, F. <fre...@bi...>]

Hi,

1.15 is great, as well as the desktop version, congratulations Rob and Colin.

I would like to ask a question about the use of Tabix GFF. It’s great to reduce disk usage and it takes less time for the admin (you don’t need to run flatfile-to-json and you just need to focus about the configuration of the track). But what about the index of names ?
If I understand well, generate-names.pl works from tracks that have been processed through flatfile-to-json ?
So if I would look at migrating my feature tracks away from flatfile-to-json like Rob said, I will lose the search function, right ?

Fred

De : Hough, Heidi [mailto:hei...@ws...]
Envoyé : mardi 24 juillet 2018 17:24
À : Robert Buels <rb...@gm...>
Cc : gmo...@li...; he...@gm...
Objet : Re: [Gmod-ajax] JBrowse Configuration/Best Practice

Oh my, I’m behind the game.  Too many balls in the air.  I’ll push for 1.15.

Regards,
Heidi

From: Robert Buels [mailto:rb...@gm...]
Sent: Tuesday, July 24, 2018 8:22 AM
To: Hough, Heidi <hei...@ws...<mailto:hei...@ws...>>
Cc: Colin <col...@gm...<mailto:col...@gm...>>; Scott Cain <sc...@sc...<mailto:sc...@sc...>>; gmo...@li...<mailto:gmo...@li...>; he...@gm...<mailto:he...@gm...>
Subject: Re: [Gmod-ajax] JBrowse Configuration/Best Practice

1.13.3?  The latest JBrowse release is 1.15.0, any reason you're not upgrading all the way to 1.15?

On Tue, Jul 24, 2018 at 8:21 AM Hough, Heidi <hei...@ws...<mailto:hei...@ws...>> wrote:
Thank you for the suggestions.  We’ve got a couple other sites using various versions.  My goal is to get them all updated to 1.13.3.  I’ll have to double-check, but I think we were having problems getting the MultiVariantViewer plugin working properly on the latest version; which is why we’re using 1.12.3 for that particular site.

Regards,
Heidi

From: Colin [mailto:col...@gm...<mailto:col...@gm...>]
Sent: Tuesday, July 24, 2018 6:42 AM
To: Robert Buels <rb...@gm...<mailto:rb...@gm...>>
Cc: Scott Cain <sc...@sc...<mailto:sc...@sc...>>; gmo...@li...<mailto:gmo...@li...>; he...@gm...<mailto:he...@gm...>; Hough, Heidi <hei...@ws...<mailto:hei...@ws...>>
Subject: Re: [Gmod-ajax] JBrowse Configuration/Best Practice

One other thing that caused some data directory size inflation in older jbrowse versions was this bug in flatfile-to-json.pl<https://urldefense.proofpoint.com/v2/url?u=http-3A__flatfile-2Dto-2Djson.pl&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=yz6-QhcZnAgcV6_fgyiob6cQIxBPUaAmfVDBXCQgmb0&e=> that is now fixed https://github.com/GMOD/jbrowse/issues/470<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_jbrowse_issues_470&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=T82QlGSRm4NZnS8Nl8bGDHfN9fAtymCg_1r6m6uoTPk&e=>

The bug occurs when you use a perl 5.18+ on jbrowse 1.12.3 or earlier

You could fix the issue by moving to 1.12.4 or later (to get the bugfix) or, if you are sticking with 1.12.1, you could remove the tracks and re-running the flatfile-to-json with an older version of perl, e.g. perl 5.14

The Tabix GFF is a great solution to reduce on disk files too, but unless you upgrade fully to the latest versions of jbrowse e.g. 1.15 I probably wouldn't use it (it didn't even exist in 1.12.1 anyways)


-Colin

On Mon, Jul 23, 2018 at 4:04 PM Robert Buels <rb...@gm...<mailto:rb...@gm...>> wrote:
My main recommendation for reducing startup time is to upgrade to the latest version of JBrowse.

For reducing the disk footprint and number of files in the `data/tracks` subdirectory, I'd look at migrating your feature tracks away from `flatfile-to-json` NCList format to an indexed format like Tabix-indexed GFF3 (using JBrowse's GFF3Tabix driver), or BigBed (using JBrowse's BigBed driver).

For the `data/names` subdirectory, there is an ElasticSearch plugin out there that would let you store your name-searching index in ElasticSearch, see https://github.com/elsiklab/jbrowse_elasticsearch<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_elsiklab_jbrowse-5Felasticsearch&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=4sEmUanU1VseDP5OJH0X2enzv3YKmzzmRzwtncKu_GY&e=>

Hope this helps! Always happy to answer any further questions.

On Mon, Jul 23, 2018 at 12:53 PM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Heidi,

I'm cc'ing this to the JBrowse mailing list for more input.

I can say that 346GB sounds like a lot to me, but nematodes have a lot smaller genomes than plants!  Have you looked at the javascript console to see what takes a lot of time?  Do you want to post a link to the one that performs badly?  Also, I'll point out (before Rob gets a chance to) that newer releases of JBrowse use webpack and thus have better startup times.  Finally, things you might want to think about is converting some of your GFF-based tracks to tabix indexed files, which will be much cleaner from a storage perspective and probably perform better too, though I don't remember if tabix indexed GFF files work with 1.12 (or work well, which I suppose is two separate things).

Scott


On Mon, Jul 23, 2018 at 11:52 AM, Hough, Heidi <hei...@ws...<mailto:hei...@ws...>> wrote:
Hello

I’d appreciate some JBrowse guidance in regards to information I can’t seem to adequately locate in the documentation regarding server hardware configuration.

We’re using JBrowse 1.12.3 on several of our websites.  We’ve got one, in particular that seems to be causing poor performance with the website.  The JBrowse footprint, on disk is 346G.  How does this compare with other users?  Is this considered large?  We also have over 5 million files.  This creates I/O issues on disk.  What configuration recommendations do you have to help alleviate this problem.

https://www.rosaceae.org/tools/jbrowse<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rosaceae.org_tools_jbrowse&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=ob7Qitvr9e8MWpxJvxak1roVaqk3Y5oMn19djFU5tp0&e=>
Heidi Hough
System/Database Administrator
Main Bioinformatics Lab - Department of Horticulture
Washington State University
48 Johnson Hall
Pullman, WA 99164-6414
509-335-7093<tel:(509)%20335-7093>
hei...@ws...<mailto:hei...@ws...>




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=8oM58hLZs7__X1S9C3bp1l2rbbk9dXF07ECcN0f9OcY&e=>)                     216-392-3087<tel:(216)%20392-3087>
Ontario Institute for Cancer Research
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Check out the vibrant tech community on one of the world's most
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Check out the vibrant tech community on one of the world's most
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Re: [Gmod-ajax] JBrowse Configuration/Best Practice

[Hough, H. <hei...@ws...>]

Thank you for the suggestions.  We’ve got a couple other sites using various versions.  My goal is to get them all updated to 1.13.3.  I’ll have to double-check, but I think we were having problems getting the MultiVariantViewer plugin working properly on the latest version; which is why we’re using 1.12.3 for that particular site.

Regards,
Heidi

From: Colin [mailto:col...@gm...]
Sent: Tuesday, July 24, 2018 6:42 AM
To: Robert Buels <rb...@gm...>
Cc: Scott Cain <sc...@sc...>; gmo...@li...; he...@gm...; Hough, Heidi <hei...@ws...>
Subject: Re: [Gmod-ajax] JBrowse Configuration/Best Practice

One other thing that caused some data directory size inflation in older jbrowse versions was this bug in flatfile-to-json.pl<https://urldefense.proofpoint.com/v2/url?u=http-3A__flatfile-2Dto-2Djson.pl&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=yz6-QhcZnAgcV6_fgyiob6cQIxBPUaAmfVDBXCQgmb0&e=> that is now fixed https://github.com/GMOD/jbrowse/issues/470<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_jbrowse_issues_470&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=T82QlGSRm4NZnS8Nl8bGDHfN9fAtymCg_1r6m6uoTPk&e=>

The bug occurs when you use a perl 5.18+ on jbrowse 1.12.3 or earlier

You could fix the issue by moving to 1.12.4 or later (to get the bugfix) or, if you are sticking with 1.12.1, you could remove the tracks and re-running the flatfile-to-json with an older version of perl, e.g. perl 5.14

The Tabix GFF is a great solution to reduce on disk files too, but unless you upgrade fully to the latest versions of jbrowse e.g. 1.15 I probably wouldn't use it (it didn't even exist in 1.12.1 anyways)


-Colin

On Mon, Jul 23, 2018 at 4:04 PM Robert Buels <rb...@gm...<mailto:rb...@gm...>> wrote:
My main recommendation for reducing startup time is to upgrade to the latest version of JBrowse.

For reducing the disk footprint and number of files in the `data/tracks` subdirectory, I'd look at migrating your feature tracks away from `flatfile-to-json` NCList format to an indexed format like Tabix-indexed GFF3 (using JBrowse's GFF3Tabix driver), or BigBed (using JBrowse's BigBed driver).

For the `data/names` subdirectory, there is an ElasticSearch plugin out there that would let you store your name-searching index in ElasticSearch, see https://github.com/elsiklab/jbrowse_elasticsearch<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_elsiklab_jbrowse-5Felasticsearch&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=4sEmUanU1VseDP5OJH0X2enzv3YKmzzmRzwtncKu_GY&e=>

Hope this helps! Always happy to answer any further questions.

On Mon, Jul 23, 2018 at 12:53 PM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Heidi,

I'm cc'ing this to the JBrowse mailing list for more input.

I can say that 346GB sounds like a lot to me, but nematodes have a lot smaller genomes than plants!  Have you looked at the javascript console to see what takes a lot of time?  Do you want to post a link to the one that performs badly?  Also, I'll point out (before Rob gets a chance to) that newer releases of JBrowse use webpack and thus have better startup times.  Finally, things you might want to think about is converting some of your GFF-based tracks to tabix indexed files, which will be much cleaner from a storage perspective and probably perform better too, though I don't remember if tabix indexed GFF files work with 1.12 (or work well, which I suppose is two separate things).

Scott


On Mon, Jul 23, 2018 at 11:52 AM, Hough, Heidi <hei...@ws...<mailto:hei...@ws...>> wrote:
Hello

I’d appreciate some JBrowse guidance in regards to information I can’t seem to adequately locate in the documentation regarding server hardware configuration.

We’re using JBrowse 1.12.3 on several of our websites.  We’ve got one, in particular that seems to be causing poor performance with the website.  The JBrowse footprint, on disk is 346G.  How does this compare with other users?  Is this considered large?  We also have over 5 million files.  This creates I/O issues on disk.  What configuration recommendations do you have to help alleviate this problem.

https://www.rosaceae.org/tools/jbrowse<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rosaceae.org_tools_jbrowse&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=ob7Qitvr9e8MWpxJvxak1roVaqk3Y5oMn19djFU5tp0&e=>
Heidi Hough
System/Database Administrator
Main Bioinformatics Lab - Department of Horticulture
Washington State University
48 Johnson Hall
Pullman, WA 99164-6414
509-335-7093<tel:(509)%20335-7093>
hei...@ws...<mailto:hei...@ws...>




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=8oM58hLZs7__X1S9C3bp1l2rbbk9dXF07ECcN0f9OcY&e=>)                     216-392-3087<tel:(216)%20392-3087>
Ontario Institute for Cancer Research
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Re: [Gmod-ajax] JBrowse Configuration/Best Practice

[Hough, H. <hei...@ws...>]

Oh my, I’m behind the game.  Too many balls in the air.  I’ll push for 1.15.

Regards,
Heidi

From: Robert Buels [mailto:rb...@gm...]
Sent: Tuesday, July 24, 2018 8:22 AM
To: Hough, Heidi <hei...@ws...>
Cc: Colin <col...@gm...>; Scott Cain <sc...@sc...>; gmo...@li...; he...@gm...
Subject: Re: [Gmod-ajax] JBrowse Configuration/Best Practice

1.13.3?  The latest JBrowse release is 1.15.0, any reason you're not upgrading all the way to 1.15?

On Tue, Jul 24, 2018 at 8:21 AM Hough, Heidi <hei...@ws...<mailto:hei...@ws...>> wrote:
Thank you for the suggestions.  We’ve got a couple other sites using various versions.  My goal is to get them all updated to 1.13.3.  I’ll have to double-check, but I think we were having problems getting the MultiVariantViewer plugin working properly on the latest version; which is why we’re using 1.12.3 for that particular site.

Regards,
Heidi

From: Colin [mailto:col...@gm...<mailto:col...@gm...>]
Sent: Tuesday, July 24, 2018 6:42 AM
To: Robert Buels <rb...@gm...<mailto:rb...@gm...>>
Cc: Scott Cain <sc...@sc...<mailto:sc...@sc...>>; gmo...@li...<mailto:gmo...@li...>; he...@gm...<mailto:he...@gm...>; Hough, Heidi <hei...@ws...<mailto:hei...@ws...>>
Subject: Re: [Gmod-ajax] JBrowse Configuration/Best Practice

One other thing that caused some data directory size inflation in older jbrowse versions was this bug in flatfile-to-json.pl<https://urldefense.proofpoint.com/v2/url?u=http-3A__flatfile-2Dto-2Djson.pl&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=yz6-QhcZnAgcV6_fgyiob6cQIxBPUaAmfVDBXCQgmb0&e=> that is now fixed https://github.com/GMOD/jbrowse/issues/470<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_jbrowse_issues_470&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=T82QlGSRm4NZnS8Nl8bGDHfN9fAtymCg_1r6m6uoTPk&e=>

The bug occurs when you use a perl 5.18+ on jbrowse 1.12.3 or earlier

You could fix the issue by moving to 1.12.4 or later (to get the bugfix) or, if you are sticking with 1.12.1, you could remove the tracks and re-running the flatfile-to-json with an older version of perl, e.g. perl 5.14

The Tabix GFF is a great solution to reduce on disk files too, but unless you upgrade fully to the latest versions of jbrowse e.g. 1.15 I probably wouldn't use it (it didn't even exist in 1.12.1 anyways)


-Colin

On Mon, Jul 23, 2018 at 4:04 PM Robert Buels <rb...@gm...<mailto:rb...@gm...>> wrote:
My main recommendation for reducing startup time is to upgrade to the latest version of JBrowse.

For reducing the disk footprint and number of files in the `data/tracks` subdirectory, I'd look at migrating your feature tracks away from `flatfile-to-json` NCList format to an indexed format like Tabix-indexed GFF3 (using JBrowse's GFF3Tabix driver), or BigBed (using JBrowse's BigBed driver).

For the `data/names` subdirectory, there is an ElasticSearch plugin out there that would let you store your name-searching index in ElasticSearch, see https://github.com/elsiklab/jbrowse_elasticsearch<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_elsiklab_jbrowse-5Felasticsearch&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=4sEmUanU1VseDP5OJH0X2enzv3YKmzzmRzwtncKu_GY&e=>

Hope this helps! Always happy to answer any further questions.

On Mon, Jul 23, 2018 at 12:53 PM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Heidi,

I'm cc'ing this to the JBrowse mailing list for more input.

I can say that 346GB sounds like a lot to me, but nematodes have a lot smaller genomes than plants!  Have you looked at the javascript console to see what takes a lot of time?  Do you want to post a link to the one that performs badly?  Also, I'll point out (before Rob gets a chance to) that newer releases of JBrowse use webpack and thus have better startup times.  Finally, things you might want to think about is converting some of your GFF-based tracks to tabix indexed files, which will be much cleaner from a storage perspective and probably perform better too, though I don't remember if tabix indexed GFF files work with 1.12 (or work well, which I suppose is two separate things).

Scott


On Mon, Jul 23, 2018 at 11:52 AM, Hough, Heidi <hei...@ws...<mailto:hei...@ws...>> wrote:
Hello

I’d appreciate some JBrowse guidance in regards to information I can’t seem to adequately locate in the documentation regarding server hardware configuration.

We’re using JBrowse 1.12.3 on several of our websites.  We’ve got one, in particular that seems to be causing poor performance with the website.  The JBrowse footprint, on disk is 346G.  How does this compare with other users?  Is this considered large?  We also have over 5 million files.  This creates I/O issues on disk.  What configuration recommendations do you have to help alleviate this problem.

https://www.rosaceae.org/tools/jbrowse<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rosaceae.org_tools_jbrowse&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=ob7Qitvr9e8MWpxJvxak1roVaqk3Y5oMn19djFU5tp0&e=>
Heidi Hough
System/Database Administrator
Main Bioinformatics Lab - Department of Horticulture
Washington State University
48 Johnson Hall
Pullman, WA 99164-6414
509-335-7093<tel:(509)%20335-7093>
hei...@ws...<mailto:hei...@ws...>




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=8oM58hLZs7__X1S9C3bp1l2rbbk9dXF07ECcN0f9OcY&e=>)                     216-392-3087<tel:(216)%20392-3087>
Ontario Institute for Cancer Research
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Re: [Gmod-ajax] JBrowse Configuration/Best Practice

[Robert B. <rb...@gm...>]

1.13.3?  The latest JBrowse release is 1.15.0, any reason you're not
upgrading all the way to 1.15?

On Tue, Jul 24, 2018 at 8:21 AM Hough, Heidi <hei...@ws...> wrote:

> Thank you for the suggestions.  We’ve got a couple other sites using
> various versions.  My goal is to get them all updated to 1.13.3.  I’ll have
> to double-check, but I think we were having problems getting the
> MultiVariantViewer plugin working properly on the latest version; which is
> why we’re using 1.12.3 for that particular site.
>
>
>
> Regards,
>
> Heidi
>
>
>
> *From:* Colin [mailto:col...@gm...]
> *Sent:* Tuesday, July 24, 2018 6:42 AM
> *To:* Robert Buels <rb...@gm...>
> *Cc:* Scott Cain <sc...@sc...>; gmo...@li...;
> he...@gm...; Hough, Heidi <hei...@ws...>
> *Subject:* Re: [Gmod-ajax] JBrowse Configuration/Best Practice
>
>
>
> One other thing that caused some data directory size inflation in older
> jbrowse versions was this bug in flatfile-to-json.pl
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__flatfile-2Dto-2Djson.pl&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=yz6-QhcZnAgcV6_fgyiob6cQIxBPUaAmfVDBXCQgmb0&e=>
> that is now fixed https://github.com/GMOD/jbrowse/issues/470
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_jbrowse_issues_470&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=T82QlGSRm4NZnS8Nl8bGDHfN9fAtymCg_1r6m6uoTPk&e=>
>
>
>
> The bug occurs when you use a perl 5.18+ on jbrowse 1.12.3 or earlier
>
>
>
> You could fix the issue by moving to 1.12.4 or later (to get the bugfix)
> or, if you are sticking with 1.12.1, you could remove the tracks and
> re-running the flatfile-to-json with an older version of perl, e.g. perl
> 5.14
>
>
>
> The Tabix GFF is a great solution to reduce on disk files too, but unless
> you upgrade fully to the latest versions of jbrowse e.g. 1.15 I probably
> wouldn't use it (it didn't even exist in 1.12.1 anyways)
>
>
>
>
>
> -Colin
>
>
>
> On Mon, Jul 23, 2018 at 4:04 PM Robert Buels <rb...@gm...> wrote:
>
> My main recommendation for reducing startup time is to upgrade to the
> latest version of JBrowse.
>
>
>
> For reducing the disk footprint and number of files in the `data/tracks`
> subdirectory, I'd look at migrating your feature tracks away from
> `flatfile-to-json` NCList format to an indexed format like Tabix-indexed
> GFF3 (using JBrowse's GFF3Tabix driver), or BigBed (using JBrowse's BigBed
> driver).
>
>
>
> For the `data/names` subdirectory, there is an ElasticSearch plugin out
> there that would let you store your name-searching index in ElasticSearch,
> see https://github.com/elsiklab/jbrowse_elasticsearch
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_elsiklab_jbrowse-5Felasticsearch&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=4sEmUanU1VseDP5OJH0X2enzv3YKmzzmRzwtncKu_GY&e=>
>
>
>
> Hope this helps! Always happy to answer any further questions.
>
>
>
> On Mon, Jul 23, 2018 at 12:53 PM Scott Cain <sc...@sc...> wrote:
>
> Hi Heidi,
>
>
>
> I'm cc'ing this to the JBrowse mailing list for more input.
>
>
>
> I can say that 346GB sounds like a lot to me, but nematodes have a lot
> smaller genomes than plants!  Have you looked at the javascript console to
> see what takes a lot of time?  Do you want to post a link to the one that
> performs badly?  Also, I'll point out (before Rob gets a chance to) that
> newer releases of JBrowse use webpack and thus have better startup times.
> Finally, things you might want to think about is converting some of your
> GFF-based tracks to tabix indexed files, which will be much cleaner from a
> storage perspective and probably perform better too, though I don't
> remember if tabix indexed GFF files work with 1.12 (or work well, which I
> suppose is two separate things).
>
>
>
> Scott
>
>
>
>
>
> On Mon, Jul 23, 2018 at 11:52 AM, Hough, Heidi <hei...@ws...>
> wrote:
>
> Hello
>
>
>
> I’d appreciate some JBrowse guidance in regards to information I can’t
> seem to adequately locate in the documentation regarding server hardware
> configuration.
>
>
>
> We’re using JBrowse 1.12.3 on several of our websites.  We’ve got one, in
> particular that seems to be causing poor performance with the website.  The
> JBrowse footprint, on disk is 346G.  How does this compare with other
> users?  Is this considered large?  We also have over 5 million files.  This
> creates I/O issues on disk.  What configuration recommendations do you have
> to help alleviate this problem.
>
>
>
> https://www.rosaceae.org/tools/jbrowse
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rosaceae.org_tools_jbrowse&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=ob7Qitvr9e8MWpxJvxak1roVaqk3Y5oMn19djFU5tp0&e=>
>
> Heidi Hough
> System/Database Administrator
> Main Bioinformatics Lab - Department of Horticulture
> Washington State University
> 48 Johnson Hall
> Pullman, WA 99164-6414
>
> 509-335-7093 <(509)%20335-7093>
> hei...@ws...
>
>
>
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=8oM58hLZs7__X1S9C3bp1l2rbbk9dXF07ECcN0f9OcY&e=>)
>                    216-392-3087 <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>
>
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> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=MczgiGElisUAjxkUtZUdoub4x_lZbT2NV1Q8jGmYKa8&e=>
> _______________________________________________
> 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=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=RIEFIUIh4wnoEZFOB_TUkr8FKyuRjnDRS3tlTglKEgo&m=ihxzJIqxYEr5mgVmy6-7QJN9K5nqDnKWMutiIiYlW24&s=20CO3d0fISjaLFo28bA4S16fUZpo4Buz9ur-2E3uImU&e=>
>
>

Re: [Gmod-ajax] JBrowse Configuration/Best Practice

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

One other thing that caused some data directory size inflation in older
jbrowse versions was this bug in flatfile-to-json.pl that is now fixed
https://github.com/GMOD/jbrowse/issues/470

The bug occurs when you use a perl 5.18+ on jbrowse 1.12.3 or earlier

You could fix the issue by moving to 1.12.4 or later (to get the bugfix)
or, if you are sticking with 1.12.1, you could remove the tracks and
re-running the flatfile-to-json with an older version of perl, e.g. perl
5.14

The Tabix GFF is a great solution to reduce on disk files too, but unless
you upgrade fully to the latest versions of jbrowse e.g. 1.15 I probably
wouldn't use it (it didn't even exist in 1.12.1 anyways)


-Colin

On Mon, Jul 23, 2018 at 4:04 PM Robert Buels <rb...@gm...> wrote:

> My main recommendation for reducing startup time is to upgrade to the
> latest version of JBrowse.
>
> For reducing the disk footprint and number of files in the `data/tracks`
> subdirectory, I'd look at migrating your feature tracks away from
> `flatfile-to-json` NCList format to an indexed format like Tabix-indexed
> GFF3 (using JBrowse's GFF3Tabix driver), or BigBed (using JBrowse's BigBed
> driver).
>
> For the `data/names` subdirectory, there is an ElasticSearch plugin out
> there that would let you store your name-searching index in ElasticSearch,
> see https://github.com/elsiklab/jbrowse_elasticsearch
>
> Hope this helps! Always happy to answer any further questions.
>
> On Mon, Jul 23, 2018 at 12:53 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Heidi,
>>
>> I'm cc'ing this to the JBrowse mailing list for more input.
>>
>> I can say that 346GB sounds like a lot to me, but nematodes have a lot
>> smaller genomes than plants!  Have you looked at the javascript console to
>> see what takes a lot of time?  Do you want to post a link to the one that
>> performs badly?  Also, I'll point out (before Rob gets a chance to) that
>> newer releases of JBrowse use webpack and thus have better startup times.
>> Finally, things you might want to think about is converting some of your
>> GFF-based tracks to tabix indexed files, which will be much cleaner from a
>> storage perspective and probably perform better too, though I don't
>> remember if tabix indexed GFF files work with 1.12 (or work well, which I
>> suppose is two separate things).
>>
>> Scott
>>
>>
>> On Mon, Jul 23, 2018 at 11:52 AM, Hough, Heidi <hei...@ws...>
>> wrote:
>>
>>> Hello
>>>
>>>
>>>
>>> I’d appreciate some JBrowse guidance in regards to information I can’t
>>> seem to adequately locate in the documentation regarding server hardware
>>> configuration.
>>>
>>>
>>>
>>> We’re using JBrowse 1.12.3 on several of our websites.  We’ve got one,
>>> in particular that seems to be causing poor performance with the website.
>>> The JBrowse footprint, on disk is 346G.  How does this compare with other
>>> users?  Is this considered large?  We also have over 5 million files.  This
>>> creates I/O issues on disk.  What configuration recommendations do you have
>>> to help alleviate this problem.
>>>
>>>
>>>
>>> https://www.rosaceae.org/tools/jbrowse
>>>
>>> Heidi Hough
>>> System/Database Administrator
>>> Main Bioinformatics Lab - Department of Horticulture
>>> Washington State University
>>> 48 Johnson Hall
>>> Pullman, WA 99164-6414
>>>
>>> 509-335-7093 <(509)%20335-7093>
>>> hei...@ws...
>>>
>>>
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> <(216)%20392-3087>
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse Configuration/Best Practice

[Robert B. <rb...@gm...>]

My main recommendation for reducing startup time is to upgrade to the
latest version of JBrowse.

For reducing the disk footprint and number of files in the `data/tracks`
subdirectory, I'd look at migrating your feature tracks away from
`flatfile-to-json` NCList format to an indexed format like Tabix-indexed
GFF3 (using JBrowse's GFF3Tabix driver), or BigBed (using JBrowse's BigBed
driver).

For the `data/names` subdirectory, there is an ElasticSearch plugin out
there that would let you store your name-searching index in ElasticSearch,
see https://github.com/elsiklab/jbrowse_elasticsearch

Hope this helps! Always happy to answer any further questions.

On Mon, Jul 23, 2018 at 12:53 PM Scott Cain <sc...@sc...> wrote:

> Hi Heidi,
>
> I'm cc'ing this to the JBrowse mailing list for more input.
>
> I can say that 346GB sounds like a lot to me, but nematodes have a lot
> smaller genomes than plants!  Have you looked at the javascript console to
> see what takes a lot of time?  Do you want to post a link to the one that
> performs badly?  Also, I'll point out (before Rob gets a chance to) that
> newer releases of JBrowse use webpack and thus have better startup times.
> Finally, things you might want to think about is converting some of your
> GFF-based tracks to tabix indexed files, which will be much cleaner from a
> storage perspective and probably perform better too, though I don't
> remember if tabix indexed GFF files work with 1.12 (or work well, which I
> suppose is two separate things).
>
> Scott
>
>
> On Mon, Jul 23, 2018 at 11:52 AM, Hough, Heidi <hei...@ws...>
> wrote:
>
>> Hello
>>
>>
>>
>> I’d appreciate some JBrowse guidance in regards to information I can’t
>> seem to adequately locate in the documentation regarding server hardware
>> configuration.
>>
>>
>>
>> We’re using JBrowse 1.12.3 on several of our websites.  We’ve got one, in
>> particular that seems to be causing poor performance with the website.  The
>> JBrowse footprint, on disk is 346G.  How does this compare with other
>> users?  Is this considered large?  We also have over 5 million files.  This
>> creates I/O issues on disk.  What configuration recommendations do you have
>> to help alleviate this problem.
>>
>>
>>
>> https://www.rosaceae.org/tools/jbrowse
>>
>> Heidi Hough
>> System/Database Administrator
>> Main Bioinformatics Lab - Department of Horticulture
>> Washington State University
>> 48 Johnson Hall
>> Pullman, WA 99164-6414
>>
>> 509-335-7093 <(509)%20335-7093>
>> hei...@ws...
>>
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse Configuration/Best Practice

[Scott C. <sc...@sc...>]

Hi Heidi,

I'm cc'ing this to the JBrowse mailing list for more input.

I can say that 346GB sounds like a lot to me, but nematodes have a lot
smaller genomes than plants!  Have you looked at the javascript console to
see what takes a lot of time?  Do you want to post a link to the one that
performs badly?  Also, I'll point out (before Rob gets a chance to) that
newer releases of JBrowse use webpack and thus have better startup times.
Finally, things you might want to think about is converting some of your
GFF-based tracks to tabix indexed files, which will be much cleaner from a
storage perspective and probably perform better too, though I don't
remember if tabix indexed GFF files work with 1.12 (or work well, which I
suppose is two separate things).

Scott


On Mon, Jul 23, 2018 at 11:52 AM, Hough, Heidi <hei...@ws...> wrote:

> Hello
>
>
>
> I’d appreciate some JBrowse guidance in regards to information I can’t
> seem to adequately locate in the documentation regarding server hardware
> configuration.
>
>
>
> We’re using JBrowse 1.12.3 on several of our websites.  We’ve got one, in
> particular that seems to be causing poor performance with the website.  The
> JBrowse footprint, on disk is 346G.  How does this compare with other
> users?  Is this considered large?  We also have over 5 million files.  This
> creates I/O issues on disk.  What configuration recommendations do you have
> to help alleviate this problem.
>
>
>
> https://www.rosaceae.org/tools/jbrowse
>
> Heidi Hough
> System/Database Administrator
> Main Bioinformatics Lab - Department of Horticulture
> Washington State University
> 48 Johnson Hall
> Pullman, WA 99164-6414
>
> 509-335-7093
> hei...@ws...
>
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] JBrowse 'Save track data' not working

[Scott C. <sc...@sc...>]

Oh, I hope they are going to maintain it, that's a cool plugin.  I did see
a commit from a month ago, so somebody is paying at least a little bit of
attention to it.

On Fri, Jul 20, 2018 at 2:55 PM, Robert Buels <rb...@gm...> wrote:

> Have you considered just ditching that plugin if they are not going to
> maintain it?
>
> On Thu, Jul 19, 2018 at 3:13 PM Vaneet Lotay <van...@uc...>
> wrote:
>
>> Yes Robert, the plugin I’m still having problems with is
>> ComboTrackSelector.  Again the plugin looks to be functional, it’s just not
>> displayed correctly, both issues posted on the Github branch are related to
>> the same problem:
>>
>>
>>
>> https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/
>> issues
>>
>>
>>
>> I was thinking I could try upgrading to a later version of JBrowse, but
>> not the latest release in the off chance that this plugin works with that
>> version as the developer did post a fix earlier for this issue so it must
>> have been working in at least 1 release.  Perhaps I could try JBrowse
>> 1.14.0 first.
>>
>>
>>
>> I’m not sure how to fork JBrowse exactly, might need instructions on how
>> to do that.  Do you mean only copy the folders and files from one of the
>> newer releases of JBrowse that fix this particular ‘save track data’ bug
>> and not the complete release?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Vaneet
>>
>>
>>
>>
>>
>>
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Vaneet
>> Lotay*
>>
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>>
>>
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Xenbase
>> Bioinformatician*
>>
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>>
>> *716 ICT Building - University of Calgary*
>>
>> *2500 University Drive NW
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>> *Calgary AB T2N 1N4
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>> *CANADA
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>>
>>
>> *From:* Robert Buels [mailto:rb...@gm...]
>> *Sent:* Thursday, July 19, 2018 3:07 PM
>> *To:* Vaneet Lotay <van...@uc...>; gmod-ajax <
>> gmo...@li...>
>> *Cc:* Scott Cain <sc...@sc...>
>>
>>
>> *Subject:* Re: [Gmod-ajax] JBrowse 'Save track data' not working
>>
>>
>>
>> I think you are probably running into a bug that was fixed in 1.14.0 (fix
>> can be seen at https://github.com/GMOD/jbrowse/commit/
>> 228af5684362c6b6a1a9210667a0e0750d373cd3).
>>
>>
>>
>> You might try applying that fix to your local code, or you could fork
>> JBrowse at that point perhaps, if you really can't upgrade?  The plugin
>> you're still having problems with is ComboTrackSelector?
>>
>>
>>
>>
>>
>>
>>
>> On Thu, Jul 19, 2018 at 1:45 PM Vaneet Lotay <van...@uc...>
>> wrote:
>>
>> That Java console was from the Chrome browser.  I’m using
>> JBrowse-1.13.1-dev currently.  I can’t upgrade to the latest JBrowse
>> release because a plugin that we’re using doesn’t work properly with the
>> latest JBrowse release.  I posted the issue on the Github branch of that
>> plugin, as did another user about 2 weeks ago, no response yet.
>>
>>
>>
>> I am viewing JBrowse on a PC with Windows 7 Enterprise.
>>
>>
>>
>> This doesn’t work with Firefox either, here is the java console from that
>> browser when I tried to save track info:
>>
>>
>>
>> <unavailable> _fileDownload@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:15820:7 _exportDialogContent/dlButton<.onClick</<@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:15
>> hitch/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48
>> exportRegion/<@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:15459:9 hitch/<@http://jbrowse-test.
>> xenbase.org/JBrowse/dist/0.bundle.js:4772:48 signalListener@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21
>> signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:45699:4 Deferred/this.resolve@http://
>> jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 all/</<@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:7
>> signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:45708:21 signalWaiting@http://jbrowse-
>> test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
>> __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</</<@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33359:15
>> signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:45708:21 Deferred/promise.then@http://
>> jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45929:5
>> __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</<@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33358:20
>> signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:45708:21 signalWaiting@http://jbrowse-
>> test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
>> signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:45752:6 signalListener@http://jbrowse-
>> test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6 signalWaiting@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
>> Deferred/this.resolve@http://jbrowse-test.xenbase.org/
>> JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-
>> test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45729:4
>> signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:45699:4 Deferred/this.resolve@http://
>> jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6
>> signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:45723:6 signalWaiting@http://jbrowse-
>> test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@
>> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
>> handleResponse@http://jbrowse-test.xenbase.org/JBrowse/dist/
>> 0.bundle.js:5096:6 onLoad@http://jbrowse-test.xenbase.org/JBrowse/dist/0.
>> bundle.js:5131:5 0.bundle.js:70956:3
>> <http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js>
>>
>>
>>
>>
>>
>> Vaneet
>>
>>
>>
>>
>>
>> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>>
>> *Vaneet Lotay*
>>
>> *Xenbase Bioinformatician*
>>
>> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>>
>> *716 ICT Building - University of Calgary*
>>
>> *2500 University Drive NW
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>> *Calgary AB T2N 1N4
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>> *CANADA
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>>
>>
>> *From:* Robert Buels [mailto:rb...@gm...]
>> *Sent:* Thursday, July 19, 2018 2:11 PM
>> *To:* Vaneet Lotay <van...@uc...>
>> *Cc:* Scott Cain <sc...@sc...>; gmo...@li...
>>
>>
>> *Subject:* Re: [Gmod-ajax] JBrowse 'Save track data' not working
>>
>>
>>
>> That's interesting, it looks like file saving might not be supported on
>> that browser and platform and JBrowse might not be detecting that fact?
>>
>>
>>
>> What are the exact versions of JBrowse, the web browser, and the
>> operating system you are trying this with?
>>
>>
>>
>> On Thu, Jul 19, 2018 at 1:04 PM Vaneet Lotay <van...@uc...>
>> wrote:
>>
>> Hey guys,
>>
>>
>>
>> I have checked the option in both Firefox and Chrome browsers for
>> automatically saving downloads to a specific folder without prompting.  I
>> tried the option enabled and disabled and in both cases it doesn’t work in
>> that it isn’t being saved in the default download folder or it’s not
>> prompting me to pick the location in where I save the file.  It appears
>> there’s an error happening though if we look at the Java console, so I
>> pasted it here below:
>>
>>
>>
>> GET https://www.google-analytics.com/analytics.js 0 ()
>>
>> instrumentation.js:23 TypeError: saveAs is not a function
>>
>>     at Object._fileDownload (_ExportMixin.js:252)
>>
>>     at Object.<anonymous> (_ExportMixin.js:178)
>>
>>     at lang.js:385
>>
>>     at Object.<anonymous> (FASTA.js:26)
>>
>>     at lang.js:385
>>
>>     at SeqFeature.js:182
>>
>>     at signalListener (Deferred.js:37)
>>
>>     at signalWaiting (Deferred.js:28)
>>
>>     at Deferred.resolve (Deferred.js:192)
>>
>>     at all.js:68 "TypeError: saveAs is not a function
>>
>>     at Object._fileDownload (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:15820:7)
>>
>>     at Object.<anonymous> (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:15737:20)
>>
>>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>>
>>     at Object.<anonymous> (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:38890:9)
>>
>>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>>
>>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12939:9
>>
>>     at signalListener (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45708:21)
>>
>>     at signalWaiting (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45699:4)
>>
>>     at Deferred.resolve (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45863:5)
>>
>>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
>>
>>     ----------------------------------------
>>
>>     rejected at signalDeferred (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45755:15)
>>
>>     at signalListener (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45726:5)
>>
>>     at signalWaiting (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45699:4)
>>
>>     at Deferred.resolve (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45863:5)
>>
>>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
>>
>>     at signalListener (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45708:21)
>>
>>     at signalWaiting (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45699:4)
>>
>>     at Deferred.resolve (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45863:5)
>>
>>     at signalListener (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45708:21)
>>
>>     at signalWaiting (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45699:4)
>>
>>     ----------------------------------------
>>
>> Error
>>
>>     at Promise.Deferred.then.promise.then (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:45923:24)
>>
>>     at Object.getFeatures (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:11005:20)
>>
>>     at Object.getReferenceSequence (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:12933:12)
>>
>>     at Object.exportRegion (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:38889:18)
>>
>>     at Object.<anonymous> (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:15849:12)
>>
>>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>>
>>     at contextRequire (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/main.bundle.js:265:25)
>>
>>     at req (http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.
>> js:159:21)
>>
>>     at Object.exportRegion (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:15844:19)
>>
>>     at Object.<anonymous> (http://jbrowse-test.xenbase.
>> org/JBrowse/dist/0.bundle.js:15734:18)"
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Vaneet
>>
>>
>>
>>
>>
>> *Vaneet Lotay*
>>
>> *Xenbase Bioinformatician*
>>
>> *716 ICT Building - University of Calgary*
>>
>> *2500 University Drive NW
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>> *Calgary AB T2N 1N4
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>> *CANADA
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>>
>>
>> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>>
>> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>>
>> *From:* Robert Buels [mailto:rb...@gm...]
>> *Sent:* Wednesday, July 18, 2018 7:35 PM
>> *To:* Scott Cain <sc...@sc...>
>> *Cc:* Vaneet Lotay <van...@uc...>;
>> gmo...@li...
>> *Subject:* Re: [Gmod-ajax] JBrowse 'Save track data' not working
>>
>>
>>
>> It should look and work the same as any other file download in the
>> browser. Which with most browsers is that it just downloads the file into
>> your downloads folder. Is it not doing that?
>>
>> On Wed, Jul 18, 2018 at 8:32 AM Scott Cain <sc...@sc...> wrote:
>>
>> Hi Vaneet,
>>
>>
>>
>> Now that I've reread your email and also tried it myself to remind me how
>> it works--it does not prompt you for a name or location.  It assigns a name
>> based on the track and location and puts a file in your default download
>> location.
>>
>>
>>
>> Scott
>>
>>
>>
>>
>>
>> On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...> wrote:
>>
>> Hi Vaneet,
>>
>>
>>
>> Can you check the javascript console when you're doing that to see if it
>> gives any useful feedback?
>>
>>
>>
>> Thanks,
>>
>> Scott
>>
>>
>>
>>
>>
>> On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...>
>> wrote:
>>
>> Hello,
>>
>>
>>
>> I’m having trouble saving track data to capture sequence data in FASTA
>> format, model data in GFF3 or any other track and format.
>>
>>
>>
>> I click on the drop down arrow next to the track label and then ‘Save
>> track data’.  Whether I click on the visible region or the whole reference
>> sequence and no matter which output format I select it doesn’t work. When I
>> click on ‘Save’ the dialog box always closes and nothing happens.
>>
>>
>>
>> I assume there should be another box popping up asking where to save the
>> file and also how to name it?
>>
>>
>>
>> I’ve tested this on both Firefox and Chrome browsers, still the same
>> problem.  I’ve also tested both browsers while disabling the pop-up
>> blocker, in case that was interfering but still the same problem remained.
>>
>>
>>
>> Please let me know if anyone can resolve this issue.
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Vaneet
>>
>>
>>
>>
>>
>> *Vaneet Lotay*
>>
>> *Xenbase Bioinformatician*
>>
>> *716 ICT Building - University of Calgary*
>>
>> *2500 University Drive NW
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>> *Calgary AB T2N 1N4
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>> *CANADA
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>>
>>
>>
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>>
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>>
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>>
>>
>>
>> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> 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
>> <(216)%20392-3087>
>> Ontario Institute for Cancer Research
>>
>>
>>
>>
>> --
>>
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> <(216)%20392-3087>
>> Ontario Institute for Cancer Research
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> 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

Re: [Gmod-ajax] JBrowse 'Save track data' not working

[Vaneet L. <van...@uc...>]

We need it for a major upcoming project, so I hope we don’t have to but if it’s not maintained we may have to face that reality and perhaps just use the Faceted track selector on its own.

Vaneet


Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

From: Robert Buels [mailto:rb...@gm...]
Sent: Friday, July 20, 2018 12:56 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>; Scott Cain <sc...@sc...>
Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working

Have you considered just ditching that plugin if they are not going to maintain it?
On Thu, Jul 19, 2018 at 3:13 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Yes Robert, the plugin I’m still having problems with is ComboTrackSelector.  Again the plugin looks to be functional, it’s just not displayed correctly, both issues posted on the Github branch are related to the same problem:

https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/issues

I was thinking I could try upgrading to a later version of JBrowse, but not the latest release in the off chance that this plugin works with that version as the developer did post a fix earlier for this issue so it must have been working in at least 1 release.  Perhaps I could try JBrowse 1.14.0 first.

I’m not sure how to fork JBrowse exactly, might need instructions on how to do that.  Do you mean only copy the folders and files from one of the newer releases of JBrowse that fix this particular ‘save track data’ bug and not the complete release?

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

From: Robert Buels [mailto:rb...@gm...<mailto:rb...@gm...>]
Sent: Thursday, July 19, 2018 3:07 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>; gmod-ajax <gmo...@li...<mailto:gmo...@li...>>
Cc: Scott Cain <sc...@sc...<mailto:sc...@sc...>>

Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working

I think you are probably running into a bug that was fixed in 1.14.0 (fix can be seen at https://github.com/GMOD/jbrowse/commit/228af5684362c6b6a1a9210667a0e0750d373cd3).

You might try applying that fix to your local code, or you could fork JBrowse at that point perhaps, if you really can't upgrade?  The plugin you're still having problems with is ComboTrackSelector?



On Thu, Jul 19, 2018 at 1:45 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
That Java console was from the Chrome browser.  I’m using JBrowse-1.13.1-dev currently.  I can’t upgrade to the latest JBrowse release because a plugin that we’re using doesn’t work properly with the latest JBrowse release.  I posted the issue on the Github branch of that plugin, as did another user about 2 weeks ago, no response yet.

I am viewing JBrowse on a PC with Windows 7 Enterprise.

This doesn’t work with Firefox either, here is the java console from that browser when I tried to save track info:

<unavailable> _fileDownload@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7 _exportDialogContent/dlButton<.onClick</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:15 hitch/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48 exportRegion/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15459:9 hitch/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 all/</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:7 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33359:15 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 Deferred/promise.then@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45929:5 __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33358:20 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45729:4 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 handleResponse@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5096:6 onLoad@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5131:5 0.bundle.js:70956:3<http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js>


Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

From: Robert Buels [mailto:rb...@gm...<mailto:rb...@gm...>]
Sent: Thursday, July 19, 2018 2:11 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: Scott Cain <sc...@sc...<mailto:sc...@sc...>>; gmo...@li...<mailto:gmo...@li...>

Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working

That's interesting, it looks like file saving might not be supported on that browser and platform and JBrowse might not be detecting that fact?

What are the exact versions of JBrowse, the web browser, and the operating system you are trying this with?

On Thu, Jul 19, 2018 at 1:04 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey guys,

I have checked the option in both Firefox and Chrome browsers for automatically saving downloads to a specific folder without prompting.  I tried the option enabled and disabled and in both cases it doesn’t work in that it isn’t being saved in the default download folder or it’s not prompting me to pick the location in where I save the file.  It appears there’s an error happening though if we look at the Java console, so I pasted it here below:

GET https://www.google-analytics.com/analytics.js 0 ()
instrumentation.js:23 TypeError: saveAs is not a function
    at Object._fileDownload (_ExportMixin.js:252)
    at Object.<anonymous> (_ExportMixin.js:178)
    at lang.js:385
    at Object.<anonymous> (FASTA.js:26)
    at lang.js:385
    at SeqFeature.js:182
    at signalListener (Deferred.js:37)
    at signalWaiting (Deferred.js:28)
    at Deferred.resolve (Deferred.js:192)
    at all.js:68 "TypeError: saveAs is not a function
    at Object._fileDownload (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7)
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:20)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38890:9)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12939:9
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
    ----------------------------------------
    rejected at signalDeferred (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45755:15)
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45726:5)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    ----------------------------------------
Error
    at Promise.Deferred.then.promise.then (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45923:24)
    at Object.getFeatures (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:11005:20)
    at Object.getReferenceSequence (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12933:12)
    at Object.exportRegion (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38889:18)
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15849:12)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
    at contextRequire (http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:265:25)
    at req (http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:159:21)
    at Object.exportRegion (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15844:19)
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15734:18)"

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

From: Robert Buels [mailto:rb...@gm...<mailto:rb...@gm...>]
Sent: Wednesday, July 18, 2018 7:35 PM
To: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Cc: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>; gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working

It should look and work the same as any other file download in the browser. Which with most browsers is that it just downloads the file into your downloads folder. Is it not doing that?
On Wed, Jul 18, 2018 at 8:32 AM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Vaneet,

Now that I've reread your email and also tried it myself to remind me how it works--it does not prompt you for a name or location.  It assigns a name based on the track and location and puts a file in your default download location.

Scott


On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Vaneet,

Can you check the javascript console when you're doing that to see if it gives any useful feedback?

Thanks,
Scott


On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I’m having trouble saving track data to capture sequence data in FASTA format, model data in GFF3 or any other track and format.

I click on the drop down arrow next to the track label and then ‘Save track data’.  Whether I click on the visible region or the whole reference sequence and no matter which output format I select it doesn’t work. When I click on ‘Save’ the dialog box always closes and nothing happens.

I assume there should be another box popping up asking where to save the file and also how to name it?

I’ve tested this on both Firefox and Chrome browsers, still the same problem.  I’ve also tested both browsers while disabling the pop-up blocker, in case that was interfering but still the same problem remained.

Please let me know if anyone can resolve this issue.

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087<tel:(216)%20392-3087>
Ontario Institute for Cancer Research
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Re: [Gmod-ajax] JBrowse 'Save track data' not working

[Robert B. <rb...@gm...>]

Have you considered just ditching that plugin if they are not going to
maintain it?
On Thu, Jul 19, 2018 at 3:13 PM Vaneet Lotay <van...@uc...>
wrote:

> Yes Robert, the plugin I’m still having problems with is
> ComboTrackSelector.  Again the plugin looks to be functional, it’s just not
> displayed correctly, both issues posted on the Github branch are related to
> the same problem:
>
>
>
> https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/issues
>
>
>
> I was thinking I could try upgrading to a later version of JBrowse, but
> not the latest release in the off chance that this plugin works with that
> version as the developer did post a fix earlier for this issue so it must
> have been working in at least 1 release.  Perhaps I could try JBrowse
> 1.14.0 first.
>
>
>
> I’m not sure how to fork JBrowse exactly, might need instructions on how
> to do that.  Do you mean only copy the folders and files from one of the
> newer releases of JBrowse that fix this particular ‘save track data’ bug
> and not the complete release?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Vaneet
> Lotay*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Xenbase
> Bioinformatician*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *Calgary AB T2N 1N4
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *CANADA
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
>
>
> *From:* Robert Buels [mailto:rb...@gm...]
> *Sent:* Thursday, July 19, 2018 3:07 PM
> *To:* Vaneet Lotay <van...@uc...>; gmod-ajax <
> gmo...@li...>
> *Cc:* Scott Cain <sc...@sc...>
>
>
> *Subject:* Re: [Gmod-ajax] JBrowse 'Save track data' not working
>
>
>
> I think you are probably running into a bug that was fixed in 1.14.0 (fix
> can be seen at
> https://github.com/GMOD/jbrowse/commit/228af5684362c6b6a1a9210667a0e0750d373cd3
> ).
>
>
>
> You might try applying that fix to your local code, or you could fork
> JBrowse at that point perhaps, if you really can't upgrade?  The plugin
> you're still having problems with is ComboTrackSelector?
>
>
>
>
>
>
>
> On Thu, Jul 19, 2018 at 1:45 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> That Java console was from the Chrome browser.  I’m using
> JBrowse-1.13.1-dev currently.  I can’t upgrade to the latest JBrowse
> release because a plugin that we’re using doesn’t work properly with the
> latest JBrowse release.  I posted the issue on the Github branch of that
> plugin, as did another user about 2 weeks ago, no response yet.
>
>
>
> I am viewing JBrowse on a PC with Windows 7 Enterprise.
>
>
>
> This doesn’t work with Firefox either, here is the java console from that
> browser when I tried to save track info:
>
>
>
> <unavailable> _fileDownload@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7
> _exportDialogContent/dlButton<.onClick</<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:15 hitch/<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48
> exportRegion/<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15459:9 hitch/<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 all/</<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:7
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</</<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33359:15
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21
> Deferred/promise.then@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45929:5
> __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33358:20
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> signalDeferred@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> signalDeferred@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45729:4
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> signalDeferred@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> handleResponse@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5096:6 onLoad@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5131:5
> 0.bundle.js:70956:3
> <http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js>
>
>
>
>
>
> Vaneet
>
>
>
>
>
> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *Calgary AB T2N 1N4
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *CANADA
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
>
>
> *From:* Robert Buels [mailto:rb...@gm...]
> *Sent:* Thursday, July 19, 2018 2:11 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* Scott Cain <sc...@sc...>; gmo...@li...
>
>
> *Subject:* Re: [Gmod-ajax] JBrowse 'Save track data' not working
>
>
>
> That's interesting, it looks like file saving might not be supported on
> that browser and platform and JBrowse might not be detecting that fact?
>
>
>
> What are the exact versions of JBrowse, the web browser, and the operating
> system you are trying this with?
>
>
>
> On Thu, Jul 19, 2018 at 1:04 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey guys,
>
>
>
> I have checked the option in both Firefox and Chrome browsers for
> automatically saving downloads to a specific folder without prompting.  I
> tried the option enabled and disabled and in both cases it doesn’t work in
> that it isn’t being saved in the default download folder or it’s not
> prompting me to pick the location in where I save the file.  It appears
> there’s an error happening though if we look at the Java console, so I
> pasted it here below:
>
>
>
> GET https://www.google-analytics.com/analytics.js 0 ()
>
> instrumentation.js:23 TypeError: saveAs is not a function
>
>     at Object._fileDownload (_ExportMixin.js:252)
>
>     at Object.<anonymous> (_ExportMixin.js:178)
>
>     at lang.js:385
>
>     at Object.<anonymous> (FASTA.js:26)
>
>     at lang.js:385
>
>     at SeqFeature.js:182
>
>     at signalListener (Deferred.js:37)
>
>     at signalWaiting (Deferred.js:28)
>
>     at Deferred.resolve (Deferred.js:192)
>
>     at all.js:68 "TypeError: saveAs is not a function
>
>     at Object._fileDownload (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7)
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:20)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38890:9)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12939:9
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     at Deferred.resolve (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
>
>     ----------------------------------------
>
>     rejected at signalDeferred (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45755:15)
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45726:5)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     at Deferred.resolve (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     at Deferred.resolve (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     ----------------------------------------
>
> Error
>
>     at Promise.Deferred.then.promise.then (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45923:24)
>
>     at Object.getFeatures (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:11005:20)
>
>     at Object.getReferenceSequence (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12933:12)
>
>     at Object.exportRegion (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38889:18)
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15849:12)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>
>     at contextRequire (
> http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:265:25)
>
>     at req (
> http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:159:21)
>
>     at Object.exportRegion (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15844:19)
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15734:18)"
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *Calgary AB T2N 1N4
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *CANADA
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
>
>
> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>
> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>
> *From:* Robert Buels [mailto:rb...@gm...]
> *Sent:* Wednesday, July 18, 2018 7:35 PM
> *To:* Scott Cain <sc...@sc...>
> *Cc:* Vaneet Lotay <van...@uc...>;
> gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse 'Save track data' not working
>
>
>
> It should look and work the same as any other file download in the
> browser. Which with most browsers is that it just downloads the file into
> your downloads folder. Is it not doing that?
>
> On Wed, Jul 18, 2018 at 8:32 AM Scott Cain <sc...@sc...> wrote:
>
> Hi Vaneet,
>
>
>
> Now that I've reread your email and also tried it myself to remind me how
> it works--it does not prompt you for a name or location.  It assigns a name
> based on the track and location and puts a file in your default download
> location.
>
>
>
> Scott
>
>
>
>
>
> On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...> wrote:
>
> Hi Vaneet,
>
>
>
> Can you check the javascript console when you're doing that to see if it
> gives any useful feedback?
>
>
>
> Thanks,
>
> Scott
>
>
>
>
>
> On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I’m having trouble saving track data to capture sequence data in FASTA
> format, model data in GFF3 or any other track and format.
>
>
>
> I click on the drop down arrow next to the track label and then ‘Save
> track data’.  Whether I click on the visible region or the whole reference
> sequence and no matter which output format I select it doesn’t work. When I
> click on ‘Save’ the dialog box always closes and nothing happens.
>
>
>
> I assume there should be another box popping up asking where to save the
> file and also how to name it?
>
>
>
> I’ve tested this on both Firefox and Chrome browsers, still the same
> problem.  I’ve also tested both browsers while disabling the pop-up
> blocker, in case that was interfering but still the same problem remained.
>
>
>
> Please let me know if anyone can resolve this issue.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *Calgary AB T2N 1N4
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *CANADA
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
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>
>

[Gmod-ajax] JBrowse 1.15.0 released – CRAM support, CSI indexes, and on the desktop!

[Robert B. <rb...@gm...>]

Hi all,

JBrowse 1.15.0 has been released! This is a really big one.

At long last, JBrowse can open and view CRAM v2 and v3 files just like BAM.
In fact, viewing CRAM files can sometimes be even faster than viewing BAM
files, because there is less data to move around! Enjoy CRAM support, we
all worked really hard to bring it to you! Getting started with CRAM is
easy, just use the `JBrowse/Store/SeqFeature/CRAM` store and the
`Alignments2` track type, just as you probably are already with BAM files.
It works with local files too, of course!

Another big development, JBrowse Desktop has matured to the point where we
can recommend it without reservation to those looking for a fast, easy to
use desktop genome browser for local and remote files. From now on, we’ll
be publishing builds of JBrowse Desktop for Windows, Mac OS, and Linux
alongside the regular JBrowse releases. Download it and give it a try, let
us know what you think! Huge congratulations to Colin Diesh (who is now a
full-time JBrowse developer!) for thinking of this, and seeing this amazing
development through. I think you will be quite pleased with how well
JBrowse runs on the desktop!

Also, JBrowse now supports CSI format indexes for BAM fiels and
Tabix-indexed (VCF, GFF3, etc) files. Now your BAM files can be even
bigger. As if they weren’t huge enough already. This continues our very
serious commitment to make JBrowse effortlessly usable on even the biggest
datasets.

Lastly, JBrowse now sports a nice new text-searching interface accessible
from the View → Search menu item in the top bar. This was a cool idea that
came out of discussions last month at the GCCBOSC 2018 CollaborationFest
<https://galaxyproject.org/events/gccbosc2018/collaboration/>, and was
executed with alacrity by Colin!

As always, read on below the fold for the full release notes, including
minor improvements and bugfixes. And thanks for using JBrowse. [image: 😁]
Files for download

   - JBrowse-1.15.0.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.0-release/JBrowse-1.15.0.zip>
–
   3.1M
   file SHA1 db1cb6eb6110e22b4d7bad3d4d1b5784afcaf6e7
   - JBrowse-1.15.0-dev.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.0-release/JBrowse-1.15.0-dev.zip>
–
   8.5M
   file SHA1 851593861bea726b428ebc51633eae9f5b1edebe
   - JBrowse-1.15.0-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.0-release/JBrowse-1.15.0-desktop-win32-x64.zip>
–
   68M
   file SHA1 bc88f03a66938c3e6e86c54927d38ed9dd51777c
   - JBrowse-1.15.0-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.0-release/JBrowse-1.15.0-desktop-linux-x64.zip>
–
   66M
   file SHA1 5a00c1b218cbb8fc740bd49ed1620111af9bf72b
   - JBrowse-1.15.0-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.0-release/JBrowse-1.15.0-desktop-darwin-x64.zip>
–
   66M
   file SHA1 97c985dcf84e67b23b609cc30454b21c097d89ef

Major improvements

   - Added support for displaying alignments from CRAM files, using the new
   npm module @gmod <https://www.npmjs.com/package/%3Ca%20href=>/cram”>@gmod
   <https://github.com/gmod>/cram. Thanks to @keiranmraine
   <https://github.com/keiranmraine>, @cmdcolin
   <https://github.com/cmdcolin>, @nathanhaigh
   <https://github.com/nathanhaigh>, and the authors of htslib and htsjdk for
   invaluable test data and suggestions during this major effort. (issue
   #546 <https://github.com/gmod/jbrowse/issues/546>, issue #1120
   <https://github.com/gmod/jbrowse/pull/1120>, @rbuels
   <https://github.com/rbuels>)
   - Added support for the CSI index format for tabix VCF/BED/GFF and BAM
   files! This allows
   individual chromosomes longer than ~537MB (229 bases) to be used in
   JBrowse. To enable,
   use the csiUrlTemplate config to point to the file. The “Open track”
   dialog also allows
   CSI to be used. Thanks to Keiran Raine for initial report and Nathan S
   Watson-Haigh for
   catching a bug in the initial implementation! (issue #926
   <https://github.com/gmod/jbrowse/issues/926>, issue #1086
   <https://github.com/gmod/jbrowse/pull/1086>, @cmdcolin
   <https://github.com/cmdcolin>)
   - Added a new search dialog box via the View->Search features menubar.
   It will search the
   currently configured store for features. You can also configure the
   dialog class in the
   configuration with names.dialog entry, or disable search dialog with
   disableSearch.
   Thanks to the #GCCBOSC hackathon for the idea and feedback (issue #1101
   <https://github.com/gmod/jbrowse/pull/1101>, @cmdcolin
   <https://github.com/cmdcolin>).

Minor improvements

   - Re-enabled JBrowse Desktop builds for releases! The Windows, Mac, and
   Linux binaries for
   JBrowse Desktop are uploaded automatically to GitHub releases page.
   JBrowse Desktop is a
   standalone app that can be used without a web server, similar to IGV or
   IGB (@cmdcolin <https://github.com/cmdcolin>)
   - Added a dontRedispatch option for GFF3Tabix stores. Example: set
   dontRedispatch=region
   if there are very large region biotype features in the GFF that do not
   have subfeatures which will
   speed up loading times significantly (issue #1076
   <https://github.com/gmod/jbrowse/issues/1076>, issue #1084
   <https://github.com/gmod/jbrowse/pull/1084>, @cmdcolin
   <https://github.com/cmdcolin>)
   - Add auto-lower-casing to the feature.get(‘…’) function, commonly used
   for callback
   customizations. Now, for example, feature.get(‘ID’) works as well as
   feature.get(‘id’).
   Thanks to @nvteja <https://github.com/nvteja> for motivating this! (issue
   #1068 <https://github.com/gmod/jbrowse/issues/1068>, issue #1074
   <https://github.com/gmod/jbrowse/pull/1074>, @cmdcolin
   <https://github.com/cmdcolin>)
   - Added cache-busting for track config files which actively prevents
   stale configuration files
   from being loaded (issue #1080
   <https://github.com/gmod/jbrowse/pull/1080>, @cmdcolin
   <https://github.com/cmdcolin>)
   - Added indexing of both Name and ID from GFF3Tabix files from
   generate-names.pl. Thanks to
   @billzt <https://github.com/billzt> for the implementation! (issue #1069
   <https://github.com/gmod/jbrowse/issues/1069>)
   - Made the color of the guanine (G) residue more orangey than yellow to
   help visibility.
   Thanks to Keiran Raine for the implementation! (issue #1079
   <https://github.com/gmod/jbrowse/issues/1079>)
   - Refactored NeatCanvasFeatures and NeatHTMLFeatures as track types. You
   can enable the track
   style on specific tracks instead of globally this way by modifying the
   track type to be
   NeatCanvasFeatures/View/Track/NeatFeatures or
   NeatHTMLFeatures/View/Track/NeatFeatures.
   (issue #889 <https://github.com/gmod/jbrowse/pull/889>, @cmdcolin
   <https://github.com/cmdcolin>).
   - In the location box, allow strings with format ctgA:1-100 e.g. with a
   hyphen instead of ...
   Big thanks to Nathan S Watson-Haigh for the idea and implementation! The
   default display
   remains .. but - is allowed. (issue #1100
   <https://github.com/gmod/jbrowse/issues/1100>, issue #1102
   <https://github.com/gmod/jbrowse/pull/1102>, @nathanhaigh
   <https://github.com/nathanhaigh>)
   - Allow sequences with a colon in their name to be used in the location
   box. This includes
   the HLA reference sequences in hg38. Thanks again to Nathan S
   Watson-Haigh for the
   implementation of this feature. (issue #1119
   <https://github.com/gmod/jbrowse/pull/1119>, @nathanhaigh
   <https://github.com/nathanhaigh>)
   - Fix sensitivity to .gff.gz vs .gff3.gz in GFF3Tabix tracks opened via
   the “Open track”
   dialog for GFF3Tabix. (issue #1125
   <https://github.com/gmod/jbrowse/issues/1125>, @cmdcolin
   <https://github.com/cmdcolin>)
   - Feature detail dialog boxes now display subfeatures of features on the
   reverse strand in
   upstream-to-downstream order, instead of in genomic coordinate order.
   Thanks to
   @nathanhaigh <https://github.com/nathanhaigh> for suggesting this and
   contributing the fix! (issue #1071
   <https://github.com/gmod/jbrowse/issues/1071>, issue #1114
   <https://github.com/gmod/jbrowse/pull/1114>, @nathanhaigh
   <https://github.com/nathanhaigh>)

Bug fixes

   - Fixed a potential cross-site-scripting (XSS) vulnerability by
   disallowing dataRoot config
   values or ?data= URL parameters that point to a different server from
   the one serving
   JBrowse. Users can disable this security check by setting
allowCrossOriginDataRoot
   = true
   in their configuration. (@cmdcolin <https://github.com/cmdcolin>, @rbuels
   <https://github.com/rbuels>)
   - Fixed a memory leak that was introduced in JBrowse 1.13.1 in
   generate-names.pl. Thanks to
   @scottcain <https://github.com/scottcain> for reporting (issue #1058
   <https://github.com/gmod/jbrowse/issues/1058>, @cmdcolin
   <https://github.com/cmdcolin>)
   - Fix the error checking in setup.sh if no node is installed at all (issue
   #1083 <https://github.com/gmod/jbrowse/pull/1083>, @cmdcolin
   <https://github.com/cmdcolin>)
   - Fix calculation of histograms on GFF3 and GFF3Tabix stores. Thanks to
   @thomasvangurp <https://github.com/thomasvangurp> for
   the bug report and sample data! (issue #1103
   <https://github.com/gmod/jbrowse/issues/1103>, @cmdcolin
   <https://github.com/cmdcolin>)
   - Fix the representation of array-valued attributes in column 9 for
   GFF3Tabix. Thanks to
   @loraine-gueguen <https://github.com/loraine-gueguen> for the bug
   report! (issue #1122 <https://github.com/gmod/jbrowse/issues/1122>,
   @cmdcolin <https://github.com/cmdcolin>)
   - Fixed a bug in which visibleRegion() in GenomeView.js sometimes
   returned a non-integer value for end, which interfered with some scripts
   and plugins. Thanks to @rdhayes <https://github.com/rdhayes> for
   noticing and contributing the fix! (issue #491
   <https://github.com/gmod/jbrowse/issues/491>, @rdhayes
   <https://github.com/rdhayes>)
   - Fixed bug where reference sequences with names containing the : character
   could not be switched to by typing their name in the search box. (issue
   #1118 <https://github.com/gmod/jbrowse/issues/1118>, issue #1119
   <https://github.com/gmod/jbrowse/pull/1119>, @nathanhaigh
   <https://github.com/nathanhaigh>)
   - Fixed setup.sh behavior when node is not installed, printing a decent
   error message. (issue #1082 <https://github.com/gmod/jbrowse/issues/1082>
   , issue #1083 <https://github.com/gmod/jbrowse/pull/1083>, @cmdcolin
   <https://github.com/cmdcolin>)

Re: [Gmod-ajax] JBrowse 'Save track data' not working

[Vaneet L. <van...@uc...>]

Yes Robert, the plugin I’m still having problems with is ComboTrackSelector.  Again the plugin looks to be functional, it’s just not displayed correctly, both issues posted on the Github branch are related to the same problem:

https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector/issues

I was thinking I could try upgrading to a later version of JBrowse, but not the latest release in the off chance that this plugin works with that version as the developer did post a fix earlier for this issue so it must have been working in at least 1 release.  Perhaps I could try JBrowse 1.14.0 first.

I’m not sure how to fork JBrowse exactly, might need instructions on how to do that.  Do you mean only copy the folders and files from one of the newer releases of JBrowse that fix this particular ‘save track data’ bug and not the complete release?

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

From: Robert Buels [mailto:rb...@gm...]
Sent: Thursday, July 19, 2018 3:07 PM
To: Vaneet Lotay <van...@uc...>; gmod-ajax <gmo...@li...>
Cc: Scott Cain <sc...@sc...>
Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working

I think you are probably running into a bug that was fixed in 1.14.0 (fix can be seen at https://github.com/GMOD/jbrowse/commit/228af5684362c6b6a1a9210667a0e0750d373cd3).

You might try applying that fix to your local code, or you could fork JBrowse at that point perhaps, if you really can't upgrade?  The plugin you're still having problems with is ComboTrackSelector?



On Thu, Jul 19, 2018 at 1:45 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
That Java console was from the Chrome browser.  I’m using JBrowse-1.13.1-dev currently.  I can’t upgrade to the latest JBrowse release because a plugin that we’re using doesn’t work properly with the latest JBrowse release.  I posted the issue on the Github branch of that plugin, as did another user about 2 weeks ago, no response yet.

I am viewing JBrowse on a PC with Windows 7 Enterprise.

This doesn’t work with Firefox either, here is the java console from that browser when I tried to save track info:

<unavailable> _fileDownload@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7 _exportDialogContent/dlButton<.onClick</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:15 hitch/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48 exportRegion/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15459:9 hitch/<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 all/</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:7 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33359:15 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 Deferred/promise.then@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45929:5 __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</<@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33358:20 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45729:4 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 signalDeferred@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6 signalListener@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6 signalWaiting@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4 Deferred/this.resolve@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 handleResponse@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5096:6 onLoad@http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5131:5 0.bundle.js:70956:3<http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js>


Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

From: Robert Buels [mailto:rb...@gm...<mailto:rb...@gm...>]
Sent: Thursday, July 19, 2018 2:11 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: Scott Cain <sc...@sc...<mailto:sc...@sc...>>; gmo...@li...<mailto:gmo...@li...>

Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working

That's interesting, it looks like file saving might not be supported on that browser and platform and JBrowse might not be detecting that fact?

What are the exact versions of JBrowse, the web browser, and the operating system you are trying this with?

On Thu, Jul 19, 2018 at 1:04 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey guys,

I have checked the option in both Firefox and Chrome browsers for automatically saving downloads to a specific folder without prompting.  I tried the option enabled and disabled and in both cases it doesn’t work in that it isn’t being saved in the default download folder or it’s not prompting me to pick the location in where I save the file.  It appears there’s an error happening though if we look at the Java console, so I pasted it here below:

GET https://www.google-analytics.com/analytics.js 0 ()
instrumentation.js:23 TypeError: saveAs is not a function
    at Object._fileDownload (_ExportMixin.js:252)
    at Object.<anonymous> (_ExportMixin.js:178)
    at lang.js:385
    at Object.<anonymous> (FASTA.js:26)
    at lang.js:385
    at SeqFeature.js:182
    at signalListener (Deferred.js:37)
    at signalWaiting (Deferred.js:28)
    at Deferred.resolve (Deferred.js:192)
    at all.js:68 "TypeError: saveAs is not a function
    at Object._fileDownload (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7)
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:20)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38890:9)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12939:9
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
    ----------------------------------------
    rejected at signalDeferred (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45755:15)
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45726:5)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    ----------------------------------------
Error
    at Promise.Deferred.then.promise.then (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45923:24)
    at Object.getFeatures (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:11005:20)
    at Object.getReferenceSequence (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12933:12)
    at Object.exportRegion (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38889:18)
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15849:12)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
    at contextRequire (http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:265:25)
    at req (http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:159:21)
    at Object.exportRegion (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15844:19)
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15734:18)"

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

From: Robert Buels [mailto:rb...@gm...<mailto:rb...@gm...>]
Sent: Wednesday, July 18, 2018 7:35 PM
To: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Cc: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>; gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working

It should look and work the same as any other file download in the browser. Which with most browsers is that it just downloads the file into your downloads folder. Is it not doing that?
On Wed, Jul 18, 2018 at 8:32 AM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Vaneet,

Now that I've reread your email and also tried it myself to remind me how it works--it does not prompt you for a name or location.  It assigns a name based on the track and location and puts a file in your default download location.

Scott


On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Vaneet,

Can you check the javascript console when you're doing that to see if it gives any useful feedback?

Thanks,
Scott


On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I’m having trouble saving track data to capture sequence data in FASTA format, model data in GFF3 or any other track and format.

I click on the drop down arrow next to the track label and then ‘Save track data’.  Whether I click on the visible region or the whole reference sequence and no matter which output format I select it doesn’t work. When I click on ‘Save’ the dialog box always closes and nothing happens.

I assume there should be another box popping up asking where to save the file and also how to name it?

I’ve tested this on both Firefox and Chrome browsers, still the same problem.  I’ve also tested both browsers while disabling the pop-up blocker, in case that was interfering but still the same problem remained.

Please let me know if anyone can resolve this issue.

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

Calgary AB T2N 1N4<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>

CANADA<https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>


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_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087<tel:(216)%20392-3087>
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087<tel:(216)%20392-3087>
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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Re: [Gmod-ajax] JBrowse 'Save track data' not working

[Robert B. <rb...@gm...>]

I think you are probably running into a bug that was fixed in 1.14.0 (fix
can be seen at
https://github.com/GMOD/jbrowse/commit/228af5684362c6b6a1a9210667a0e0750d373cd3
).

You might try applying that fix to your local code, or you could fork
JBrowse at that point perhaps, if you really can't upgrade?  The plugin
you're still having problems with is ComboTrackSelector?



On Thu, Jul 19, 2018 at 1:45 PM Vaneet Lotay <van...@uc...>
wrote:

> That Java console was from the Chrome browser.  I’m using
> JBrowse-1.13.1-dev currently.  I can’t upgrade to the latest JBrowse
> release because a plugin that we’re using doesn’t work properly with the
> latest JBrowse release.  I posted the issue on the Github branch of that
> plugin, as did another user about 2 weeks ago, no response yet.
>
>
>
> I am viewing JBrowse on a PC with Windows 7 Enterprise.
>
>
>
> This doesn’t work with Firefox either, here is the java console from that
> browser when I tried to save track info:
>
>
>
> <unavailable> _fileDownload@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7
> _exportDialogContent/dlButton<.onClick</<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:15 hitch/<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48
> exportRegion/<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15459:9 hitch/<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:48
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5 all/</<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:7
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</</<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33359:15
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21
> Deferred/promise.then@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45929:5
> __WEBPACK_AMD_DEFINE_RESULT__</NCList.prototype.iterHelper/</<@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:33358:20
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> signalDeferred@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> signalDeferred@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45729:4
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> signalDeferred@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45752:6
> signalListener@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45723:6
> signalWaiting@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4
> Deferred/this.resolve@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5
> handleResponse@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5096:6 onLoad@
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:5131:5
> 0.bundle.js:70956:3
> <http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js>
>
>
>
>
>
> Vaneet
>
>
>
>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Vaneet
> Lotay*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Xenbase
> Bioinformatician*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *Calgary AB T2N 1N4
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *CANADA
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
>
>
> *From:* Robert Buels [mailto:rb...@gm...]
> *Sent:* Thursday, July 19, 2018 2:11 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* Scott Cain <sc...@sc...>; gmo...@li...
>
>
> *Subject:* Re: [Gmod-ajax] JBrowse 'Save track data' not working
>
>
>
> That's interesting, it looks like file saving might not be supported on
> that browser and platform and JBrowse might not be detecting that fact?
>
>
>
> What are the exact versions of JBrowse, the web browser, and the operating
> system you are trying this with?
>
>
>
> On Thu, Jul 19, 2018 at 1:04 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey guys,
>
>
>
> I have checked the option in both Firefox and Chrome browsers for
> automatically saving downloads to a specific folder without prompting.  I
> tried the option enabled and disabled and in both cases it doesn’t work in
> that it isn’t being saved in the default download folder or it’s not
> prompting me to pick the location in where I save the file.  It appears
> there’s an error happening though if we look at the Java console, so I
> pasted it here below:
>
>
>
> GET https://www.google-analytics.com/analytics.js 0 ()
>
> instrumentation.js:23 TypeError: saveAs is not a function
>
>     at Object._fileDownload (_ExportMixin.js:252)
>
>     at Object.<anonymous> (_ExportMixin.js:178)
>
>     at lang.js:385
>
>     at Object.<anonymous> (FASTA.js:26)
>
>     at lang.js:385
>
>     at SeqFeature.js:182
>
>     at signalListener (Deferred.js:37)
>
>     at signalWaiting (Deferred.js:28)
>
>     at Deferred.resolve (Deferred.js:192)
>
>     at all.js:68 "TypeError: saveAs is not a function
>
>     at Object._fileDownload (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7)
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:20)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38890:9)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12939:9
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     at Deferred.resolve (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
>
>     ----------------------------------------
>
>     rejected at signalDeferred (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45755:15)
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45726:5)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     at Deferred.resolve (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     at Deferred.resolve (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     ----------------------------------------
>
> Error
>
>     at Promise.Deferred.then.promise.then (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45923:24)
>
>     at Object.getFeatures (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:11005:20)
>
>     at Object.getReferenceSequence (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12933:12)
>
>     at Object.exportRegion (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38889:18)
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15849:12)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>
>     at contextRequire (
> http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:265:25)
>
>     at req (
> http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:159:21)
>
>     at Object.exportRegion (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15844:19)
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15734:18)"
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>
> *Calgary AB T2N 1N4
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *CANADA
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> <https://maps.google.com/?q=2500%0D%0A+University+Drive+NW+%0D%0A+Calgary%0D%0A+AB+T2N+1N4+%0D%0A+CANADA&entry=gmail&source=g>
>
>
>
> *From:* Robert Buels [mailto:rb...@gm...]
> *Sent:* Wednesday, July 18, 2018 7:35 PM
> *To:* Scott Cain <sc...@sc...>
> *Cc:* Vaneet Lotay <van...@uc...>;
> gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse 'Save track data' not working
>
>
>
> It should look and work the same as any other file download in the
> browser. Which with most browsers is that it just downloads the file into
> your downloads folder. Is it not doing that?
>
> On Wed, Jul 18, 2018 at 8:32 AM Scott Cain <sc...@sc...> wrote:
>
> Hi Vaneet,
>
>
>
> Now that I've reread your email and also tried it myself to remind me how
> it works--it does not prompt you for a name or location.  It assigns a name
> based on the track and location and puts a file in your default download
> location.
>
>
>
> Scott
>
>
>
>
>
> On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...> wrote:
>
> Hi Vaneet,
>
>
>
> Can you check the javascript console when you're doing that to see if it
> gives any useful feedback?
>
>
>
> Thanks,
>
> Scott
>
>
>
>
>
> On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I’m having trouble saving track data to capture sequence data in FASTA
> format, model data in GFF3 or any other track and format.
>
>
>
> I click on the drop down arrow next to the track label and then ‘Save
> track data’.  Whether I click on the visible region or the whole reference
> sequence and no matter which output format I select it doesn’t work. When I
> click on ‘Save’ the dialog box always closes and nothing happens.
>
>
>
> I assume there should be another box popping up asking where to save the
> file and also how to name it?
>
>
>
> I’ve tested this on both Firefox and Chrome browsers, still the same
> problem.  I’ve also tested both browsers while disabling the pop-up
> blocker, in case that was interfering but still the same problem remained.
>
>
>
> Please let me know if anyone can resolve this issue.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Calgary
> AB T2N 1N4
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*CANADA
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] JBrowse 'Save track data' not working

[Robert B. <rb...@gm...>]

That's interesting, it looks like file saving might not be supported on
that browser and platform and JBrowse might not be detecting that fact?

What are the exact versions of JBrowse, the web browser, and the operating
system you are trying this with?

On Thu, Jul 19, 2018 at 1:04 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey guys,
>
>
>
> I have checked the option in both Firefox and Chrome browsers for
> automatically saving downloads to a specific folder without prompting.  I
> tried the option enabled and disabled and in both cases it doesn’t work in
> that it isn’t being saved in the default download folder or it’s not
> prompting me to pick the location in where I save the file.  It appears
> there’s an error happening though if we look at the Java console, so I
> pasted it here below:
>
>
>
> GET https://www.google-analytics.com/analytics.js 0 ()
>
> instrumentation.js:23 TypeError: saveAs is not a function
>
>     at Object._fileDownload (_ExportMixin.js:252)
>
>     at Object.<anonymous> (_ExportMixin.js:178)
>
>     at lang.js:385
>
>     at Object.<anonymous> (FASTA.js:26)
>
>     at lang.js:385
>
>     at SeqFeature.js:182
>
>     at signalListener (Deferred.js:37)
>
>     at signalWaiting (Deferred.js:28)
>
>     at Deferred.resolve (Deferred.js:192)
>
>     at all.js:68 "TypeError: saveAs is not a function
>
>     at Object._fileDownload (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7)
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:20)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38890:9)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12939:9
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     at Deferred.resolve (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
>
>     ----------------------------------------
>
>     rejected at signalDeferred (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45755:15)
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45726:5)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     at Deferred.resolve (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     at Deferred.resolve (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
>
>     at signalListener (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
>
>     at signalWaiting (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
>
>     ----------------------------------------
>
> Error
>
>     at Promise.Deferred.then.promise.then (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45923:24)
>
>     at Object.getFeatures (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:11005:20)
>
>     at Object.getReferenceSequence (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12933:12)
>
>     at Object.exportRegion (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38889:18)
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15849:12)
>
>     at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
>
>     at contextRequire (
> http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:265:25)
>
>     at req (
> http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:159:21)
>
>     at Object.exportRegion (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15844:19)
>
>     at Object.<anonymous> (
> http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15734:18)"
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Vaneet
> Lotay*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Xenbase
> Bioinformatician*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *Calgary AB T2N 1N4
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *CANADA
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
>
>
> *From:* Robert Buels [mailto:rb...@gm...]
> *Sent:* Wednesday, July 18, 2018 7:35 PM
> *To:* Scott Cain <sc...@sc...>
> *Cc:* Vaneet Lotay <van...@uc...>;
> gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse 'Save track data' not working
>
>
>
> It should look and work the same as any other file download in the
> browser. Which with most browsers is that it just downloads the file into
> your downloads folder. Is it not doing that?
>
> On Wed, Jul 18, 2018 at 8:32 AM Scott Cain <sc...@sc...> wrote:
>
> Hi Vaneet,
>
>
>
> Now that I've reread your email and also tried it myself to remind me how
> it works--it does not prompt you for a name or location.  It assigns a name
> based on the track and location and puts a file in your default download
> location.
>
>
>
> Scott
>
>
>
>
>
> On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...> wrote:
>
> Hi Vaneet,
>
>
>
> Can you check the javascript console when you're doing that to see if it
> gives any useful feedback?
>
>
>
> Thanks,
>
> Scott
>
>
>
>
>
> On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I’m having trouble saving track data to capture sequence data in FASTA
> format, model data in GFF3 or any other track and format.
>
>
>
> I click on the drop down arrow next to the track label and then ‘Save
> track data’.  Whether I click on the visible region or the whole reference
> sequence and no matter which output format I select it doesn’t work. When I
> click on ‘Save’ the dialog box always closes and nothing happens.
>
>
>
> I assume there should be another box popping up asking where to save the
> file and also how to name it?
>
>
>
> I’ve tested this on both Firefox and Chrome browsers, still the same
> problem.  I’ve also tested both browsers while disabling the pop-up
> blocker, in case that was interfering but still the same problem remained.
>
>
>
> Please let me know if anyone can resolve this issue.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Vaneet
> Lotay*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*Xenbase
> Bioinformatician*
>
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *Calgary AB T2N 1N4
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
> *CANADA
> <https://maps.google.com/?q=2500+University+Drive+NW+%0D%0A+%0D%0A+Calgary+AB+T2N+1N4+%0D%0A+%0D%0A+CANADA&entry=gmail&source=g>*
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] JBrowse 'Save track data' not working

[Vaneet L. <van...@uc...>]

Hey guys,

I have checked the option in both Firefox and Chrome browsers for automatically saving downloads to a specific folder without prompting.  I tried the option enabled and disabled and in both cases it doesn’t work in that it isn’t being saved in the default download folder or it’s not prompting me to pick the location in where I save the file.  It appears there’s an error happening though if we look at the Java console, so I pasted it here below:

GET https://www.google-analytics.com/analytics.js 0 ()
instrumentation.js:23 TypeError: saveAs is not a function
    at Object._fileDownload (_ExportMixin.js:252)
    at Object.<anonymous> (_ExportMixin.js:178)
    at lang.js:385
    at Object.<anonymous> (FASTA.js:26)
    at lang.js:385
    at SeqFeature.js:182
    at signalListener (Deferred.js:37)
    at signalWaiting (Deferred.js:28)
    at Deferred.resolve (Deferred.js:192)
    at all.js:68 "TypeError: saveAs is not a function
    at Object._fileDownload (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15820:7)
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15737:20)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38890:9)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12939:9
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
    ----------------------------------------
    rejected at signalDeferred (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45755:15)
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45726:5)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:49394:16
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    at Deferred.resolve (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45863:5)
    at signalListener (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45708:21)
    at signalWaiting (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45699:4)
    ----------------------------------------
Error
    at Promise.Deferred.then.promise.then (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:45923:24)
    at Object.getFeatures (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:11005:20)
    at Object.getReferenceSequence (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:12933:12)
    at Object.exportRegion (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:38889:18)
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15849:12)
    at http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:4772:55
    at contextRequire (http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:265:25)
    at req (http://jbrowse-test.xenbase.org/JBrowse/dist/main.bundle.js:159:21)
    at Object.exportRegion (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15844:19)
    at Object.<anonymous> (http://jbrowse-test.xenbase.org/JBrowse/dist/0.bundle.js:15734:18)"

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

From: Robert Buels [mailto:rb...@gm...]
Sent: Wednesday, July 18, 2018 7:35 PM
To: Scott Cain <sc...@sc...>
Cc: Vaneet Lotay <van...@uc...>; gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse 'Save track data' not working

It should look and work the same as any other file download in the browser. Which with most browsers is that it just downloads the file into your downloads folder. Is it not doing that?
On Wed, Jul 18, 2018 at 8:32 AM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Vaneet,

Now that I've reread your email and also tried it myself to remind me how it works--it does not prompt you for a name or location.  It assigns a name based on the track and location and puts a file in your default download location.

Scott


On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Vaneet,

Can you check the javascript console when you're doing that to see if it gives any useful feedback?

Thanks,
Scott


On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I’m having trouble saving track data to capture sequence data in FASTA format, model data in GFF3 or any other track and format.

I click on the drop down arrow next to the track label and then ‘Save track data’.  Whether I click on the visible region or the whole reference sequence and no matter which output format I select it doesn’t work. When I click on ‘Save’ the dialog box always closes and nothing happens.

I assume there should be another box popping up asking where to save the file and also how to name it?

I’ve tested this on both Firefox and Chrome browsers, still the same problem.  I’ve also tested both browsers while disabling the pop-up blocker, in case that was interfering but still the same problem remained.

Please let me know if anyone can resolve this issue.

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto: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



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse 'Save track data' not working

[Robert B. <rb...@gm...>]

It should look and work the same as any other file download in the browser.
Which with most browsers is that it just downloads the file into your
downloads folder. Is it not doing that?
On Wed, Jul 18, 2018 at 8:32 AM Scott Cain <sc...@sc...> wrote:

> Hi Vaneet,
>
> Now that I've reread your email and also tried it myself to remind me how
> it works--it does not prompt you for a name or location.  It assigns a name
> based on the track and location and puts a file in your default download
> location.
>
> Scott
>
>
> On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...> wrote:
>
>> Hi Vaneet,
>>
>> Can you check the javascript console when you're doing that to see if it
>> gives any useful feedback?
>>
>> Thanks,
>> Scott
>>
>>
>> On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...>
>> wrote:
>>
>>> Hello,
>>>
>>>
>>>
>>> I’m having trouble saving track data to capture sequence data in FASTA
>>> format, model data in GFF3 or any other track and format.
>>>
>>>
>>>
>>> I click on the drop down arrow next to the track label and then ‘Save
>>> track data’.  Whether I click on the visible region or the whole reference
>>> sequence and no matter which output format I select it doesn’t work. When I
>>> click on ‘Save’ the dialog box always closes and nothing happens.
>>>
>>>
>>>
>>> I assume there should be another box popping up asking where to save the
>>> file and also how to name it?
>>>
>>>
>>>
>>> I’ve tested this on both Firefox and Chrome browsers, still the same
>>> problem.  I’ve also tested both browsers while disabling the pop-up
>>> blocker, in case that was interfering but still the same problem remained.
>>>
>>>
>>>
>>> Please let me know if anyone can resolve this issue.
>>>
>>>
>>>
>>> Thanks,
>>>
>>>
>>>
>>> Vaneet
>>>
>>>
>>>
>>>
>>>
>>> *Vaneet Lotay*
>>>
>>> *Xenbase Bioinformatician*
>>>
>>> *716 ICT Building - University of Calgary*
>>>
>>> *2500 University Drive NW*
>>>
>>> *Calgary AB T2N 1N4*
>>>
>>> *CANADA*
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> 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
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>