gmod-ajax — JBrowse list

Re: [Gmod-ajax] 416 Requested range not satisfiable message appearing in newer versions of JBrowse, with same configuration

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

Both these issues are very weird. I cannot think exactly what might be
going on, it might be helpful to have data to test on.

The Amazon S3 URLs linked are access denied for me but something like that
would be good for testing


-Colin

On Fri, Jan 11, 2019 at 8:32 AM Douwe van der Leest <
dou...@gm...> wrote:

> Hey there,
>
> On advance, thanks for taking the time for reading and perhaps answering
> my question. I am updating my Jbrowse version from JBrowse-1.12.5; to
> JBrowse-1.16.1-release with as intermediate versions JBrowse-1.14.2-dev and
> JBrowse-1.15.0-dev for troubleshooting some issues.
>
> I use Firefox for viewing my data and am looking at two specific bam files that for some reason provide an error starting from version 1.15.0. Also, I noticed the peaks of some related files changing with the version number (all included in the screenshots below), should I be concerned about this difference in displaying the exact same files? I am not sure whether it is related to CORS configuration as proposed in #1091 <https://github.com/GMOD/jbrowse/issues/1091> because it works in certain versions of JBrowse, but not in all.
>
>
>
> [image: jbrowse v1 14 2]
> <https://user-images.githubusercontent.com/38953127/51028366-80fdc000-1593-11e9-8c33-75fefeb3276f.png>
> [image: jbrowse v1 15 0]
> <https://user-images.githubusercontent.com/38953127/51028367-80fdc000-1593-11e9-9ccc-967804a3ed79.png>
> [image: jbrowse v1 16 1]
> <https://user-images.githubusercontent.com/38953127/51028368-80fdc000-1593-11e9-8517-82cde00315a3.png>
>
> Can someone please explain how to solve this?
>
> PS: some extra info:
> The CORS configuration of the bucket in which the data is stored:
>
> <?xml version="1.0" encoding="UTF-8"?>
>
> <CORSConfiguration xmlns="http://s3.amazonaws.com/doc/2006-03-01/">
>
> <CORSRule>
>
>     <AllowedOrigin>*</AllowedOrigin>
>
>     <AllowedMethod>GET</AllowedMethod>
>
>     <MaxAgeSeconds>3000</MaxAgeSeconds>
>
>     <AllowedHeader>*</AllowedHeader>
>
> </CORSRule>
>
> </CORSConfiguration>
>
> I am using apache:
>
> > rpm -q httpd
>
> httpd-2.4.6-80.el7.centos.1.x86_64
>
> The code in /etc/httpd/conf/httpd.conf, related to JBrowse; which I think
> is meant for the configuration of my apache server
>
> Alias /jbrowse /var/www/jbrowse/default
>
> <Directory "/var/www/jbrowse/default/">
>
> Options Indexes FollowSymLinks ExecCGI
>
> Require all granted
>
> AllowOverride All
>
>  <IfModule mod_gzip.c>
>
>    mod_gzip_item_exclude "(\.jsonz|\.txtz)"
>
>  </IfModule>
>
>  <IfModule setenvif.c>
>
>    SetEnvIf Request_URI "(\.jsonz|\.txtz)" no-gzip dont-vary
>
>  </IfModule>
>
>  <IfModule mod_headers.c>
>
>    <FilesMatch "(\.jsonz|\.txtz)">
>
>      Header onsuccess set Content-Encoding gzip
>
>    </FilesMatch>
>
>  </IfModule>
>
> </Directory>
>
>
>
> Using curl –I on the urls for the bam and the bai file returns the following, respectively:
>
> [root@cloud jbrowse]# curl -I https://s3.eu-central-1.amazonaws.com/lim-asp-data/PacBio/WGS/K30-1/AsparagusMaleV1/bam/K30-1.PacBio_Ref_run1.contigs.fasta.sorted.minimap2.sorted.bam
>
> HTTP/1.1 200 OK
>
> x-amz-id-2: 1JbjscRo+vjcUIXpIs+zFdwk9WxLS8mveBViQM+gJlrVubz4KTYywfdLx6LAh7cEw1PETP2Cn1U=
>
> x-amz-request-id: 28B9E9172181C705
>
> Date: Fri, 11 Jan 2019 11:36:24 GMT
>
> Last-Modified: Wed, 09 Jan 2019 15:18:49 GMT
>
> ETag: "02aef1647f185c451ec55cf69731f939"
>
> x-amz-meta-mode: 33188
>
> x-amz-meta-gid: 0
>
> x-amz-meta-uid: 0
>
> x-amz-meta-mtime: 1547047128
>
> x-amz-version-id: n96JSHBApAMOClTPUpJCOkoBJ5X_2DEe
>
> Accept-Ranges: bytes
>
> Content-Type: application/octet-stream
>
> Content-Length: 163169
>
> Server: AmazonS3
>
>
>
> [root@cloud jbrowse]# curl -I https://s3.eu-central-1.amazonaws.com/lim-asp-data/PacBio/WGS/K30-1/AsparagusMaleV1/bam/K30-1.PacBio_Ref_run1.contigs.fasta.sorted.minimap2.sorted.bam.bai
>
> HTTP/1.1 200 OK
>
> x-amz-id-2: kcUF8e4oClVu6INZ78npWcPgNLO3UJP3KQKsDCUDWHhsCjNfC5r4XB9IbB93LYdOwQLXRLi8EgU=
>
> x-amz-request-id: 9C523CCFAA1B2301
>
> Date: Fri, 11 Jan 2019 11:36:27 GMT
>
> Last-Modified: Wed, 09 Jan 2019 15:18:49 GMT
>
> ETag: "ac2c06762fc282602aa0f1db2d562b19"
>
> x-amz-meta-mode: 33188
>
> x-amz-meta-gid: 0
>
> x-amz-meta-uid: 0
>
> x-amz-meta-mtime: 1547047128
>
> x-amz-version-id: pD4RMlnV1r8qW7Q9cnwSRhaZW.dMI6dA
>
> Accept-Ranges: bytes
>
> Content-Type: application/octet-stream
>
> Content-Length: 502496
>
> Server: AmazonS3
>
>
>
> Please feel free to mail me if you need additional data.
>
> Thanks a bunch in advance,
>
>
>
> Cheers,
>
> Douwe
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] question about import bw file

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

Your webserver that you are using is responding incorrectly to HTTP Range
requests, e.g. it should return HTTP status 206 but it is returning HTTP
200 which is incorrect.

What webserver are you using? We have a FAQ entry that explains some
options here
http://jbrowse.org/docs/faq.html#what-webserver-is-needed-for-jbrowse


-Colin

On Fri, Jan 11, 2019 at 8:48 AM Ke Jiang <bio...@gm...> wrote:

> I would think about file protocol problems instead of a specific problem
> with BigWig files? Can you try using a different file (BAM/VCF) in the
> directory?
>
> On Fri, Jan 11, 2019 at 9:32 AM 袁杰 <jie...@16...> wrote:
>
>> When I use the jbrowse in Ubuntu to import the bigwig file, the error
>> shown in these pictures.
>> Could you please tell me how to solve this problem?
>> Greatful！
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] question about import bw file

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

I would think about file protocol problems instead of a specific problem
with BigWig files? Can you try using a different file (BAM/VCF) in the
directory?

On Fri, Jan 11, 2019 at 9:32 AM 袁杰 <jie...@16...> wrote:

> When I use the jbrowse in Ubuntu to import the bigwig file, the error
> shown in these pictures.
> Could you please tell me how to solve this problem?
> Greatful！
>
>
>
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] 416 Requested range not satisfiable message appearing in newer versions of JBrowse, with same configuration

[Douwe v. d. L. <dou...@gm...>]

Hey there,

On advance, thanks for taking the time for reading and perhaps answering
my question. I am updating my Jbrowse version from JBrowse-1.12.5; to
JBrowse-1.16.1-release with as intermediate versions JBrowse-1.14.2-dev
and JBrowse-1.15.0-dev for troubleshooting some issues.

I use Firefox for viewing my data and am looking at two specific bam
files that for some reason provide an error starting from version
1.15.0. Also, I noticed the peaks of some related files changing with
the version number (all included in the screenshots below), should I be
concerned about this difference in displaying the exact same files? I am
not sure whether it is related to CORS configuration as proposed in
<https://github.com/GMOD/jbrowse/issues/1091> #1091 because it works in
certain versions of JBrowse, but not in all.

 

 
<https://user-images.githubusercontent.com/38953127/51028366-80fdc000-15
93-11e9-8c33-75fefeb3276f.png> 
 
<https://user-images.githubusercontent.com/38953127/51028367-80fdc000-15
93-11e9-9ccc-967804a3ed79.png> 
 
<https://user-images.githubusercontent.com/38953127/51028368-80fdc000-15
93-11e9-8517-82cde00315a3.png> 

Can someone please explain how to solve this?

PS: some extra info:
The CORS configuration of the bucket in which the data is stored:

<?xml version="1.0" encoding="UTF-8"?>
<CORSConfiguration xmlns="http://s3.amazonaws.com/doc/2006-03-01/">
<CORSRule>
    <AllowedOrigin>*</AllowedOrigin>
    <AllowedMethod>GET</AllowedMethod>
    <MaxAgeSeconds>3000</MaxAgeSeconds>
    <AllowedHeader>*</AllowedHeader>
</CORSRule>
</CORSConfiguration>

I am using apache:

> rpm -q httpd
httpd-2.4.6-80.el7.centos.1.x86_64

The code in /etc/httpd/conf/httpd.conf, related to JBrowse; which I
think is meant for the configuration of my apache server

Alias /jbrowse /var/www/jbrowse/default
<Directory "/var/www/jbrowse/default/">
Options Indexes FollowSymLinks ExecCGI
Require all granted
AllowOverride All
 <IfModule mod_gzip.c>
   mod_gzip_item_exclude "(\.jsonz|\.txtz)"
 </IfModule>
 <IfModule setenvif.c>
   SetEnvIf Request_URI "(\.jsonz|\.txtz)" no-gzip dont-vary
 </IfModule>
 <IfModule mod_headers.c>
   <FilesMatch "(\.jsonz|\.txtz)">
     Header onsuccess set Content-Encoding gzip
   </FilesMatch>
 </IfModule>
</Directory>
 
Using curl -I on the urls for the bam and the bai file returns the
following, respectively:
[root@cloud jbrowse]# curl -I
https://s3.eu-central-1.amazonaws.com/lim-asp-data/PacBio/WGS/K30-1/Aspa
ragusMaleV1/bam/K30-1.PacBio_Ref_run1.contigs.fasta.sorted.minimap2.sort
ed.bam
HTTP/1.1 200 OK
x-amz-id-2:
1JbjscRo+vjcUIXpIs+zFdwk9WxLS8mveBViQM+gJlrVubz4KTYywfdLx6LAh7cEw1PETP2C
n1U=
x-amz-request-id: 28B9E9172181C705
Date: Fri, 11 Jan 2019 11:36:24 GMT
Last-Modified: Wed, 09 Jan 2019 15:18:49 GMT
ETag: "02aef1647f185c451ec55cf69731f939"
x-amz-meta-mode: 33188
x-amz-meta-gid: 0
x-amz-meta-uid: 0
x-amz-meta-mtime: 1547047128
x-amz-version-id: n96JSHBApAMOClTPUpJCOkoBJ5X_2DEe
Accept-Ranges: bytes
Content-Type: application/octet-stream
Content-Length: 163169
Server: AmazonS3
 
[root@cloud jbrowse]# curl -I
https://s3.eu-central-1.amazonaws.com/lim-asp-data/PacBio/WGS/K30-1/Aspa
ragusMaleV1/bam/K30-1.PacBio_Ref_run1.contigs.fasta.sorted.minimap2.sort
ed.bam.bai
HTTP/1.1 200 OK
x-amz-id-2:
kcUF8e4oClVu6INZ78npWcPgNLO3UJP3KQKsDCUDWHhsCjNfC5r4XB9IbB93LYdOwQLXRLi8
EgU=
x-amz-request-id: 9C523CCFAA1B2301
Date: Fri, 11 Jan 2019 11:36:27 GMT
Last-Modified: Wed, 09 Jan 2019 15:18:49 GMT
ETag: "ac2c06762fc282602aa0f1db2d562b19"
x-amz-meta-mode: 33188
x-amz-meta-gid: 0
x-amz-meta-uid: 0
x-amz-meta-mtime: 1547047128
x-amz-version-id: pD4RMlnV1r8qW7Q9cnwSRhaZW.dMI6dA
Accept-Ranges: bytes
Content-Type: application/octet-stream
Content-Length: 502496
Server: AmazonS3
 

Please feel free to mail me if you need additional data.

Thanks a bunch in advance,

 

Cheers,

Douwe

[Gmod-ajax] question about import bw file

[袁杰 <jie...@16...>]

When I use the jbrowse in Ubuntu to import the bigwig file, the error shown in these pictures.
Could you please tell me how to solve this problem? 
Greatful！






 

[Gmod-ajax] JBrowse 1.16.1 released

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

Hello all,

A new JBrowse version is here! This is a minor release with just a couple
of bugfixes and improvements. One interesting change allows the
Hierarchical track selector to be much faster when loaded with very large
track lists (e.g. thousands of tracks). Thanks to everyone for feedback and
bug reports, even on Christmas day :)

Happy holidays and enjoy browsing!


   - JBrowse-1.16.1.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.1-release/JBrowse-1.16.1.zip>
-
   minified release
   - JBrowse-1.16.1-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.1-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.1-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.1-release/JBrowse-1.16.1-desktop-win32-x64.zip>
   - JBrowse-1.16.1-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.1-release/JBrowse-1.16.1-desktop-linux-x64.zip>
   - JBrowse-1.16.1-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.1-release/JBrowse-1.16.1-desktop-darwin-x64.zip>

Blog post http://jbrowse.org/blog/2018/12/27/jbrowse-1-16-1.html
Minor improvements

   -

   Made a change to make Hierarchical track selector much faster on initial
   browser load for very large tracklists (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Updated to webpack 4 for some faster build times (issue #1270
   <https://github.com/gmod/jbrowse/pull/1270>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Updated to use dojo/dijit/dojox 1.14 (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Updated NeatCanvasFeatures to allow non-coding transcripts to be colored
   differently with style->unprocessedTranscriptColor. Thanks to @billzt
   <https://github.com/billzt> for the bug report (issue #1298
   <https://github.com/gmod/jbrowse/issues/1298>, @cmdcolin
   <https://github.com/cmdcolin>)

Bug fixes

   -

   Fixed issue where data directories with spaces in them were giving
   errors due to CORS on JBrowse Desktop (issue #1285
   <https://github.com/gmod/jbrowse/issues/1285>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed issue where the name store could be queried before being
   initialized (issue #1286 <https://github.com/gmod/jbrowse/issues/1286>,
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Fixed an issue for large BAM headers failing to load post-@gmod/bam
   integration. Thanks to @nie-jeff for reporting (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed access to some cross-origin resources (issue #1289
   <https://github.com/gmod/jbrowse/issues/1289>, issue #1292
   <https://github.com/gmod/jbrowse/pull/1292>, @cmdcolin
   <https://github.com/cmdcolin>)

[Gmod-ajax] Apollo 2.2.0 Released

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

	
Apollo 2.2.0 has been officially released.

https://github.com/GMOD/Apollo/releases/tag/2.2.0 <https://github.com/GMOD/Apollo/releases/tag/2.2.0>

Please note that to build this version you need to install yarn (npm i -g yarn) and you should either download and build a clean version or run ./apollo clean-all first.

There are a few bug fixes here, but most importantly is the upgrade from Jbrowse 1.12 to 1.15.4-release, which means numerous features and bug fixes and WebPack processing by default (far fewer files to download). 

JBrowse 1.16, also released today, will be integrated in the New Year in a future version of Apollo.  The current branch is here: https://github.com/GMOD/Apollo/tree/test-jb-1.16 <https://github.com/GMOD/Apollo/tree/test-jb-1.16> (still working on variant integration).  Feel free to contribute. 


Apollo is also available via docker (https://github.com/GMOD/docker-apollo <https://github.com/GMOD/docker-apollo>) and findable via the AWS community marketplace for EC2 images. 


Please report any issues here or via GitHub:

https://github.com/GMOD/Apollo/issues <https://github.com/GMOD/Apollo/issues>


Cheers,

The Apollo Team

[Gmod-ajax] JBrowse 1.16.0 released

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

Hello all!

I am very pleased to announce the release of JBrowse version 1.16.0! A
major new feature of this release is the introduction of paired read
visualization options.

And rather than delivering just one type of paired read visualization,
there are several options for visualizing pairs including:

* Pileup - standard alignments view but with connections between pairs
* Read cloud - plotting by insert size
* Arc view - plotting paired reads as connected arcs

Please refer to our blog post and documentation for more info
http://jbrowse.org/blog/2018/12/13/jbrowse-1-16-0.html

Additionally. there are other important bug fixes and features including
some for generate-names.pl, CRAM bugfixes, JBrowse desktop, and more.
Thanks to all the contributors, bug reporters, and feature requesters in
the community.

Enjoy browsing!


   - JBrowse-1.16.0.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.0-release/JBrowse-1.16.0.zip>
-
   minified release
   - JBrowse-1.16.0-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.0-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.0-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.0-release/JBrowse-1.16.0-desktop-win32-x64.zip>
   - JBrowse-1.16.0-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.0-release/JBrowse-1.16.0-desktop-linux-x64.zip>
   - JBrowse-1.16.0-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.0-release/JBrowse-1.16.0-desktop-darwin-x64.zip>

Major improvements

   - Added ability to view paired read data as connected entities for BAM
   and CRAM store classes. There are multiple different viewing options for
   this including plotting by insert size, plotting as connected arcs, or
   pileup views for the paired reads. Additionally multiple color schemes are
   available for coloring by insert size, pair orientation, mapping quality,
   and more. Thanks to @garrettjstevens <https://github.com/garrettjstevens>
   , @rbuels <https://github.com/rbuels>, @AndyMenzies
   <https://github.com/AndyMenzies>, and @keiranmraine
   <https://github.com/keiranmraine> for testing. Also a big thanks to
   @jrobinso <https://github.com/jrobinso> from @igvteam
   <https://github.com/igvteam> for contributions to CRAM code related to
   paired reads (issue #1235 <https://github.com/gmod/jbrowse/pull/1235>,
   @cmdcolin <https://github.com/cmdcolin>)

<http://jbrowse.org/blog/2018/12/13/jbrowse-1-16-0.html#minor-improvements>Minor
improvements

   -

   For users with the "dev" or compiling JBrowse from source code, the
   ./setup.sh now performs a full webpack production build (issue #1223
   <https://github.com/gmod/jbrowse/pull/1223>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Created new BAM parsing mechanism using the npm module @gmod/bam
   <https://www.npmjs.com/package/@gmod/bam>. Users might see some modest
   performance improvements due to enhanced tooling. Thanks to @rbuels
   <https://github.com/rbuels> and others for testing and feedback (issue
   #1215 <https://github.com/gmod/jbrowse/pull/1215>, issue #1178
   <https://github.com/gmod/jbrowse/issues/1178>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   setup.sh now supports setting a JBROWSE_PUBLIC_PATH environment variable
   for more flexibility in iframeless embedding scenarios (issue #1213
   <https://github.com/gmod/jbrowse/issues/1213>, @rbuels
   <https://github.com/rbuels>)
   -

   Added support for indexing arbitrary fields from GFF3Tabix files by
   setting nameAttributes in the track config e.g.
   nameAttributes=name,id,customfield. (issue #1115
   <https://github.com/gmod/jbrowse/issues/1115>, issue #1222
   <https://github.com/gmod/jbrowse/pull/1222>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Add support for generate-names to index VCF features that have multiple
   IDs in the ID column (@cmdcolin <https://github.com/cmdcolin>)
   -

   Added documentation on embedding JBrowse in an iframe and in a div,
   including how to embed JBrowse using a custom JavaScript object as a
   configuration (issue #1228
<https://github.com/gmod/jbrowse/pull/1228>, issue
   #1243 <https://github.com/gmod/jbrowse/pull/1243>, @rbuels
   <https://github.com/rbuels> and @garrettjstevens
   <https://github.com/garrettjstevens>)
   -

   Added ability to render non-coding transcript types to the default Gene
   glyph which helps when a gene feature has a mix of coding and non-coding
   subfeatures (issue #1106
<https://github.com/gmod/jbrowse/issues/1106>, issue
   #1230 <https://github.com/gmod/jbrowse/pull/1230>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Created new VCF parsing mechanism using the NPM module @gmod/vcf
   <https://www.npmjs.com/package/@gmod/vcf>. Thanks to @cmdcolin
   <https://github.com/cmdcolin> and others for testing and feedback (issue
   #1227 <https://github.com/gmod/jbrowse/pull/1227>, issue #1199
   <https://github.com/gmod/jbrowse/issues/1199>, @garrettjstevens
   <https://github.com/garrettjstevens>)
   -

   Added ability to open "chrom.sizes" files from the Open sequence
dialog (issue
   #1250 <https://github.com/gmod/jbrowse/issues/1250>, issue #1257
   <https://github.com/gmod/jbrowse/pull/1257>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added a config datasetLinkToParentIframe to make the dataset selector
   use window.parent for when jbrowse is in an iframe (issue #1248
   <https://github.com/gmod/jbrowse/pull/1248>, @enuggetry
   <https://github.com/enuggetry>)
   -

   Improved error message that is displayed when a data file cannot be
   fetched via CORS (@rbuels <https://github.com/rbuels>)
   -

   Added some word wrapping for long unbroken fields in the View details
   popups. Thanks to @luke-c-sargent <https://github.com/luke-c-sargent> for
   the idea (issue #1246 <https://github.com/gmod/jbrowse/issues/1246>).
   -

   Added hideImproperPairs filter for Alignments2/SNPCoverage tracks which
   disambiguates from missing mate pairs (issue #1235
   <https://github.com/gmod/jbrowse/pull/1235>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added useTS coloring option for RNA-seq strandedness, similar to the
   useXS that existed previously (issue #1235
   <https://github.com/gmod/jbrowse/pull/1235>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Added a --bgzip_fasta option for prepare-refseqs.pl and also the ability
   to index reference sequence names if they are manually specified as a fasta
   index e.g. refSeqs=genome.fai. Thanks to @FredericBGA
   <https://github.com/FredericBGA>for the report! (issue #1281
   <https://github.com/gmod/jbrowse/issues/1281>, issue #1282
   <https://github.com/gmod/jbrowse/pull/1282>, @cmdcolin
   <https://github.com/cmdcolin>).

<http://jbrowse.org/blog/2018/12/13/jbrowse-1-16-0.html#bug-fixes>Bug fixes

   -

   Fixed issue where some generate-names setups would fail to index
   features. Thanks to @BioInfoSuite <https://github.com/BioInfoSuite> for
   reporting (issue #1275 <https://github.com/gmod/jbrowse/issues/1275>, issue
   #1283 <https://github.com/gmod/jbrowse/pull/1283>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed issue with getting feature density from BAM files via the index
   stats estimation (issue #1233
   <https://github.com/gmod/jbrowse/issues/1233>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed issue where some feature mouseovers where not working properly
   (issue #1236, @cmdcolin <https://github.com/cmdcolin>)
   -

   Fixed issue where instantiating JBrowse via standalone.js didn't work
   when in a production build with JBROWSE_PUBLIC_PATH overridden (issue
   #1239 <https://github.com/gmod/jbrowse/issues/1239>, @garrettjstevens
   <https://github.com/garrettjstevens>)
   -

   Small fix for issue where SNPCoverage would crash on some feature
   filters (issue #1241 <https://github.com/gmod/jbrowse/issues/1241>,
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Fixed issue where JBrowse Desktop was not able to access remote files
   (issue #1234, issue #1245 <https://github.com/gmod/jbrowse/pull/1245>,
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Fix issue where the Hierarchical track selector contained a bunch of
   blank whitespace. Thanks to @nathanhaigh
<https://github.com/nathanhaigh> for
   reporting! (issue #1240 <https://github.com/gmod/jbrowse/issues/1240>, issue
   #1253 <https://github.com/gmod/jbrowse/pull/1253>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed issue where whitespace surrounding GFF3 attributes and attribute
   names was incorporated (issue #1221
   <https://github.com/gmod/jbrowse/issues/1221>, issue #1254
   <https://github.com/gmod/jbrowse/pull/1254>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed issue with some GFF3Tabix tracks having some inconsistent layout
   of features (issue #1244
<https://github.com/gmod/jbrowse/issues/1244>, issue
   #1260 <https://github.com/gmod/jbrowse/pull/1260>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed CRAM store not renaming reference sequences in the same way as
   other stores (issue #1277 <https://github.com/gmod/jbrowse/pull/1277>,
   @rbuels <https://github.com/rbuels>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed bug where older browsers e.g. IE11 were not being properly
   supported via babel (issue #1259
   <https://github.com/gmod/jbrowse/issues/1259>, issue #1267
   <https://github.com/gmod/jbrowse/pull/1267>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed bug where some files were not being fetched properly when changing
   refseqs. Thanks to @luke-c-sargent <https://github.com/luke-c-sargent> for
   the report (issue #1252 <https://github.com/gmod/jbrowse/issues/1252>)
   -

   Fixed storeTimeout on CRAM files being unused which can result in
   excessive fetches (issue #1235
   <https://github.com/gmod/jbrowse/pull/1235>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed issue where JBrowse would load the wrong area of the refseq on
   startup resulting in bad layouts and excessive data fetches. Thanks to
   @hkmoon <https://github.com/hkmoon>, @cmdcolin
   <https://github.com/cmdcolin>, and @garrettjstevens
   <https://github.com/garrettjstevens> for debugging (issue #1190
   <https://github.com/gmod/jbrowse/issues/1190>, issue #1235
   <https://github.com/gmod/jbrowse/pull/1235>, pull #1187)
   -

   Fixed issue where CRAM layout and mouseover would be glitchy due to ID
   collisions on features (issue #1271
   <https://github.com/gmod/jbrowse/issues/1271>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed parsing of certain bigBed files that were hanging on track startup
   (issue #1226 <https://github.com/gmod/jbrowse/issues/1226>, issue #1229
   <https://github.com/gmod/jbrowse/pull/1229>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed issue where some parts of a CRAM file would not be displayed in
   JBrowse due to a CRAM index parsing issue (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed an issue where BAM features were not lazily evaluating their tags (
   @cmdcolin <https://github.com/cmdcolin>)

<http://jbrowse.org/blog/2018/12/13/jbrowse-1-16-0.html#notable-changes>Notable
changes

   - Rendering of features in popups, mouseover tooltips, and feature
   labels were made to escape HTML. If you are using literal HTML labels in
   these places then set the attribute unsafePopup, unsafeMouseover, or
   unsafeHTMLFeatures on your tracks. Thanks to @garrettjstevens
   <https://github.com/garrettjstevens> (issue #1263
   <https://github.com/gmod/jbrowse/pull/1263>, @cmdcolin
   <https://github.com/cmdcolin>).

Re: [Gmod-ajax] JBrowse: customizing help menu

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

There is not a strong configuration available for customizing the menu bar,
so generally adding a new menu item is done via plugins

http://jbrowse.org/docs/faq.html#how-do-i-customize-the-main-menu-bar


Plugin writing is a little involved though. If you want to instead just
replace the contents of the "Help->General" dialog box, you can for example
just modify your jbrowse_conf.json

{
    "quickHelp": {
        "content": "Your content here. Note that <a
href='http://google.com'>html
is allowed :)</a>"
    }
}

Hope that helps


-Colin

On Wed, Dec 12, 2018 at 11:10 PM Scott Cain <sc...@sc...> wrote:

> Hi Alex,
>
> Off hand I don’t know how to modify the help menu, but I’ve been thinking
> about for a project I’ve been working on. I’ve cc’ed this email to the
> jbrowse mailing list, where I know there are people that know how to do it.
>
> Scott
>
>
> On Dec 12, 2018, at 6:54 PM, 李东 <Do...@wi...> wrote:
>
> Dear JBrowse Support,
>
>
>
> We have been using JBrowse on several projects and thanks for this open
> source project!
>
>
>
> Now I have a quick question: how to customize the help menu, say to add
> one more item into the help menu? I would like want to add our local
> project-specific help page. Currently it has only 2 items as this
> screenshot shows:
>
> <image002.png>
>
>
>
> Thanks in advance!
>
>
>
> Alex
>
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse: customizing help menu

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

Hi Alex, 

Off hand I don’t know how to modify the help menu, but I’ve been thinking about for a project I’ve been working on. I’ve cc’ed this email to the jbrowse mailing list, where I know there are people that know how to do it. 

Scott


> On Dec 12, 2018, at 6:54 PM, 李东 <Do...@wi...> wrote:
> 
> Dear JBrowse Support,
>  
> We have been using JBrowse on several projects and thanks for this open source project!
>  
> Now I have a quick question: how to customize the help menu, say to add one more item into the help menu? I would like want to add our local project-specific help page. Currently it has only 2 items as this screenshot shows:
> <image002.png>
>  
> Thanks in advance!
>  
> Alex
>  
>  

Re: [Gmod-ajax] Assistance with Jbrowse

[Shorter, T. <ts...@le...>]

Thanks Colin,

I have tried that but I may have made a typo so I'll check again tomorrow!

Tom

Get Outlook for Android<https://aka.ms/ghei36>

________________________________
From: Colin <col...@gm...>
Sent: Monday, November 26, 2018 5:45:36 PM
To: Shorter, Thomas; gmo...@li...
Subject: Re: [Gmod-ajax] Assistance with Jbrowse

Sure thing! Glad to help

I think the key is to set this value in the config on your REST API track

region_feature_densities=true


-Colin

On Mon, Nov 26, 2018 at 8:50 AM Shorter, Thomas <ts...@le...<mailto:ts...@le...>> wrote:

Hi,


Thank you for your help previously, I managed to sort a lot of my issues out because of it.


I have now moved onto generating custom/dynamic CanvasFeature tracks and I am using a rest API to supply the feature data. Is there a way to have CanvasFeature tracks display data from the API's (base)/stats/regionFeatureDensities/(refseq_name) endpoint?


Many thanks,


Tom

________________________________
From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: 08 November 2018 16:37:29
To: Scott Cain
Cc: Shorter, Thomas; gmo...@li...<mailto:gmo...@li...>; he...@gm...<mailto:he...@gm...>
Subject: Re: [Gmod-ajax] Assistance with Jbrowse

1. The glyph configuration is just glyph, not style->glyph
2. The height can be changed via a callback in style->height e.g. "style": { "height": "function(feat) { return feature.get('my_feat_height') || 10; }" } would return some GFF attribute my_feature_height
3. Set style.featureScale=1000 and it will never be able to zoom in as far as to display the features (zoom are represented as pixels per basepair)

For histogram customizations I would recommend probably making a custom bigwig track for coverage and use the "summary histograms" feature http://gmod.org/wiki/JBrowse_Configuration_Guide#Configuring_Summary_Histograms this will give you more flexibility than the built in histograms generated by flatfile-to-json (I am assuming you are using this based on a thread posted recently?)

Hope that helps

-Colin


On Thu, Nov 8, 2018 at 11:24 AM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Tom,

You can definitely do those things but I’m on my phone, so it’s hard to write out using this keyboard. I’ve CC’d the jbrowse mailing list so if I don’t get back to you today it’s likely that somebody else on the list will.

Scott


On Nov 7, 2018, at 9:42 AM, Shorter, Thomas <ts...@le...<mailto:ts...@le...>> wrote:


Hi,


I'm surrently looking at using Jbrowse to display SNP data within a website I'm working on.


I don't have much experience with JavaScript and I'm having some trouble following some of the guides/what I want to do isn't covered.


If you could answer a few of my questions I'd be most greatful!


Firstly, how do I set the glyph type? I've tried changing style.glyph to diamond in both the .conf and .json and within the track config itself in the browser window but this doesn't seem to work but I'm pretty sure I saw a diamond glyph whilst looking through the code.


Next I'd like to be able to change the height of a glyph/feature based on data within the 9th column of the gff imported, is this possible and how?


I'd also like to be able to always have the histogram showing, even at the single base level and if possible to have the bin size set to 2-5% of the window (i'll have to play about with the exact number) or to the size of a single base, whichever is bigger.


Many thanks!


Tom

_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] Assistance with Jbrowse

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

Sure thing! Glad to help

I think the key is to set this value in the config on your REST API track

region_feature_densities=true


-Colin

On Mon, Nov 26, 2018 at 8:50 AM Shorter, Thomas <ts...@le...>
wrote:

> Hi,
>
>
> Thank you for your help previously, I managed to sort a lot of my issues
> out because of it.
>
>
> I have now moved onto generating custom/dynamic CanvasFeature tracks and I
> am using a rest API to supply the feature data. Is there a way to have
> CanvasFeature tracks display data from the API's (base)/stats/regionFeatureDensities/(refseq_name)
> endpoint?
>
>
> Many thanks,
>
>
> Tom
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* 08 November 2018 16:37:29
> *To:* Scott Cain
> *Cc:* Shorter, Thomas; gmo...@li...; he...@gm...
> *Subject:* Re: [Gmod-ajax] Assistance with Jbrowse
>
> 1. The glyph configuration is just glyph, not style->glyph
> 2. The height can be changed via a callback in style->height e.g. "style":
> { "height": "function(feat) { return feature.get('my_feat_height') || 10;
> }" } would return some GFF attribute my_feature_height
> 3. Set style.featureScale=1000 and it will never be able to zoom in as far
> as to display the features (zoom are represented as pixels per basepair)
>
> For histogram customizations I would recommend probably making a custom
> bigwig track for coverage and use the "summary histograms" feature
> http://gmod.org/wiki/JBrowse_Configuration_Guide#Configuring_Summary_Histograms
> this will give you more flexibility than the built in histograms generated
> by flatfile-to-json (I am assuming you are using this based on a thread
> posted recently?)
>
> Hope that helps
>
> -Colin
>
>
> On Thu, Nov 8, 2018 at 11:24 AM Scott Cain <sc...@sc...> wrote:
>
> Hi Tom,
>
> You can definitely do those things but I’m on my phone, so it’s hard to
> write out using this keyboard. I’ve CC’d the jbrowse mailing list so if I
> don’t get back to you today it’s likely that somebody else on the list
> will.
>
> Scott
>
>
> On Nov 7, 2018, at 9:42 AM, Shorter, Thomas <ts...@le...> wrote:
>
> Hi,
>
>
> I'm surrently looking at using Jbrowse to display SNP data within a
> website I'm working on.
>
>
> I don't have much experience with JavaScript and I'm having some trouble
> following some of the guides/what I want to do isn't covered.
>
>
> If you could answer a few of my questions I'd be most greatful!
>
>
> Firstly, how do I set the glyph type? I've tried changing style.glyph to
> diamond in both the .conf and .json and within the track config itself in
> the browser window but this doesn't seem to work but I'm pretty sure I saw
> a diamond glyph whilst looking through the code.
>
>
> Next I'd like to be able to change the height of a glyph/feature based on
> data within the 9th column of the gff imported, is this possible and how?
>
>
> I'd also like to be able to always have the histogram showing, even at the
> single base level and if possible to have the bin size set to 2-5% of the
> window (i'll have to play about with the exact number) or to the size of a
> single base, whichever is bigger.
>
>
> Many thanks!
>
>
> Tom
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] Unable to fetch vcf file

[Garrett S. <ste...@gm...>]

Hello,

I am not able to reproduce this behavior. Going to the site you provided,
wheat_90k loads fine for me:
[image: image.png]

Perhaps the VCF was unavailable before but is available now?

Best,
Garrett

On Tue, Nov 20, 2018 at 10:47 AM 2013201008 <201...@nj...> wrote:

>
>
> - JBrowse version:  jbrowse-1.12.3-release
> - Web browser being used: apache2
> - Operating system if relevant: Jbrowse was installed on docker of ubuntu
> 16.04
>
> This is my jbrowse
> http://202.194.139.32/jbrowse-1.12.3-release/?data=Chinese_Spring
> I can load `wheat660K` track but not for wheat_90K.
>
>
> http://202.194.139.32/jbrowse-1.12.3-release/?data=Chinese_Spring&loc=chr1A%3A498530961..498537150&tracks=IWGSC_v1.1_HC_gene%2Cwheat660K%2Cwheat_90K&highlight=
>
>
>
> Sheng-Wei Ma
> Nanjing Agricultural University <http://english.njau.edu.cn/>
> 201...@nj...
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Unable to fetch vcf file

[2013201008 <201...@nj...>]

<html>
<head>
    <meta http-equiv='Content-Type' content='text/html; charset=UTF-8'>
</head>
<body>
<style>
    font{
        line-height: 1.6;
    }
    ul,ol{
        padding-left: 20px;
        list-style-position: inside;
    }
</style>
<div style = 'font-family:Helvetica,Helvetica,微软雅黑, 宋体; line-height:1.6;'>
    <div ></div><div>
    <div>
        <span>
            <br>
        </span>
    </div>
    <div>
        <div><br></div><div>- JBrowse version: &nbsp;jbrowse-1.12.3-release</div><div>- Web browser being used: apache2</div><div>- Operating system if relevant: Jbrowse was installed on docker of ubuntu 16.04</div><div><br></div><div>This is my jbrowse http://202.194.139.32/jbrowse-1.12.3-release/?data=Chinese_Spring</div><div>I can load `wheat660K` track but not for wheat_90K.</div><div><br></div><div><a href="http://202.194.139.32/jbrowse-1.12.3-release/?data=Chinese_Spring&amp;loc=chr1A%3A498530961..498537150&amp;tracks=IWGSC_v1.1_HC_gene%2Cwheat660K%2Cwheat_90K&amp;highlight=" _src="http://202.194.139.32/jbrowse-1.12.3-release/?data=Chinese_Spring&amp;loc=chr1A%3A498530961..498537150&amp;tracks=IWGSC_v1.1_HC_gene%2Cwheat660K%2Cwheat_90K&amp;highlight=">http://202.194.139.32/jbrowse-1.12.3-release/?data=Chinese_Spring&amp;loc=chr1A%3A498530961..498537150&amp;tracks=IWGSC_v1.1_HC_gene%2Cwheat660K%2Cwheat_90K&amp;highlight=</a></div><div>&nbsp;</div><span>
            
        </span>
    </div>
    <div>
        <span>
            <br>
        </span>
    </div>
    <div id="ntes-pcmac-signature" style="font-family:'Helvetica','Microsoft Yahei', '微软雅黑'">
          <div style="font-size:14px; padding: 0;  margin:0;">
        <div style="display:inline-block;">
            <div style="font-family:&quot;Helvetica&quot;; font-size: 14px; color:#31353b">
    <style>
        font{
            line-height: 1.6;
        }
    </style>
<div style="font-family:&quot;Helvetica&quot;; font-size: 14px; color:#000000">
    <style>
        font{
            line-height: 1.5;
        }
    </style>
<div style="font-family:&quot;Helvetica&quot;; font-size: 14px; color:#000000">
    <style>
        font{
            line-height: 1.5;
        }
    </style>
<div><br></div><div><img src="cid:0A3D717E-6BFC-4C67-B4F9-B64D417B8F55@mailmaster" naturalheight="1994px" naturalwidth="1094px" currentsize="14" style="height: 858.3516167400003px; width: 470.9311277400002px;"></div><div><img src="https://wheat-1252088472.picsh.myqcloud.com/2018-11-20-164941.png"></div><div><img src="https://wheat-1252088472.picsh.myqcloud.com/2018-11-20-165433.png"></div><div><img src="cid:0C18E25C-099C-4DE9-AFDB-EDE215BDA6C2@mailmaster"></div><div><img src="cid:582E45EE-C1A3-4EAF-98DF-51C4DCECE54E@mailmaster"></div><div><font size="2" color="#347eec" style="font-size: 16px;">Sheng-Wei Ma</font></div><div><h3 class="r" style="font-weight: normal; margin: 0px; padding: 0px; line-height: 1.2; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; font-family: arial, sans-serif; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><font color="#347eec" size="2" style="cursor: pointer; text-decoration: none; font-size: 16px;"><a href="http://english.njau.edu.cn/" style="cursor: pointer; text-decoration: none;">Nanjing Agricultural University</a></font></h3><h3 class="r" style="font-weight: normal; margin: 0px; padding: 0px; line-height: 1.2; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; font-family: arial, sans-serif; font-variant-ligatures: normal; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><span style="font-size: 14px;"></span><a href="mailto:201...@nj...">201...@nj...</a></h3></div><div><br></div>
</div>
</div>
</div>
        </div>
    </div>
     </div>
    <br>
</div><!--�-->
</div>
</body>
</html>

Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

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

It’s true that a list for each category in the config could get very long with large tracklists in a given category.  I think track metadata like a numerical ‘sortOrder’ attribute would probably be an easy alternative to be specified in each track stanza, similar to how that’s done in UCSC genome browsers if I recall correctly.  If that were implemented it would be nice to specify that attribute in the add bigwig script as you’re adding the bigwigs to the trackList file so you don’t have to manually change it in the configuration, automated techniques are always helpful.  Didn’t think of a callback function but that would be an option as well I suppose.

Thanks for looking into it,

Vaneet


Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

From: Colin [mailto:col...@gm...]
Sent: Monday, November 19, 2018 11:05 AM
To: Vaneet Lotay <van...@uc...>
Cc: Predeus, Olexandr <A.P...@li...>; gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

I do want to enable that, but I am thinking you could have multiple ways to go about it...what seems like the best way to do it? e.g. track metadata on the track specifies sort order, callback function for sort order (seems difficult but flexible) or a list in the config?

-Colin

On Mon, Nov 19, 2018 at 12:48 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Colin,

I would reiterate my interest in terms of issue #4 posed by Alex.  While it’s great that we can now sort JBrowser categories in the hierarchical track selector, it would be another useful improvement to be able to sort tracks within these categories.  I realize besides sorting them in alphabetical order if you set the config setting “sortHierarchical: false” then it will sort based on the order of the tracks in the trackList.json file, but this can become tricky when you’re dealing with 60 or 70 tracks trying to ensure they’re placed in the right physical order in the .json file.

Thanks,

Vaneet

From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: Monday, November 19, 2018 6:32 AM
To: Predeus, Olexandr <A.P...@li...<mailto:A.P...@li...>>
Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

1. It is true that faceted allows the shift-select of multiple tracks but sort of has that arbitrary limit. Hierarchical track selector has a plugin for multiple select that could help https://github.com/bhofmei/jbplugin-hierarchicalcheckbox or the hard coded limit could be removed. I'd be curious what you are doing that requires this many tracks to be selected, it could slow down the browser somewhat having many tracks so I'm wondering if there are alternative.

2. There are several options for tracks to load by default `defaultTracks`, `forceTracks`, and `alwaysOnTracks`. Example `defaultTracks=snps,genes,bam1,bam2` at the top of your tracks.conf. Note: defaultTracks is overridden by cookies/previous sessions, and forceTracks is overridden by URL lists of tracks, and alwaysOnTracks always loads the tracks, so kind of three levels of forcing the track to be displayed.

3. There aren't really very great hooks to add logos and such presently. For a really hacky solution you could just add some extra script

    <script>
var timer = setInterval(() => {
    var ret = document.querySelector('.jbrowseStandaloneDatasetSelector');
    if(ret) {
        var img = document.createElement('img')
        img.src = 'yourlogo.png'
        ret.prepend(img)
        clearInterval(timer)
    }
},200)
    </script>


4. The categoryOrder config was added recently for ordering the categories of the hierarchical track selector. If you have more details on the case please describe further. There is also "sortHierarchical: false" option where there is no sorting applied and the order is just based on the order of the tracks in the trackList.json/tracks.conf


-Colin

On Fri, Nov 16, 2018 at 8:20 PM Predeus, Olexandr <A.P...@li...<mailto:A.P...@li...>> wrote:

Hello all,



I was wondering several things about JBrowse configuration I couldn't figure out after searching the manual.



  1.  Is there an option or selecting all the tracks at once? Maybe a plugin? I've tried faceted selection, but that doesn't allow you to do more than 30, and all of my datasets do have more. And it's quite inconvenient to click on them too. So I'd appreciate any suggestions.
  2.  How can I set up which files are selected upon loading the dataset? E.g. if I want half of the tracks to be selected to begin with?
  3.  Is there any way to customize the dataset selector screen? E.g. add a picture or some other links?
  4.  How can I change the order of tracks within each category? I managed to sort categories by adding a number to their name - do I have to do the same with the keys?

Thank you very much in advance!

-- Alex
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

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

I do want to enable that, but I am thinking you could have multiple ways to
go about it...what seems like the best way to do it? e.g. track metadata on
the track specifies sort order, callback function for sort order (seems
difficult but flexible) or a list in the config?

-Colin

On Mon, Nov 19, 2018 at 12:48 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Colin,
>
>
>
> I would reiterate my interest in terms of issue #4 posed by Alex.  While
> it’s great that we can now sort JBrowser categories in the hierarchical
> track selector, it would be another useful improvement to be able to sort
> tracks within these categories.  I realize besides sorting them in
> alphabetical order if you set the config setting “sortHierarchical: false”
> then it will sort based on the order of the tracks in the trackList.json
> file, but this can become tricky when you’re dealing with 60 or 70 tracks
> trying to ensure they’re placed in the right physical order in the .json
> file.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Monday, November 19, 2018 6:32 AM
> *To:* Predeus, Olexandr <A.P...@li...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse: select all tracks? Default selection
> when dataset is loaded? etc
>
>
>
> 1. It is true that faceted allows the shift-select of multiple tracks but
> sort of has that arbitrary limit. Hierarchical track selector has a plugin
> for multiple select that could help
> https://github.com/bhofmei/jbplugin-hierarchicalcheckbox or the hard
> coded limit could be removed. I'd be curious what you are doing that
> requires this many tracks to be selected, it could slow down the browser
> somewhat having many tracks so I'm wondering if there are alternative.
>
>
>
> 2. There are several options for tracks to load by default
> `defaultTracks`, `forceTracks`, and `alwaysOnTracks`. Example
> `defaultTracks=snps,genes,bam1,bam2` at the top of your tracks.conf. Note:
> defaultTracks is overridden by cookies/previous sessions, and forceTracks
> is overridden by URL lists of tracks, and alwaysOnTracks always loads the
> tracks, so kind of three levels of forcing the track to be displayed.
>
>
>
> 3. There aren't really very great hooks to add logos and such presently.
> For a really hacky solution you could just add some extra script
>
>
>
>     <script>
>
> var timer = setInterval(() => {
>
>     var ret = document.querySelector('.jbrowseStandaloneDatasetSelector');
>
>     if(ret) {
>
>         var img = document.createElement('img')
>
>         img.src = 'yourlogo.png'
>
>         ret.prepend(img)
>
>         clearInterval(timer)
>
>     }
>
> },200)
>
>     </script>
>
>
>
>
>
> 4. The categoryOrder config was added recently for ordering the categories
> of the hierarchical track selector. If you have more details on the case
> please describe further. There is also "sortHierarchical: false" option
> where there is no sorting applied and the order is just based on the order
> of the tracks in the trackList.json/tracks.conf
>
>
>
>
>
> -Colin
>
>
>
> On Fri, Nov 16, 2018 at 8:20 PM Predeus, Olexandr <
> A.P...@li...> wrote:
>
> Hello all,
>
>
>
> I was wondering several things about JBrowse configuration I couldn't
> figure out after searching the manual.
>
>
>
>    1. Is there an option or selecting all the tracks at once? Maybe a
>    plugin? I've tried faceted selection, but that doesn't allow you to do more
>    than 30, and all of my datasets do have more. And it's quite inconvenient
>    to click on them too. So I'd appreciate any suggestions.
>    2. How can I set up which files are selected upon loading the dataset?
>    E.g. if I want half of the tracks to be selected to begin with?
>    3. Is there any way to customize the dataset selector screen? E.g. add
>    a picture or some other links?
>    4. How can I change the order of tracks within each category? I
>    managed to sort categories by adding a number to their name - do I have to
>    do the same with the keys?
>
>
>
> Thank you very much in advance!
>
>
>
> -- Alex
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

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

Hey Colin,

I would reiterate my interest in terms of issue #4 posed by Alex.  While it’s great that we can now sort JBrowser categories in the hierarchical track selector, it would be another useful improvement to be able to sort tracks within these categories.  I realize besides sorting them in alphabetical order if you set the config setting “sortHierarchical: false” then it will sort based on the order of the tracks in the trackList.json file, but this can become tricky when you’re dealing with 60 or 70 tracks trying to ensure they’re placed in the right physical order in the .json file.

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: Monday, November 19, 2018 6:32 AM
To: Predeus, Olexandr <A.P...@li...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

1. It is true that faceted allows the shift-select of multiple tracks but sort of has that arbitrary limit. Hierarchical track selector has a plugin for multiple select that could help https://github.com/bhofmei/jbplugin-hierarchicalcheckbox or the hard coded limit could be removed. I'd be curious what you are doing that requires this many tracks to be selected, it could slow down the browser somewhat having many tracks so I'm wondering if there are alternative.

2. There are several options for tracks to load by default `defaultTracks`, `forceTracks`, and `alwaysOnTracks`. Example `defaultTracks=snps,genes,bam1,bam2` at the top of your tracks.conf. Note: defaultTracks is overridden by cookies/previous sessions, and forceTracks is overridden by URL lists of tracks, and alwaysOnTracks always loads the tracks, so kind of three levels of forcing the track to be displayed.

3. There aren't really very great hooks to add logos and such presently. For a really hacky solution you could just add some extra script

    <script>
var timer = setInterval(() => {
    var ret = document.querySelector('.jbrowseStandaloneDatasetSelector');
    if(ret) {
        var img = document.createElement('img')
        img.src = 'yourlogo.png'
        ret.prepend(img)
        clearInterval(timer)
    }
},200)
    </script>


4. The categoryOrder config was added recently for ordering the categories of the hierarchical track selector. If you have more details on the case please describe further. There is also "sortHierarchical: false" option where there is no sorting applied and the order is just based on the order of the tracks in the trackList.json/tracks.conf


-Colin

On Fri, Nov 16, 2018 at 8:20 PM Predeus, Olexandr <A.P...@li...<mailto:A.P...@li...>> wrote:

Hello all,



I was wondering several things about JBrowse configuration I couldn't figure out after searching the manual.



  1.  Is there an option or selecting all the tracks at once? Maybe a plugin? I've tried faceted selection, but that doesn't allow you to do more than 30, and all of my datasets do have more. And it's quite inconvenient to click on them too. So I'd appreciate any suggestions.
  2.  How can I set up which files are selected upon loading the dataset? E.g. if I want half of the tracks to be selected to begin with?
  3.  Is there any way to customize the dataset selector screen? E.g. add a picture or some other links?
  4.  How can I change the order of tracks within each category? I managed to sort categories by adding a number to their name - do I have to do the same with the keys?

Thank you very much in advance!

-- Alex
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

[Predeus, O. <A.P...@li...>]

Dear Colin, thank you very much for your help!


All of your suggestions are extremely helpful.


>  I'd be curious what you are doing that requires this many tracks to be selected, it could slow down the browser somewhat having many tracks so I'm wondering if there are alternative.


We are processing a large bunch of RNA-seq conditions in bacterial strains. Genomes and annotations are not huge so having e.g. 40-60 tracks does not slow it down too much. At the same time, people quite often need to look at all replicates and conditions. This means they have to click on 60 checkboxes, which is not ideal, of course.


Thank you again!


-- Alex

________________________________
From: Colin <col...@gm...>
Sent: Monday, November 19, 2018 1:31:48 PM
To: Predeus, Olexandr
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

1. It is true that faceted allows the shift-select of multiple tracks but sort of has that arbitrary limit. Hierarchical track selector has a plugin for multiple select that could help https://github.com/bhofmei/jbplugin-hierarchicalcheckbox or the hard coded limit could be removed. I'd be curious what you are doing that requires this many tracks to be selected, it could slow down the browser somewhat having many tracks so I'm wondering if there are alternative.

2. There are several options for tracks to load by default `defaultTracks`, `forceTracks`, and `alwaysOnTracks`. Example `defaultTracks=snps,genes,bam1,bam2` at the top of your tracks.conf. Note: defaultTracks is overridden by cookies/previous sessions, and forceTracks is overridden by URL lists of tracks, and alwaysOnTracks always loads the tracks, so kind of three levels of forcing the track to be displayed.

3. There aren't really very great hooks to add logos and such presently. For a really hacky solution you could just add some extra script

    <script>
var timer = setInterval(() => {
    var ret = document.querySelector('.jbrowseStandaloneDatasetSelector');
    if(ret) {
        var img = document.createElement('img')
        img.src = 'yourlogo.png'
        ret.prepend(img)
        clearInterval(timer)
    }
},200)
    </script>


4. The categoryOrder config was added recently for ordering the categories of the hierarchical track selector. If you have more details on the case please describe further. There is also "sortHierarchical: false" option where there is no sorting applied and the order is just based on the order of the tracks in the trackList.json/tracks.conf


-Colin

On Fri, Nov 16, 2018 at 8:20 PM Predeus, Olexandr <A.P...@li...<mailto:A.P...@li...>> wrote:

Hello all,


I was wondering several things about JBrowse configuration I couldn't figure out after searching the manual.


  1.  Is there an option or selecting all the tracks at once? Maybe a plugin? I've tried faceted selection, but that doesn't allow you to do more than 30, and all of my datasets do have more. And it's quite inconvenient to click on them too. So I'd appreciate any suggestions.
  2.  How can I set up which files are selected upon loading the dataset? E.g. if I want half of the tracks to be selected to begin with?
  3.  Is there any way to customize the dataset selector screen? E.g. add a picture or some other links?
  4.  How can I change the order of tracks within each category? I managed to sort categories by adding a number to their name - do I have to do the same with the keys?

Thank you very much in advance!

-- Alex

_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

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

1. It is true that faceted allows the shift-select of multiple tracks but
sort of has that arbitrary limit. Hierarchical track selector has a plugin
for multiple select that could help
https://github.com/bhofmei/jbplugin-hierarchicalcheckbox or the hard coded
limit could be removed. I'd be curious what you are doing that requires
this many tracks to be selected, it could slow down the browser somewhat
having many tracks so I'm wondering if there are alternative.

2. There are several options for tracks to load by default `defaultTracks`,
`forceTracks`, and `alwaysOnTracks`. Example
`defaultTracks=snps,genes,bam1,bam2` at the top of your tracks.conf. Note:
defaultTracks is overridden by cookies/previous sessions, and forceTracks
is overridden by URL lists of tracks, and alwaysOnTracks always loads the
tracks, so kind of three levels of forcing the track to be displayed.

3. There aren't really very great hooks to add logos and such presently.
For a really hacky solution you could just add some extra script

    <script>
var timer = setInterval(() => {
    var ret = document.querySelector('.jbrowseStandaloneDatasetSelector');
    if(ret) {
        var img = document.createElement('img')
        img.src = 'yourlogo.png'
        ret.prepend(img)
        clearInterval(timer)
    }
},200)
    </script>


4. The categoryOrder config was added recently for ordering the categories
of the hierarchical track selector. If you have more details on the case
please describe further. There is also "sortHierarchical: false" option
where there is no sorting applied and the order is just based on the order
of the tracks in the trackList.json/tracks.conf


-Colin

On Fri, Nov 16, 2018 at 8:20 PM Predeus, Olexandr <A.P...@li...>
wrote:

> Hello all,
>
>
> I was wondering several things about JBrowse configuration I couldn't
> figure out after searching the manual.
>
>
>
>    1. Is there an option or selecting all the tracks at once? Maybe a
>    plugin? I've tried faceted selection, but that doesn't allow you to do more
>    than 30, and all of my datasets do have more. And it's quite inconvenient
>    to click on them too. So I'd appreciate any suggestions.
>    2. How can I set up which files are selected upon loading the dataset?
>    E.g. if I want half of the tracks to be selected to begin with?
>    3. Is there any way to customize the dataset selector screen? E.g. add
>    a picture or some other links?
>    4. How can I change the order of tracks within each category? I
>    managed to sort categories by adding a number to their name - do I have to
>    do the same with the keys?
>
>
> Thank you very much in advance!
>
> -- Alex
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse: select all tracks? Default selection when dataset is loaded? etc

[Predeus, O. <A.P...@li...>]

Hello all,


I was wondering several things about JBrowse configuration I couldn't figure out after searching the manual.


  1.  Is there an option or selecting all the tracks at once? Maybe a plugin? I've tried faceted selection, but that doesn't allow you to do more than 30, and all of my datasets do have more. And it's quite inconvenient to click on them too. So I'd appreciate any suggestions.
  2.  How can I set up which files are selected upon loading the dataset? E.g. if I want half of the tracks to be selected to begin with?
  3.  Is there any way to customize the dataset selector screen? E.g. add a picture or some other links?
  4.  How can I change the order of tracks within each category? I managed to sort categories by adding a number to their name - do I have to do the same with the keys?

Thank you very much in advance!

-- Alex

Re: [Gmod-ajax] Error in jbrowse

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

The error you posted shows that you opened the file from the filesystem
e.g. it says file:/// and this doesn't really work even if it displays
enough info to show an error message. you need a real webserver e.g. apache2

You could run "sudo apt install apache2" and then "sudo service apache2
start" and then navigate to http://localhost/jbrowse

See http://jbrowse.org/docs/faq.html#what-webserver-is-needed-for-jbrowse

-Colin


On Wed, Nov 14, 2018 at 4:04 PM Scott Cain <sc...@sc...> wrote:

> Hi Yousaf,
>
> In order for there to be "something" there, you need to add data,
> typically by running included tools like prepare-refseqs.pl and
> flatfile-to-json.pl.  Did you click on the link for the Volvox sample
> data?
>
> Scott
>
>
> On Thu, Nov 15, 2018 at 6:41 AM yousaf raza <yry...@gm...>
> wrote:
>
>> hello sir
>> i have run ./setup.sh it ran successfully but after that i am not
>> receiving full page of indax.htm
>> it is giving RequestError: Unable to load
>> file:///var/www/html/jbrowse/data/trackList.json?v=0.015361163899122343
>> status: 0.
>> this result at downside the page
>> _______________________________________________
>> 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
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Error in jbrowse

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

Hi Yousaf,

In order for there to be "something" there, you need to add data, typically
by running included tools like prepare-refseqs.pl and flatfile-to-json.pl.
Did you click on the link for the Volvox sample data?

Scott


On Thu, Nov 15, 2018 at 6:41 AM yousaf raza <yry...@gm...> wrote:

> hello sir
> i have run ./setup.sh it ran successfully but after that i am not
> receiving full page of indax.htm
> it is giving RequestError: Unable to load
> file:///var/www/html/jbrowse/data/trackList.json?v=0.015361163899122343
> status: 0.
> this result at downside the page
> _______________________________________________
> 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

[Gmod-ajax] Error in jbrowse

[yousaf r. <yry...@gm...>]

hello sir
i have run ./setup.sh it ran successfully but after that i am not receiving
full page of indax.htm
it is giving RequestError: Unable to load
file:///var/www/html/jbrowse/data/trackList.json?v=0.015361163899122343
status: 0.
this result at downside the page

Re: [Gmod-ajax] Assistance with Jbrowse

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

1. The glyph configuration is just glyph, not style->glyph
2. The height can be changed via a callback in style->height e.g. "style":
{ "height": "function(feat) { return feature.get('my_feat_height') || 10;
}" } would return some GFF attribute my_feature_height
3. Set style.featureScale=1000 and it will never be able to zoom in as far
as to display the features (zoom are represented as pixels per basepair)

For histogram customizations I would recommend probably making a custom
bigwig track for coverage and use the "summary histograms" feature
http://gmod.org/wiki/JBrowse_Configuration_Guide#Configuring_Summary_Histograms
this will give you more flexibility than the built in histograms generated
by flatfile-to-json (I am assuming you are using this based on a thread
posted recently?)

Hope that helps

-Colin


On Thu, Nov 8, 2018 at 11:24 AM Scott Cain <sc...@sc...> wrote:

> Hi Tom,
>
> You can definitely do those things but I’m on my phone, so it’s hard to
> write out using this keyboard. I’ve CC’d the jbrowse mailing list so if I
> don’t get back to you today it’s likely that somebody else on the list
> will.
>
> Scott
>
>
> On Nov 7, 2018, at 9:42 AM, Shorter, Thomas <ts...@le...> wrote:
>
> Hi,
>
>
> I'm surrently looking at using Jbrowse to display SNP data within a
> website I'm working on.
>
>
> I don't have much experience with JavaScript and I'm having some trouble
> following some of the guides/what I want to do isn't covered.
>
>
> If you could answer a few of my questions I'd be most greatful!
>
>
> Firstly, how do I set the glyph type? I've tried changing style.glyph to
> diamond in both the .conf and .json and within the track config itself in
> the browser window but this doesn't seem to work but I'm pretty sure I saw
> a diamond glyph whilst looking through the code.
>
>
> Next I'd like to be able to change the height of a glyph/feature based on
> data within the 9th column of the gff imported, is this possible and how?
>
>
> I'd also like to be able to always have the histogram showing, even at the
> single base level and if possible to have the bin size set to 2-5% of the
> window (i'll have to play about with the exact number) or to the size of a
> single base, whichever is bigger.
>
>
> Many thanks!
>
>
> Tom
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Assistance with Jbrowse

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

Hi Tom, 

You can definitely do those things but I’m on my phone, so it’s hard to write out using this keyboard. I’ve CC’d the jbrowse mailing list so if I don’t get back to you today it’s likely that somebody else on the list will. 

Scott


> On Nov 7, 2018, at 9:42 AM, Shorter, Thomas <ts...@le...> wrote:
> 
> Hi,
> 
> I'm surrently looking at using Jbrowse to display SNP data within a website I'm working on.
> 
> I don't have much experience with JavaScript and I'm having some trouble following some of the guides/what I want to do isn't covered.
> 
> If you could answer a few of my questions I'd be most greatful!
> 
> Firstly, how do I set the glyph type? I've tried changing style.glyph to diamond in both the .conf and .json and within the track config itself in the browser window but this doesn't seem to work but I'm pretty sure I saw a diamond glyph whilst looking through the code.
> 
> Next I'd like to be able to change the height of a glyph/feature based on data within the 9th column of the gff imported, is this possible and how?
> 
> I'd also like to be able to always have the histogram showing, even at the single base level and if possible to have the bin size set to 2-5% of the window (i'll have to play about with the exact number) or to the size of a single base, whichever is bigger.
> 
> Many thanks!
> 
> Tom