gmod-ajax — JBrowse list

Re: [Gmod-ajax] FW: JBrowse: override metadata display in 'About this track' box

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

It’s weird though, if I refresh page it goes back to using metadata references from the tracklist2.json via external CSV file.  If I change URL to just load all the default tracks for that genome version, it shows my new metadata from the tracklist.json file.

I guess not everything has been worked out in JBrowse elegantly for this type of scenario?

Vaneet

From: Vaneet Lotay <van...@uc...>
Sent: Tuesday, February 26, 2019 10:57 AM
To: Colin <col...@gm...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] FW: JBrowse: override metadata display in 'About this track' box

CAUTION: This Email is External.


Thanks Colin, it actually seemed to blank out all of the previous metadata referenced in trackList2.json and allow me to add my own fields if I enable all the unsafe attributes (unsafePopup, unsafeHTMLFeatures, unsafeMouseover).

Is there any way to sort the list of metadata fields in ‘About this track’ box? It defaults to alphabetical order right now.

Vaneet

From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: Thursday, February 21, 2019 12:58 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmod-ajax <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: FW: JBrowse: override metadata display in 'About this track' box

I wish I could say that there was a really elegant solution to all this. It is kind of a clunky solution to use all these fmt callbacks so to make it work currently is not elegant. But, if you want, some workarounds include

1. Adding a new field cannot be done straightforwardly, you can create a "dummy" value in the metadata section of your track and then use fmtMetaValue_dummy to customize it
2. fmtMetaValue_fieldname can modify existing fields also
3. To remove a field, return null from a fmtMetaField_fieldname

As this applies to hundreds of tracks that sounds pretty annoying. If you want to formulate this as a github issue then please provide detail to reproduce and what you expect to have.

-Colin

On Thu, Feb 21, 2019 at 1:49 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Colin,

I don’t think this is ComboTrackSelector specific as you can always specify the fields in the ‘About this track’ box and also have a faceted track selector as well, without the plugin.

I was testing out these functions, and while fmtMetaValue_* allows you to change the value of an existing field already on the ‘About’ popup box, I don’t know how to remove fields that are being shown on it.  As I said I have an external metadata CSV file being used in the faceted track selector to display the metadata for each track, but I don’t want that same metadata to be displayed in the ‘About’ popup box, I want to choose the fields and values that are displayed there.  Do you know how I would specify for a field to be not visible in the popup box using the fmtMetaValue or fmtMetaField callback functions or others?

Also I thought that fmtMetaField_* would allow me to specify a new data field to be shown in the popup box but I guess I didn’t figure out how to use it properly.  There isn’t any documentation of use cases or examples for these 2 callback functions on the JBrowse websites, can you show me some examples of how to use them…specifically for these scenarios would help:

-Specify a new ‘About this track’ field and value
-Modify the value of an existing field in ‘About this track’ box
-Specify which existing ‘About this track’ field should be removed or not visible when it pops up

Basically if there is metadata used in the faceted track selector via tracklist2.json file, JBrowse seems to by default display that metadata in the ‘About this track’ box and I’m looking for a way to override that functionality or at least change the text content of it. Any help would be appreciated as I’m dealing with hundreds of tracks in this scenario.

Thanks,

Vaneet

From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: Friday, January 25, 2019 10:51 AM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>; gmod-ajax <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: FW: JBrowse: override metadata display in 'About this track' box

I'm not sure if it is ComboTrackSelector specific but there are callbacks called fmtMetaValue_* and fmtMetaField_* callbacks in the config

That can help customize the About popups

-Colin

On Fri, Jan 25, 2019 at 12:37 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Colin,

Any thoughts on how I can get around this?  Or this metadata locked in once I have a reference to an external metadata CSV file?

Thanks,

Vaneet

From: Vaneet Lotay
Sent: Tuesday, January 22, 2019 2:47 PM
To: gmo...@li...<mailto:gmo...@li...>
Subject: JBrowse: override metadata display in 'About this track' box

Hello,

I am using the ComboTrackSelector plugin to have both the Hierarchical and Faceted track selectors active at the same time currently in my JBrowse.  This is because I have metadata to display in the faceted track selector which comes from a CSV file.  What I notice is that every column of this same metadata is displayed in the pop up box when I click on the track label drop down bar and select ‘About this track’.  I’ve tried adding additional metadata fields or overwriting the content of some of the fields there because I didn’t like the format in which they are displayed but that doesn’t work it seems locked in to displaying the metadata from the CSV file referenced in the tracklist2.json file.

Do you know if there’s any way I can stop it from displaying the metadata show in the faceted track selector and specify my own metadata fields to be displayed in the ‘About this track’ box possibly via the original tracklist.json file?

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building – University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA


CAUTION: External Email This Email originated from outside the University of Calgary. Please exercise caution when opening attachments, clicking on links or when asked to enter usernames/passwords. Report suspicious emails to "reportphishing​@​ucalgary.ca<mailto:reportphishing​@​ucalgary.ca>" or via the Junk Email Reporting Tool in the Outlook Tool Bar. For More Information call the Service Desk.

Re: [Gmod-ajax] FW: JBrowse: override metadata display in 'About this track' box

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

Thanks Colin, it actually seemed to blank out all of the previous metadata referenced in trackList2.json and allow me to add my own fields if I enable all the unsafe attributes (unsafePopup, unsafeHTMLFeatures, unsafeMouseover).

Is there any way to sort the list of metadata fields in ‘About this track’ box? It defaults to alphabetical order right now.

Vaneet

From: Colin <col...@gm...>
Sent: Thursday, February 21, 2019 12:58 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: FW: JBrowse: override metadata display in 'About this track' box

I wish I could say that there was a really elegant solution to all this. It is kind of a clunky solution to use all these fmt callbacks so to make it work currently is not elegant. But, if you want, some workarounds include

1. Adding a new field cannot be done straightforwardly, you can create a "dummy" value in the metadata section of your track and then use fmtMetaValue_dummy to customize it
2. fmtMetaValue_fieldname can modify existing fields also
3. To remove a field, return null from a fmtMetaField_fieldname

As this applies to hundreds of tracks that sounds pretty annoying. If you want to formulate this as a github issue then please provide detail to reproduce and what you expect to have.

-Colin

On Thu, Feb 21, 2019 at 1:49 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Colin,

I don’t think this is ComboTrackSelector specific as you can always specify the fields in the ‘About this track’ box and also have a faceted track selector as well, without the plugin.

I was testing out these functions, and while fmtMetaValue_* allows you to change the value of an existing field already on the ‘About’ popup box, I don’t know how to remove fields that are being shown on it.  As I said I have an external metadata CSV file being used in the faceted track selector to display the metadata for each track, but I don’t want that same metadata to be displayed in the ‘About’ popup box, I want to choose the fields and values that are displayed there.  Do you know how I would specify for a field to be not visible in the popup box using the fmtMetaValue or fmtMetaField callback functions or others?

Also I thought that fmtMetaField_* would allow me to specify a new data field to be shown in the popup box but I guess I didn’t figure out how to use it properly.  There isn’t any documentation of use cases or examples for these 2 callback functions on the JBrowse websites, can you show me some examples of how to use them…specifically for these scenarios would help:

-Specify a new ‘About this track’ field and value
-Modify the value of an existing field in ‘About this track’ box
-Specify which existing ‘About this track’ field should be removed or not visible when it pops up

Basically if there is metadata used in the faceted track selector via tracklist2.json file, JBrowse seems to by default display that metadata in the ‘About this track’ box and I’m looking for a way to override that functionality or at least change the text content of it. Any help would be appreciated as I’m dealing with hundreds of tracks in this scenario.

Thanks,

Vaneet

From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: Friday, January 25, 2019 10:51 AM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>; gmod-ajax <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: FW: JBrowse: override metadata display in 'About this track' box

I'm not sure if it is ComboTrackSelector specific but there are callbacks called fmtMetaValue_* and fmtMetaField_* callbacks in the config

That can help customize the About popups

-Colin

On Fri, Jan 25, 2019 at 12:37 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Colin,

Any thoughts on how I can get around this?  Or this metadata locked in once I have a reference to an external metadata CSV file?

Thanks,

Vaneet

From: Vaneet Lotay
Sent: Tuesday, January 22, 2019 2:47 PM
To: gmo...@li...<mailto:gmo...@li...>
Subject: JBrowse: override metadata display in 'About this track' box

Hello,

I am using the ComboTrackSelector plugin to have both the Hierarchical and Faceted track selectors active at the same time currently in my JBrowse.  This is because I have metadata to display in the faceted track selector which comes from a CSV file.  What I notice is that every column of this same metadata is displayed in the pop up box when I click on the track label drop down bar and select ‘About this track’.  I’ve tried adding additional metadata fields or overwriting the content of some of the fields there because I didn’t like the format in which they are displayed but that doesn’t work it seems locked in to displaying the metadata from the CSV file referenced in the tracklist2.json file.

Do you know if there’s any way I can stop it from displaying the metadata show in the faceted track selector and specify my own metadata fields to be displayed in the ‘About this track’ box possibly via the original tracklist.json file?

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building – University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

Re: [Gmod-ajax] Issues wrt JBrowse

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

Hello again Divya,

Sorry, I gave you some bad information: the refSeqDropdown = false isn't
supported anymore. It was there to prevent dropdown menus with thousands of
entries which is generally undesirable.  The general thrust of my advice
remains the same: I don't think you want a dropdown with 3000 items in it
:-)

Also, in retrospect, having the dropdown with 30 items in it isn't so bad,
since it gives users and idea of what contig names look like.

Scott


On Fri, Feb 22, 2019 at 10:09 AM Scott Cain <sc...@sc...> wrote:

> Hi Divya,
>
> There is a configuration parameter to change the number of items displayed
> in that dropdown menu.  See:
>
>
> http://gmod.org/wiki/JBrowse_Configuration_Guide#Reference_Sequence_Selector_Configuration
>
> for more information.  I would suggest that you either want to suppress
> that menu altogether and make sure name completion works (by running
> generate_names.pl) or leave the limit of 30 items in place.  A dropdown
> menu with 3000 items is worse than useless.  To suppress the menu, add
> refSeqDropdown = false to the jbrowse.conf file.  A final option would be
> to list the contigs by size if this were a genome with many contigs (but
> some nice large ones), but since this is a transcriptome, I don't think
> that option makes much sense.
>
> Please feel free to reply to the list if you have any more questions,
> Scott
>
>
> On Fri, Feb 22, 2019 at 9:44 AM Divya Chanda via Gmod-ajax <
> gmo...@li...> wrote:
> >
> > Hi,
> > I have been given a website work which was started by someone else and
> struck in the middle of something.
> > The search bar displays only 32 contigs of a camel species whereas we
> have more than30000 values corressponding to the same.
> > Please let me know can we show more than 30 values in the dropdown menu?
> > If yes, please let me know  which files need to be changed or linked .
> > For reference the image is attached showing 30 reference sequences.
> >
> >
> > _______________________________________________
> > 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

Re: [Gmod-ajax] Issues wrt JBrowse

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

Hi Divya,

There is a configuration parameter to change the number of items displayed
in that dropdown menu.  See:


http://gmod.org/wiki/JBrowse_Configuration_Guide#Reference_Sequence_Selector_Configuration

for more information.  I would suggest that you either want to suppress
that menu altogether and make sure name completion works (by running
generate_names.pl) or leave the limit of 30 items in place.  A dropdown
menu with 3000 items is worse than useless.  To suppress the menu, add
refSeqDropdown = false to the jbrowse.conf file.  A final option would be
to list the contigs by size if this were a genome with many contigs (but
some nice large ones), but since this is a transcriptome, I don't think
that option makes much sense.

Please feel free to reply to the list if you have any more questions,
Scott


On Fri, Feb 22, 2019 at 9:44 AM Divya Chanda via Gmod-ajax <
gmo...@li...> wrote:
>
> Hi,
> I have been given a website work which was started by someone else and
struck in the middle of something.
> The search bar displays only 32 contigs of a camel species whereas we
have more than30000 values corressponding to the same.
> Please let me know can we show more than 30 values in the dropdown menu?
> If yes, please let me know  which files need to be changed or linked .
> For reference the image is attached showing 30 reference sequences.
>
>
> _______________________________________________
> 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] Issues wrt JBrowse

[Divya C. <div...@ya...>]

Hi,I have been given a website work which was started by someone else and struck in the middle of something.The search bar displays only 32 contigs of a camel species whereas we have more than30000 values corressponding to the same.Please let me know can we show more than 30 values in the dropdown menu?If yes, please let me know  which files need to be changed or linked .For reference the image is attached showing 30 reference sequences.

Re: [Gmod-ajax] FW: JBrowse: override metadata display in 'About this track' box

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

I wish I could say that there was a really elegant solution to all this. It
is kind of a clunky solution to use all these fmt callbacks so to make it
work currently is not elegant. But, if you want, some workarounds include

1. Adding a new field cannot be done straightforwardly, you can create a
"dummy" value in the metadata section of your track and then use
fmtMetaValue_dummy to customize it
2. fmtMetaValue_fieldname can modify existing fields also
3. To remove a field, return null from a fmtMetaField_fieldname

As this applies to hundreds of tracks that sounds pretty annoying. If you
want to formulate this as a github issue then please provide detail to
reproduce and what you expect to have.

-Colin

On Thu, Feb 21, 2019 at 1:49 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Colin,
>
>
>
> I don’t think this is ComboTrackSelector specific as you can always
> specify the fields in the ‘About this track’ box and also have a faceted
> track selector as well, without the plugin.
>
>
>
> I was testing out these functions, and while fmtMetaValue_* allows you to
> change the value of an existing field already on the ‘About’ popup box, I
> don’t know how to remove fields that are being shown on it.  As I said I
> have an external metadata CSV file being used in the faceted track selector
> to display the metadata for each track, but I don’t want that same metadata
> to be displayed in the ‘About’ popup box, I want to choose the fields and
> values that are displayed there.  Do you know how I would specify for a
> field to be not visible in the popup box using the fmtMetaValue or
> fmtMetaField callback functions or others?
>
>
>
> Also I thought that fmtMetaField_* would allow me to specify a new data
> field to be shown in the popup box but I guess I didn’t figure out how to
> use it properly.  There isn’t any documentation of use cases or examples
> for these 2 callback functions on the JBrowse websites, can you show me
> some examples of how to use them…specifically for these scenarios would
> help:
>
>
>
> -Specify a new ‘About this track’ field and value
>
> -Modify the value of an existing field in ‘About this track’ box
>
> -Specify which existing ‘About this track’ field should be removed or not
> visible when it pops up
>
>
>
> Basically if there is metadata used in the faceted track selector via
> tracklist2.json file, JBrowse seems to by default display that metadata in
> the ‘About this track’ box and I’m looking for a way to override that
> functionality or at least change the text content of it. Any help would be
> appreciated as I’m dealing with hundreds of tracks in this scenario.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Friday, January 25, 2019 10:51 AM
> *To:* Vaneet Lotay <van...@uc...>; gmod-ajax <
> gmo...@li...>
> *Subject:* Re: FW: JBrowse: override metadata display in 'About this
> track' box
>
>
>
> I'm not sure if it is ComboTrackSelector specific but there are callbacks
> called fmtMetaValue_* and fmtMetaField_* callbacks in the config
>
>
>
> That can help customize the About popups
>
>
>
> -Colin
>
>
>
> On Fri, Jan 25, 2019 at 12:37 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> Any thoughts on how I can get around this?  Or this metadata locked in
> once I have a reference to an external metadata CSV file?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Vaneet Lotay
> *Sent:* Tuesday, January 22, 2019 2:47 PM
> *To:* gmo...@li...
> *Subject:* JBrowse: override metadata display in 'About this track' box
>
>
>
> Hello,
>
>
>
> I am using the ComboTrackSelector plugin to have both the Hierarchical and
> Faceted track selectors active at the same time currently in my JBrowse.
> This is because I have metadata to display in the faceted track selector
> which comes from a CSV file.  What I notice is that every column of this
> same metadata is displayed in the pop up box when I click on the track
> label drop down bar and select ‘About this track’.  I’ve tried adding
> additional metadata fields or overwriting the content of some of the fields
> there because I didn’t like the format in which they are displayed but that
> doesn’t work it seems locked in to displaying the metadata from the CSV
> file referenced in the tracklist2.json file.
>
>
>
> Do you know if there’s any way I can stop it from displaying the metadata
> show in the faceted track selector and specify my own metadata fields to be
> displayed in the ‘About this track’ box possibly via the original
> tracklist.json file?
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building – University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
>
>

Re: [Gmod-ajax] FW: JBrowse: override metadata display in 'About this track' box

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

Hey Colin,

I don’t think this is ComboTrackSelector specific as you can always specify the fields in the ‘About this track’ box and also have a faceted track selector as well, without the plugin.

I was testing out these functions, and while fmtMetaValue_* allows you to change the value of an existing field already on the ‘About’ popup box, I don’t know how to remove fields that are being shown on it.  As I said I have an external metadata CSV file being used in the faceted track selector to display the metadata for each track, but I don’t want that same metadata to be displayed in the ‘About’ popup box, I want to choose the fields and values that are displayed there.  Do you know how I would specify for a field to be not visible in the popup box using the fmtMetaValue or fmtMetaField callback functions or others?

Also I thought that fmtMetaField_* would allow me to specify a new data field to be shown in the popup box but I guess I didn’t figure out how to use it properly.  There isn’t any documentation of use cases or examples for these 2 callback functions on the JBrowse websites, can you show me some examples of how to use them…specifically for these scenarios would help:

-Specify a new ‘About this track’ field and value
-Modify the value of an existing field in ‘About this track’ box
-Specify which existing ‘About this track’ field should be removed or not visible when it pops up

Basically if there is metadata used in the faceted track selector via tracklist2.json file, JBrowse seems to by default display that metadata in the ‘About this track’ box and I’m looking for a way to override that functionality or at least change the text content of it. Any help would be appreciated as I’m dealing with hundreds of tracks in this scenario.

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: Friday, January 25, 2019 10:51 AM
To: Vaneet Lotay <van...@uc...>; gmod-ajax <gmo...@li...>
Subject: Re: FW: JBrowse: override metadata display in 'About this track' box

I'm not sure if it is ComboTrackSelector specific but there are callbacks called fmtMetaValue_* and fmtMetaField_* callbacks in the config

That can help customize the About popups

-Colin

On Fri, Jan 25, 2019 at 12:37 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Colin,

Any thoughts on how I can get around this?  Or this metadata locked in once I have a reference to an external metadata CSV file?

Thanks,

Vaneet

From: Vaneet Lotay
Sent: Tuesday, January 22, 2019 2:47 PM
To: gmo...@li...<mailto:gmo...@li...>
Subject: JBrowse: override metadata display in 'About this track' box

Hello,

I am using the ComboTrackSelector plugin to have both the Hierarchical and Faceted track selectors active at the same time currently in my JBrowse.  This is because I have metadata to display in the faceted track selector which comes from a CSV file.  What I notice is that every column of this same metadata is displayed in the pop up box when I click on the track label drop down bar and select ‘About this track’.  I’ve tried adding additional metadata fields or overwriting the content of some of the fields there because I didn’t like the format in which they are displayed but that doesn’t work it seems locked in to displaying the metadata from the CSV file referenced in the tracklist2.json file.

Do you know if there’s any way I can stop it from displaying the metadata show in the faceted track selector and specify my own metadata fields to be displayed in the ‘About this track’ box possibly via the original tracklist.json file?

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building – University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

[Gmod-ajax] JBrowse 1.16.3 released

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

Hello all,
I am happy to announce JBrowse 1.16.3. This release is important in order
to address a change that was made upstream in BioPerl where some modules
that JBrowse uses were removed from the core BioPerl distribution. If you
are stuck with an older version of JBrowse please see
https://github.com/GMOD/jbrowse/issues/1313 for a workaround, but otherwise
this version of JBrowse has such a workaround built in to it.

If there are any questions about this, let me know.

Otherwise, happy browsing!


   - JBrowse-1.16.3.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.3-release/JBrowse-1.16.3.zip>
-
   minified release
   - JBrowse-1.16.3-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.3-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.3-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.3-release/JBrowse-1.16.3-desktop-win32-x64.zip>
   - JBrowse-1.16.3-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.3-release/JBrowse-1.16.3-desktop-linux-x64.zip>
   - JBrowse-1.16.3-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.3-release/JBrowse-1.16.3-desktop-darwin-x64.zip>

Blogpost http://jbrowse.org/blog/2019/02/20/jbrowse-1-16-3.html
<http://jbrowse.org/blog/#bug-fixes>Bug fixes

   -

   Fix BioPerl setup after changes to the BioPerl distribution caused
   setup.sh to fail in all past JBrowse versions (issue #1310
   <https://github.com/gmod/jbrowse/issues/1310>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fix issue with NeatCanvasFeatures not drawing gradients on some
   features. Thanks to @mara-sangiovanni
   <https://github.com/mara-sangiovanni> for reporting (issue #1311
   <https://github.com/gmod/jbrowse/issues/1311>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fix issue for exporting GFF3 for some nested attributes by dumping JSON
   into the value field. Thanks to @dionnezaal
   <https://github.com/dionnezaal> for reporting (issue #1309
   <https://github.com/gmod/jbrowse/issues/1309>, @cmdcolin
   <https://github.com/cmdcolin>)

[Gmod-ajax] Apollo 2.3.1 released

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

Apollo 2.3.1 is officially released.  It is available via download (https://github.com/GMOD/Apollo/releases/tag/2.3.1 <https://github.com/GMOD/Apollo/releases/tag/2.3.1>), https://github.com/GMOD/Apollo/ <https://github.com/GMOD/Apollo/>, docker https://github.com/GMOD/docker-apollo <https://github.com/GMOD/docker-apollo>, and as a community AMI via Amazon Web Services (only in N. Virginia, but let me know if you need it moved). 

Cheers,

Apollo Team


Many bug fixes and some minor enhancements. Many thanks to the community for reporting, testing, and fixing these issues.
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md#231 <https://github.com/GMOD/Apollo/blob/master/ChangeLog.md#231>
To test in Docker:

docker run -it -p 8888:8080 quay.io/gmod/docker-apollo:2.3.0 -v /path/to/jbrowse/directories:/data/
Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/stable/ <http://genomearchitect.readthedocs.io/en/stable/>
Note: You can find a guide upgrading existing Apollo installations here:
http://genomearchitect.readthedocs.io/en/stable/Migration.html <http://genomearchitect.readthedocs.io/en/stable/Migration.html>
Please open a GitHub issue if you find any problems: https://github.com/GMOD/Apollo/issues/ <https://github.com/GMOD/Apollo/issues/>
Active mailing list (ap...@li... <mailto:ap...@li...>) and archive.

Bug Fixes

Fixed issue when dragging features to resize was not providing an indicator box 1988 <https://github.com/GMOD/Apollo/pull/1988>
Fixed issue when sequence alterations were not rendering the full height of the sequence track 2049 <https://github.com/GMOD/Apollo/pull/2049>
Making organisms obsolete should remove associated permissions 2043 <https://github.com/GMOD/Apollo/pull/2043>
User-created features taken from split reads should create features with introns 2036 <https://github.com/GMOD/Apollo/pull/2036>
Should indicate split reads properly in evidence 2034 <https://github.com/GMOD/Apollo/pull/2034>2054 <https://github.com/GMOD/Apollo/pull/2054>
Temporary files not removed during export of GFF3 or other file types 1966 <https://github.com/GMOD/Apollo/pull/1966>
Fixed issue where you could not alter an isoform after deleting a gene name 1961 <https://github.com/GMOD/Apollo/pull/1961>
Fixed some minor issues associated with sequence alterations 1497 <https://github.com/GMOD/Apollo/pull/1497>
Multiple owners tagged on GFF3 export 29 <https://github.com/GMOD/Apollo/pull/29>
Setting gene description puts UcA into a bad state 2056 <https://github.com/GMOD/Apollo/issues/2056>
Fixes plugin inclusion error by reverting prior fix 2055 <https://github.com/GMOD/Apollo/issues/2055>
Minor Features

Allowed duplication of organism from the Organism Panel 1968 <https://github.com/GMOD/Apollo/pull/1968>
Allows making an organism obsolete 1967 <https://github.com/GMOD/Apollo/pull/1967>
Create a filter and flag for inactive users 1937 <https://github.com/GMOD/Apollo/pull/1937>
Allowed deletion of feature from the Sequence and Annotator Panels 2040 <https://github.com/GMOD/Apollo/pull/2040>
Allow export of orig_id as an optional attribute 2002 <https://github.com/GMOD/Apollo/pull/2002>

Re: [Gmod-ajax] JBrowse not processing html tags and links in track info

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

Thanks Colin!

From: Colin <col...@gm...>
Sent: Tuesday, February 12, 2019 1:51 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse not processing html tags and links in track info

This was a design decision that it's better to have this way but there is a config workaround

See
https://github.com/GMOD/jbrowse/blob/master/release-notes.md#notable-changes

-Colin



On Tue, Feb 12, 2019, 3:24 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

Since I’ve upgraded to JBrowse v1.16.1, I’ve noticed that the metadata I’ve added to the ‘About this track’ pop up box is not fully processed in terms of the html tags I’ve added for external links (<a href>) and line breaks (<br>).  I added the info via this configuration block:

         "metadata" : {
            "Info" :
},

I added the ‘Info’ field so it’s displayed in the ‘About this track’ box.  So after upgrading to this JBrowse version the html tags are displayed as is as free text, but before they were actually processed as line breaks and hyperlinks.  Can anyone help explain why the html is not processed anymore in the trackList.json file?

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building – University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

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

Re: [Gmod-ajax] JBrowse not processing html tags and links in track info

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

This was a design decision that it's better to have this way but there is a
config workaround

See
https://github.com/GMOD/jbrowse/blob/master/release-notes.md#notable-changes

-Colin



On Tue, Feb 12, 2019, 3:24 PM Vaneet Lotay <van...@uc...> wrote:

> Hello,
>
>
>
> Since I’ve upgraded to JBrowse v1.16.1, I’ve noticed that the metadata
> I’ve added to the ‘About this track’ pop up box is not fully processed in
> terms of the html tags I’ve added for external links (<a href>) and line
> breaks (<br>).  I added the info via this configuration block:
>
>
>
>          "metadata" : {
>
>             "Info" :
>
> },
>
>
>
> I added the ‘Info’ field so it’s displayed in the ‘About this track’ box.
> So after upgrading to this JBrowse version the html tags are displayed as
> is as free text, but before they were actually processed as line breaks and
> hyperlinks.  Can anyone help explain why the html is not processed anymore
> in the trackList.json file?
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building – University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse not processing html tags and links in track info

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

Hello,

Since I've upgraded to JBrowse v1.16.1, I've noticed that the metadata I've added to the 'About this track' pop up box is not fully processed in terms of the html tags I've added for external links (<a href>) and line breaks (<br>).  I added the info via this configuration block:

         "metadata" : {
            "Info" :
},

I added the 'Info' field so it's displayed in the 'About this track' box.  So after upgrading to this JBrowse version the html tags are displayed as is as free text, but before they were actually processed as line breaks and hyperlinks.  Can anyone help explain why the html is not processed anymore in the trackList.json file?

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building - University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

[Gmod-ajax] Call for Participation/Talks/Posters: ACDL 2019, 2nd Advanced Course on Data Science & Machine Learning, Siena - Tuscany, Italy, July 15-19 - Early Registration: March 31

[ICAS <in...@ic...>]

ACDL 2018 Sold-out! Probably also ACDL 2019! Hurry up! Book your Early Bird Seats!
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Certosa di Pontignano, Siena - Tuscany, Italy
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https://acdl2019.icas.xyz https://acdl2019.icas.xyz      acdl@icas.xyz mailto:acdl@icas.xyz?subject=ACDL%202019%20Registration

ACDL 2018 Sold-out! Probably also ACDL 2019, Hurry up! 
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LECTURERS https://acdl2019.icas.xyz/lecturers/:

Each Lecturer will hold three lessons on a specific topic.

Ioannis Antonoglou, Google DeepMind, UK

Topic: General Reinforcement Learning Algorithms  

Sanjeev Arora, Princeton University, USA (TBC)

Topics: Theory of Machine Learning, Generative Adversarial Networks & Theoretical Deep Learning

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Phillip Isola, MIT, USA                        

Topic: Generative Adversarial Networks

Leslie Kaelbling, MIT, USA (TBC)

Topics: Situated agents & Reinforcement Learning

Ilias S. Kotsireas, Wilfrid Laurier University, Canada

Topics: Data Mining and High-Performance Computing

Dolores Romero Morales, Copenhagen Business School, Denmark            

Topic: Big Data

Panos Pardalos, University of Florida, USA  

Topics:  Optimization, Networks & Data Science

Ruslan Salakhutdinov, Carnegie Mellon University & AI Research at Apple, USA

Topic: Deep Learning

Josh Tenenbaum, MIT, USA

Topics: Computational Cognitive Science, probabilistic generative models, and probabilistic programming

Naftali Tishby, Hebrew University, Israel

Topic: Theory of Deep Learning – Information Bottleneck

Leslie Valiant, Harvard University, USA - Turing Award (TBC)

Topics:  Machine Learning, Computational Neuroscience, Artificial Intelligence, Theory of Computation

Joaquin Vanschoren, Eindhoven University of Technology, The Netherlands

Topic: Automatic machine learning

Oriol Vinyals, Google DeepMind, UK                        

Topic: Deep Learning & Reinforcement Learning

SCOPE. The Advanced Course is not a summer school suited only for younger scholars. Rather, a significant proportion of seasoned investigators are regularly present among the attendees, often senior faculty at their own institutions. The balanced audience that we strive to maintain in each Advanced Course greatly contributes to the development of intense cross-disciplinary debates among faculty and participants that typically address the most advanced and emerging areas of each topic.

Each faculty member presents lectures and discusses with the participants for one entire day. Such long interaction together with the small, exclusive Course size provides the uncommon opportunity to fully explore the expertise of each faculty, often through one-to-one mentoring. This is unparalleled and priceless.

The Certosa di Pontignano provides the perfect setting to a relaxed yet intense learning atmosphere, with the stunning backdrop of the Tuscan landscapes. World-class wines and traditional foods will make the Advanced Course on Data Science and Machine Learning the experience of a lifetime.

CALL FOR POSTER & ORAL PRESENTATIONS https://acdl2019.icas.xyz/registration/:

During the Registration Process we accept abstract submissions for posters and oral presentations to be presented during the poster sessions and the talk sessions.  

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fax: +39-0577-1521098

in...@la... mailto:in...@la...?subject=ACDL%202019%20Accommodation

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https://www.lacertosadipontignano.com/en/index.php https://www.lacertosadipontignano.com/en/index.php

A few Kilometres from Siena, on a hill dominating the town stands the ancient Certosa di Pontignano, a unique place where nature, history and hospitality blend together in memorable harmony. Built in the 1300, its medieval structure remains intact with additions of the following centuries. The Certosa is centred on its historic cloisters and gardens.

https://acdl2019.icas.xyz/venue/ https://acdl2019.icas.xyz/venue/

ACCOMMODATION: https://acdl2019.icas.xyz/accommodation/ https://acdl2019.icas.xyz/accommodation/

Past Edition - ACDL 2018. https://acdl2018.icas.xyz

ACDL 2019 REGISTRATION.
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We remind you that ACDL 2018 sold out a long time before the registration deadline!

Anyone interested in participating in ACDL 2019 should register as soon as possible!

Similarly for accommodation at the Certosa di Pontignano (the School Venue), book your full board accommodation at the Certosa as soon as possible!

All course participants should/must stay at the Certosa di Pontignano.

See you in Tuscany next July!

ACDL 2019 Organizing Committee.

* Apologies for multiple copies. Please forward to anybody who might be interested *

* Please help us distributing in your circles (emails, blogs, and social networks) the call for participation and call for oral talks/posters  for ACDL2019.  

Together we will make ACDL 2019 a great event! *

ACDL 2019 Registration https://acdl2019.icas.xyz/registration/

ACDL 2019 – A Unique Experience: Data Science, Machine Learning & AI with the World’s Leaders in the fascinating atmosphere of the ancient Certosa di Pontignano - Tuscany

2nd Advanced Course on Data Science & Machine Learning https://acdl2019.icas.xyz

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Re: [Gmod-ajax] [apollo] Request for clarification on draggable BAM tracks

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

This is fixed on on Apollo’s master branch per this PR:

https://github.com/GMOD/Apollo/pull/2035 <https://github.com/GMOD/Apollo/pull/2035>

Let me know if there are any problems with it. 

Cheers,

Nathan


> On Feb 7, 2019, at 11:55 AM, Nathan Dunn <nat...@lb...> wrote:
> 
> 
> 
> I responded in https://github.com/GMOD/Apollo/issues/2034#issuecomment-461572858 <https://github.com/GMOD/Apollo/issues/2034#issuecomment-461572858> 
> 
> Please let me know if you need more help either there or. in the GH issue directly. 
> 
> Cheers,
> 
> Nathan
> 
> 
> 
>> On Feb 7, 2019, at 10:03 AM, Rob Syme <rob...@gm... <mailto:rob...@gm...>> wrote:
>> 
>> Hi Nathan.
>> 
>> If you point in me (vaguely) the right direction, I might be able to have a look myself (if that would be helpful). Will certainly send a PR if I make any progress.
>> 
>> -rob
>> 
>> On Thu, 7 Feb 2019 at 12:58, Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
>> 
>> Rob,
>> 
>> I believe you are correct in that the older Neat Features plugin was able to draw these effectively.  There were some small bugs with the current version. 
>> 
>> I’ll take a look at getting one, if not both working:
>> 
>> https://github.com/GMOD/Apollo/issues/2034 <https://github.com/GMOD/Apollo/issues/2034>
>> 
>> Nathan
>> 
>> 
>>> On Feb 7, 2019, at 9:52 AM, Rob Syme <rob...@gm... <mailto:rob...@gm...>> wrote:
>>> 
>>> Hi Nathan
>>> 
>>> Thanks for the tip. You're correct that the draggable vs non-draggable behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy to forgo the paired-end rendering in Alignments2 for the draggability of Track/Alignments, but in switching down to Track/Alignments, I also loose the intron rendering (and intron annotation from dragged reads). Here is a region showing data from the same BAM file using the two versions of Webapollo tracks:
>>> 
>>> <Screenshot from 2019-02-07 12-42-28.png>
>>> 
>>> 
>>> This is with the a trackList.json that looks like:
>>> 
>>> {
>>>    "formatVersion" : 1,
>>>    "names" : {
>>>       "type" : "Hash",
>>>       "url" : "names/"
>>>    },
>>>    "tracks" : [
>>>       {
>>>          "category" : "Reference sequence",
>>>          "chunkSize" : 20000,
>>>          "key" : "Reference sequence",
>>>          "label" : "DNA",
>>>          "seqType" : "dna",
>>>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>>>          "type" : "SequenceTrack",
>>>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
>>>       },
>>>       {
>>>          "bicolor_pivot" : 0.4,
>>>          "label" : "GC Content",
>>>          "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
>>>          "type" : "GCContent/View/Track/GCContentXY",
>>>          "urlTemplate" : "fasta/genome.fasta"
>>>       },
>>>       {
>>>          "key" : "Track/Alignments",
>>>          "label" : "Alignments",
>>>          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>>>          "type" : "JBrowse/View/Track/Alignments",
>>>          "urlTemplate" : "bams/inplanta-early.bam"
>>>       },
>>>       {
>>>          "key" : "Track/Alignments2",
>>>          "label" : "Alignments2",
>>>          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>>>          "type" : "JBrowse/View/Track/Alignments2",
>>>          "urlTemplate" : "bams/inplanta-early.bam"
>>>       }
>>>    ]
>>> }
>>> 
>>> Is it possible to have both intron rendering and draggable reads? Last time I set up a WebApollo instance (12 months ago), I thought I had both. I might be misremembering.
>>> 
>>> -rob
>>> 
>>> 
>>> On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
>>> 
>>> Rob,
>>> 
>>> I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 
>>> 
>>> If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   
>>> 
>>> I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 
>>> 
>>> Nathan
>>> 
>>> 
>>> 
>>> <PastedGraphic-1.png>
>>> 
>>> 
>>> 
>>>> On Feb 6, 2019, at 8:25 AM, Rob Syme <rob...@gm... <mailto:rob...@gm...>> wrote:
>>>> 
>>>> Hi all
>>>> 
>>>> I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl <http://add-bam-track.pl/> script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.
>>>> 
>>>> I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA <https://youtu.be/tc1aQwxEICA>
>>>> 
>>>> Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.
>>>> 
>>>> Rob Syme
>>>> 
>>>> 
>>>> 
>>>> 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. 
>>>> 
>>> 
>>> 
>>> 
>>> 
>>> 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. 
>>> 
>>> 
>>> 
>>> 
>>> 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. 
>>> 
>> 
>> 
>> 
>> 
>> 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. 
>> 
>> 
>> 
>> 
>> 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] [apollo] Request for clarification on draggable BAM tracks

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

I responded in https://github.com/GMOD/Apollo/issues/2034#issuecomment-461572858 <https://github.com/GMOD/Apollo/issues/2034#issuecomment-461572858> 

Please let me know if you need more help either there or. in the GH issue directly. 

Cheers,

Nathan



> On Feb 7, 2019, at 10:03 AM, Rob Syme <rob...@gm...> wrote:
> 
> Hi Nathan.
> 
> If you point in me (vaguely) the right direction, I might be able to have a look myself (if that would be helpful). Will certainly send a PR if I make any progress.
> 
> -rob
> 
> On Thu, 7 Feb 2019 at 12:58, Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
> 
> Rob,
> 
> I believe you are correct in that the older Neat Features plugin was able to draw these effectively.  There were some small bugs with the current version. 
> 
> I’ll take a look at getting one, if not both working:
> 
> https://github.com/GMOD/Apollo/issues/2034 <https://github.com/GMOD/Apollo/issues/2034>
> 
> Nathan
> 
> 
>> On Feb 7, 2019, at 9:52 AM, Rob Syme <rob...@gm... <mailto:rob...@gm...>> wrote:
>> 
>> Hi Nathan
>> 
>> Thanks for the tip. You're correct that the draggable vs non-draggable behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy to forgo the paired-end rendering in Alignments2 for the draggability of Track/Alignments, but in switching down to Track/Alignments, I also loose the intron rendering (and intron annotation from dragged reads). Here is a region showing data from the same BAM file using the two versions of Webapollo tracks:
>> 
>> <Screenshot from 2019-02-07 12-42-28.png>
>> 
>> 
>> This is with the a trackList.json that looks like:
>> 
>> {
>>    "formatVersion" : 1,
>>    "names" : {
>>       "type" : "Hash",
>>       "url" : "names/"
>>    },
>>    "tracks" : [
>>       {
>>          "category" : "Reference sequence",
>>          "chunkSize" : 20000,
>>          "key" : "Reference sequence",
>>          "label" : "DNA",
>>          "seqType" : "dna",
>>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>>          "type" : "SequenceTrack",
>>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
>>       },
>>       {
>>          "bicolor_pivot" : 0.4,
>>          "label" : "GC Content",
>>          "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
>>          "type" : "GCContent/View/Track/GCContentXY",
>>          "urlTemplate" : "fasta/genome.fasta"
>>       },
>>       {
>>          "key" : "Track/Alignments",
>>          "label" : "Alignments",
>>          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>>          "type" : "JBrowse/View/Track/Alignments",
>>          "urlTemplate" : "bams/inplanta-early.bam"
>>       },
>>       {
>>          "key" : "Track/Alignments2",
>>          "label" : "Alignments2",
>>          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>>          "type" : "JBrowse/View/Track/Alignments2",
>>          "urlTemplate" : "bams/inplanta-early.bam"
>>       }
>>    ]
>> }
>> 
>> Is it possible to have both intron rendering and draggable reads? Last time I set up a WebApollo instance (12 months ago), I thought I had both. I might be misremembering.
>> 
>> -rob
>> 
>> 
>> On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
>> 
>> Rob,
>> 
>> I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 
>> 
>> If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   
>> 
>> I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 
>> 
>> Nathan
>> 
>> 
>> 
>> <PastedGraphic-1.png>
>> 
>> 
>> 
>>> On Feb 6, 2019, at 8:25 AM, Rob Syme <rob...@gm... <mailto:rob...@gm...>> wrote:
>>> 
>>> Hi all
>>> 
>>> I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl <http://add-bam-track.pl/> script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.
>>> 
>>> I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA <https://youtu.be/tc1aQwxEICA>
>>> 
>>> Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.
>>> 
>>> Rob Syme
>>> 
>>> 
>>> 
>>> 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. 
>>> 
>> 
>> 
>> 
>> 
>> 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. 
>> 
>> 
>> 
>> 
>> 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. 
>> 
> 
> 
> 
> 
> 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. 
> 
> 
> 
> 
> 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. 
> 

Re: [Gmod-ajax] [apollo] Request for clarification on draggable BAM tracks

[Rob S. <rob...@gm...>]

Hi Nathan.

If you point in me (vaguely) the right direction, I might be able to have a
look myself (if that would be helpful). Will certainly send a PR if I make
any progress.

-rob

On Thu, 7 Feb 2019 at 12:58, Nathan Dunn <nat...@lb...> wrote:

>
> Rob,
>
> I believe you are correct in that the older Neat Features plugin was able
> to draw these effectively.  There were some small bugs with the current
> version.
>
> I’ll take a look at getting one, if not both working:
>
> https://github.com/GMOD/Apollo/issues/2034
>
> Nathan
>
>
> On Feb 7, 2019, at 9:52 AM, Rob Syme <rob...@gm...> wrote:
>
> Hi Nathan
>
> Thanks for the tip. You're correct that the draggable vs non-draggable
> behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy
> to forgo the paired-end rendering in Alignments2 for the draggability of
> Track/Alignments, but in switching down to Track/Alignments, I also loose
> the intron rendering (and intron annotation from dragged reads). Here is a
> region showing data from the same BAM file using the two versions of
> Webapollo tracks:
>
> <Screenshot from 2019-02-07 12-42-28.png>
>
>
> This is with the a trackList.json that looks like:
>
> {
>    "formatVersion" : 1,
>    "names" : {
>       "type" : "Hash",
>       "url" : "names/"
>    },
>    "tracks" : [
>       {
>          "category" : "Reference sequence",
>          "chunkSize" : 20000,
>          "key" : "Reference sequence",
>          "label" : "DNA",
>          "seqType" : "dna",
>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>          "type" : "SequenceTrack",
>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
>       },
>       {
>          "bicolor_pivot" : 0.4,
>          "label" : "GC Content",
>          "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
>          "type" : "GCContent/View/Track/GCContentXY",
>          "urlTemplate" : "fasta/genome.fasta"
>       },
>       {
>          "key" : "Track/Alignments",
>          "label" : "Alignments",
>          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>          "type" : "JBrowse/View/Track/Alignments",
>          "urlTemplate" : "bams/inplanta-early.bam"
>       },
>       {
>          "key" : "Track/Alignments2",
>          "label" : "Alignments2",
>          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>          "type" : "JBrowse/View/Track/Alignments2",
>          "urlTemplate" : "bams/inplanta-early.bam"
>       }
>    ]
> }
>
> Is it possible to have both intron rendering and draggable reads? Last
> time I set up a WebApollo instance (12 months ago), I thought I had both. I
> might be misremembering.
>
> -rob
>
>
> On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <nat...@lb...> wrote:
>
>>
>> Rob,
>>
>> I’m guessing the old track was an HTML track
>> (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse
>> creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets
>> extended into an Apollo Canvas Track, which has the nice features that
>> Colin Colin added, but is not draggable.
>>
>> If you want them to be draggable, you would set it to an HTML Track
>> (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get
>> Colin’s a paired end read code displayed.  Many curators will just have one
>> of each track (same data, but different type).
>>
>> I’m not sure if anyone will have the time to move them both over to HTML,
>> but I’m sure we could help point you in the right direction if interested
>> (would be in the JBrowse code-base, with a small fix in the Apollo
>> code-base).
>>
>> Nathan
>>
>>
>>
>> <PastedGraphic-1.png>
>>
>>
>>
>> On Feb 6, 2019, at 8:25 AM, Rob Syme <rob...@gm...> wrote:
>>
>> Hi all
>>
>> I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After
>> adding a bam track using the add-bam-track.pl script, the reads display
>> beautifully, but are not able to be dragged into the user-created
>> annotations track. I can create new annotations by right-clicking a read
>> and selecting  "create new annotation", but splicing is not preserved in
>> the newly created annotations.
>>
>> I've recorded a quick video to demonstrate the issue here:
>> https://youtu.be/tc1aQwxEICA
>>
>> Has anybody else had difficulty getting draggable BAM tracks in
>> webapollo? Any help would be greatly appreciated.
>>
>> Rob Syme
>>
>>
>>
>> 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.
>>
>>
>>
>>
>>
>> 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.
>>
>>
>
>
> 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.
>
>
>
>
>
> 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.
>
>

Re: [Gmod-ajax] [apollo] Request for clarification on draggable BAM tracks

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

Rob,

I believe you are correct in that the older Neat Features plugin was able to draw these effectively.  There were some small bugs with the current version. 

I’ll take a look at getting one, if not both working:

https://github.com/GMOD/Apollo/issues/2034 <https://github.com/GMOD/Apollo/issues/2034>

Nathan


> On Feb 7, 2019, at 9:52 AM, Rob Syme <rob...@gm...> wrote:
> 
> Hi Nathan
> 
> Thanks for the tip. You're correct that the draggable vs non-draggable behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy to forgo the paired-end rendering in Alignments2 for the draggability of Track/Alignments, but in switching down to Track/Alignments, I also loose the intron rendering (and intron annotation from dragged reads). Here is a region showing data from the same BAM file using the two versions of Webapollo tracks:
> 
> <Screenshot from 2019-02-07 12-42-28.png>
> 
> 
> This is with the a trackList.json that looks like:
> 
> {
>    "formatVersion" : 1,
>    "names" : {
>       "type" : "Hash",
>       "url" : "names/"
>    },
>    "tracks" : [
>       {
>          "category" : "Reference sequence",
>          "chunkSize" : 20000,
>          "key" : "Reference sequence",
>          "label" : "DNA",
>          "seqType" : "dna",
>          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
>          "type" : "SequenceTrack",
>          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
>       },
>       {
>          "bicolor_pivot" : 0.4,
>          "label" : "GC Content",
>          "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
>          "type" : "GCContent/View/Track/GCContentXY",
>          "urlTemplate" : "fasta/genome.fasta"
>       },
>       {
>          "key" : "Track/Alignments",
>          "label" : "Alignments",
>          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>          "type" : "JBrowse/View/Track/Alignments",
>          "urlTemplate" : "bams/inplanta-early.bam"
>       },
>       {
>          "key" : "Track/Alignments2",
>          "label" : "Alignments2",
>          "storeClass" : "JBrowse/Store/SeqFeature/BAM",
>          "type" : "JBrowse/View/Track/Alignments2",
>          "urlTemplate" : "bams/inplanta-early.bam"
>       }
>    ]
> }
> 
> Is it possible to have both intron rendering and draggable reads? Last time I set up a WebApollo instance (12 months ago), I thought I had both. I might be misremembering.
> 
> -rob
> 
> 
> On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
> 
> Rob,
> 
> I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 
> 
> If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   
> 
> I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 
> 
> Nathan
> 
> 
> 
> <PastedGraphic-1.png>
> 
> 
> 
>> On Feb 6, 2019, at 8:25 AM, Rob Syme <rob...@gm... <mailto:rob...@gm...>> wrote:
>> 
>> Hi all
>> 
>> I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl <http://add-bam-track.pl/> script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.
>> 
>> I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA <https://youtu.be/tc1aQwxEICA>
>> 
>> Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.
>> 
>> Rob Syme
>> 
>> 
>> 
>> 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. 
>> 
> 
> 
> 
> 
> 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. 
> 
> 
> 
> 
> 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. 
> 

Re: [Gmod-ajax] [apollo] Request for clarification on draggable BAM tracks

[Rob S. <rob...@gm...>]

Hi Nathan

Thanks for the tip. You're correct that the draggable vs non-draggable
behavior is explained by Track/Alignments vs Track/Alignments2. I'm happy
to forgo the paired-end rendering in Alignments2 for the draggability of
Track/Alignments, but in switching down to Track/Alignments, I also loose
the intron rendering (and intron annotation from dragged reads). Here is a
region showing data from the same BAM file using the two versions of
Webapollo tracks:

[image: Screenshot from 2019-02-07 12-42-28.png]


This is with the a trackList.json that looks like:

{
   "formatVersion" : 1,
   "names" : {
      "type" : "Hash",
      "url" : "names/"
   },
   "tracks" : [
      {
         "category" : "Reference sequence",
         "chunkSize" : 20000,
         "key" : "Reference sequence",
         "label" : "DNA",
         "seqType" : "dna",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
      },
      {
         "bicolor_pivot" : 0.4,
         "label" : "GC Content",
         "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta",
         "type" : "GCContent/View/Track/GCContentXY",
         "urlTemplate" : "fasta/genome.fasta"
      },
      {
         "key" : "Track/Alignments",
         "label" : "Alignments",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments",
         "urlTemplate" : "bams/inplanta-early.bam"
      },
      {
         "key" : "Track/Alignments2",
         "label" : "Alignments2",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments2",
         "urlTemplate" : "bams/inplanta-early.bam"
      }
   ]
}

Is it possible to have both intron rendering and draggable reads? Last time
I set up a WebApollo instance (12 months ago), I thought I had both. I
might be misremembering.

-rob


On Wed, 6 Feb 2019 at 15:52, Nathan Dunn <nat...@lb...> wrote:

>
> Rob,
>
> I’m guessing the old track was an HTML track
> (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse
> creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets
> extended into an Apollo Canvas Track, which has the nice features that
> Colin Colin added, but is not draggable.
>
> If you want them to be draggable, you would set it to an HTML Track
> (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get
> Colin’s a paired end read code displayed.  Many curators will just have one
> of each track (same data, but different type).
>
> I’m not sure if anyone will have the time to move them both over to HTML,
> but I’m sure we could help point you in the right direction if interested
> (would be in the JBrowse code-base, with a small fix in the Apollo
> code-base).
>
> Nathan
>
>
>
>
>
>
>
> On Feb 6, 2019, at 8:25 AM, Rob Syme <rob...@gm...> wrote:
>
> Hi all
>
> I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After
> adding a bam track using the add-bam-track.pl script, the reads display
> beautifully, but are not able to be dragged into the user-created
> annotations track. I can create new annotations by right-clicking a read
> and selecting  "create new annotation", but splicing is not preserved in
> the newly created annotations.
>
> I've recorded a quick video to demonstrate the issue here:
> https://youtu.be/tc1aQwxEICA
>
> Has anybody else had difficulty getting draggable BAM tracks in webapollo?
> Any help would be greatly appreciated.
>
> Rob Syme
>
>
>
> 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.
>
>
>
>
>
> 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.
>
>

Re: [Gmod-ajax] [apollo] Request for clarification on draggable BAM tracks

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

Rob,

I’m guessing the old track was an HTML track (JBrowse/View/Track/Alignments) and the new one is the default, JBrowse creates a Canvas Track (JBrowse/View/Track/Alignments2), which gets extended into an Apollo Canvas Track, which has the nice features that Colin Colin added, but is not draggable. 

If you want them to be draggable, you would set it to an HTML Track (JBrowse/View/Track/Alignments).  Unfortunately, you won’t be able to get Colin’s a paired end read code displayed.  Many curators will just have one of each track (same data, but different type).   

I’m not sure if anyone will have the time to move them both over to HTML, but I’m sure we could help point you in the right direction if interested (would be in the JBrowse code-base, with a small fix in the Apollo code-base). 

Nathan







> On Feb 6, 2019, at 8:25 AM, Rob Syme <rob...@gm...> wrote:
> 
> Hi all
> 
> I've just set up a webapollo 2.3.0 instance with JBrowse 1.16.2. After adding a bam track using the add-bam-track.pl script, the reads display beautifully, but are not able to be dragged into the user-created annotations track. I can create new annotations by right-clicking a read and selecting  "create new annotation", but splicing is not preserved in the newly created annotations.
> 
> I've recorded a quick video to demonstrate the issue here: https://youtu.be/tc1aQwxEICA
> 
> Has anybody else had difficulty getting draggable BAM tracks in webapollo? Any help would be greatly appreciated.
> 
> Rob Syme
> 
> 
> 
> 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. 
> 

[Gmod-ajax] Apollo 2.3.0 release

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

Apollo 2.3.0 has been released

https://github.com/GMOD/Apollo/releases/tag/2.3.0 <https://github.com/GMOD/Apollo/releases/tag/2.3.0>

All annotations are now Neat Features annotations due to great improvements in the JBrowse code-base. 

We have also moved to JBrowse 1.16.2 by default 1988, which also fixed track styling issues #1942.

Other bug fixes and features added as well: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md <https://github.com/GMOD/Apollo/blob/master/ChangeLog.md> 

General questions or requests for help should go to the mailing list (ap...@li...).  Note that the mailing list will be moved to google groups soon, but the archive will remain: http://gmod.827538.n3.nabble.com/Apollo-f815553.html <http://gmod.827538.n3.nabble.com/Apollo-f815553.html>.  More details as I have them. 

Please open a GitHub issue if you find any problems: https://github.com/GMOD/Apollo/issues <https://github.com/GMOD/Apollo/issues> 

The docker image will be updated on Quay and Docker hub shortly.  More instructions here: https://github.com/GMOD/docker-apollo <https://github.com/GMOD/docker-apollo>

I’ll update one of the AWS zones (N. Virginia) with the latest Apollo version for easy installation.  

Apollo and JBrowse Teams

[Gmod-ajax] JBrowse 1.16.2 released

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

Hello all,
JBrowse 1.16.2 has been released. This release contains just a couple small
bugfixes, including one for CSI in BAM files, and then a couple smaller
things. See the release notes below.


   - JBrowse-1.16.2.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.2-release/JBrowse-1.16.2.zip>
-
   minified release
   - JBrowse-1.16.2-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.2-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.2-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.2-release/JBrowse-1.16.2-desktop-win32-x64.zip>
   - JBrowse-1.16.2-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.2-release/JBrowse-1.16.2-desktop-linux-x64.zip>
   - JBrowse-1.16.2-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.2-release/JBrowse-1.16.2-desktop-darwin-x64.zip>

Blog post http://jbrowse.org/blog/2019/01/31/jbrowse-1-16-2.html
Happy browsing!
<http://jbrowse.org/blog/#minor-improvements>Minor improvements

   -

   Allow configuring the cache busting behavior for adding random ?v= value
   to config file requests. This can be configured in index.html. Thanks to
   user @sandilyaamit <https://github.com/sandilyaamit> for reporting, this
   is actually important to disable when using Amazon presigned URLs (
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Adds fixBounds config for XYPlot tracks which can be set to false to
   disable the behavior of rounding up or down on the min_score/max_score
   variables for the ruler. Thanks to @scottcain
   <https://github.com/scottcain> for the suggestion (issue #1306
   <https://github.com/gmod/jbrowse/pull/1306>, @cmdcolin
   <https://github.com/cmdcolin>)

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

   -

   Fix ability to use CSI indexes with BAM files since 1.16.0 (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fix ability to read some CRAM files with unmapped mates (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fix issue with the browser loading NaN locations on startup (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Add fix for exporting GFF3 for newer browsers that have Array.values()
   enabled. Thanks to Scott Cain for reporting (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Improve error message when refSeqs=file.fai config fails to load (
   @cmdcolin <https://github.com/cmdcolin>)

Re: [Gmod-ajax] Nomination for new GMOD project

[Cook, M. <ME...@st...>]

Pro – I have used it and deployed it and integrated it with JBrowse and agree with all points Yannick raises – and it deserves more/better exposure and funding for further dev as needed.

Malcolm Cook - Database Application Manager
Computation Biology Group
Stowers Institute for Medical Research
1000 E 50th Street
Kansas City, Missouri 64110



From: Scott Cain <sc...@sc...>
Sent: Monday, January 28, 2019 5:58 PM
To: gmod-announce <gmo...@li...>; gmod-devel <gmo...@li...>; gmod-ajax <gmo...@li...>; gmod tripal devel <gmo...@li...>; Apollo Developers <apo...@li...>; Yannick Wurm <y....@qm...>; Anurag Priyam <anu...@gm...>
Subject: [Gmod-ajax] Nomination for new GMOD project

**CAUTION: Non-Stowers email**
Hello GMOD,

Last week, Yannick Wurm of SequenceServer fame approached me about adding SequenceServer as a GMOD project.  It seems like a great fit to me as a general and widely used tool.  Please take a moment to read a little about it if you aren't already familiar and if you have any thoughts (pro or con), please let me know. I included email groups of projects that I thought might be interested in SequenceServer.  If you know of somebody else involved with GMOD who isn't covered by one of these lists, please feel free to forward it to them.

In case you weren't aware, GMOD has guidelines for adding new projects:

http://gmod.org/wiki/GMOD_Membership

Here is what Yannick wrote in support of his nomination:
-----------------------------------------------------------

Dear all,

I would like to nominate SequenceServer as a GMOD tool.

Background:
A major hurdle I stumbled upon a few years ago as  collaborators and I began to obtain transcriptome and genome assemblies from new species, was the lack of a simple manner of BLASTing unpublished data. Using  a perl/cgi blast script was horrible - and it had a counterintuitive user interface. Same with the tool for custom databases that NCBI supplied at the time.
To overcome this, Anurag Priyam (an undergraduate at the time) and I began developing  SequenceServer. Its had 3 main aims:
 - provide an intuitive user interface and elegant user experience that increases researchers productivity
 - make it easy for individual users to run it autonomously on unpublished or custom data
 - make it easy to share a BLAST interface with others - in a lab or on a community database   (including the - now deprecated antgenomes.org<http://antgenomes.org> which I ran)

It was open source from the start, and has decent success:
 - 60,000 downloads
 - >50 citations.
 - >70 github forks and 130 stars
 - >190 members on mailing list

It is used on dozens of GMOD-esque community sites - often in combination with jBrowse, including:
reefgenomics.org<http://reefgenomics.org>  http://www.daphnia-stressordb.uni-hamburg.de, hymenopterabase, http://spottedwingflybase.org , bovine genome database, Lepbase, http://www.wheat-tilling.com,  PHIbase, GenomeHubs,http://pristionchus.org/about.html, http://planmine.mpi-cbg.de/planmine/begin.do,  and many more.

Allow me to provide specific comments regarding the GMOD membership criteria below.

Please do not hesitate if you have any questions.

Kind regards,

Yannick
-----

Meets a Common Need
Growing citations & userbase demonstrate this.

Useful Over Time
Usage has steadily increased since 2012. The tool wraps BLAST (we are seeking funding to hopefully also wrap DIAMOND). We are implementing novel visualisations to increase analysis power/researchers productivity (including thanks to a recent GSoC).

Configurable and Extensible
All source code is open. Key configurable things are separated out.
 - e.g. can use built-tin "sinatra" web server - or go via apache or nginx (as we do on antgenomes.org<http://antgenomes.org>)
 - the most common customization is to add links from BLAST hits to specific databases (e.g. genome browser or other cross-ref) - this is done in a modular manner, using custom "links.rb" plugins that remain stable even when the rest of sequenceserver is upgraded. E.g. see  http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse

Open Source License for All Users
GNU AGPL v3

Interoperable With Other GMOD Components
All it needs is a directory of one or more FASTA files.
There is no internal database (the directory is scanned on launch) - thus we don't connect to Chado. We do nothing with annotations and thus don't support GFF.
(the jbrowse page actually has a decent section on linking things up - http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse )

Commitment of Support
We've been supporting this without specfic funds since 2012 and hope to be able to continue doing so. Being part of GMOD will hopefully also help attract funding. Mailing list is here:
 https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
The code is well documented, the site and doc page are decent - http://www.sequenceserver.com and http://www.sequenceserver.com/doc/
Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues
We are happy to commit to continuing these efforts.
We have encouraged (and attracted) code contributions in the past and will continue to do so.

Users and Support Mailing List(s)
 https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
 Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues

Public repository
https://github.com/wurmlab/sequenceserver

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

[Gmod-ajax] Nomination for new GMOD project

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

Hello GMOD,

Last week, Yannick Wurm of SequenceServer fame approached me about adding
SequenceServer as a GMOD project.  It seems like a great fit to me as a
general and widely used tool.  Please take a moment to read a little about
it if you aren't already familiar and if you have any thoughts (pro or
con), please let me know. I included email groups of projects that I
thought might be interested in SequenceServer.  If you know of somebody
else involved with GMOD who isn't covered by one of these lists, please
feel free to forward it to them.

In case you weren't aware, GMOD has guidelines for adding new projects:

http://gmod.org/wiki/GMOD_Membership

Here is what Yannick wrote in support of his nomination:
-----------------------------------------------------------

Dear all,

I would like to nominate SequenceServer as a GMOD tool.

Background:
A major hurdle I stumbled upon a few years ago as  collaborators and I
began to obtain transcriptome and genome assemblies from new species, was
the lack of a simple manner of BLASTing unpublished data. Using  a perl/cgi
blast script was horrible - and it had a counterintuitive user interface.
Same with the tool for custom databases that NCBI supplied at the time.
To overcome this, Anurag Priyam (an undergraduate at the time) and I began
developing  SequenceServer. Its had 3 main aims:
 - provide an intuitive user interface and elegant user experience that
increases researchers productivity
 - make it easy for individual users to run it autonomously on unpublished
or custom data
 - make it easy to share a BLAST interface with others - in a lab or on a
community database   (including the - now deprecated antgenomes.org which I
ran)

It was open source from the start, and has decent success:
 - 60,000 downloads
 - >50 citations.
 - >70 github forks and 130 stars
 - >190 members on mailing list

It is used on dozens of GMOD-esque community sites - often in combination
with jBrowse, including:
reefgenomics.org  http://www.daphnia-stressordb.uni-hamburg.de,
hymenopterabase, http://spottedwingflybase.org , bovine genome database,
Lepbase, http://www.wheat-tilling.com,  PHIbase, GenomeHubs,
http://pristionchus.org/about.html,
http://planmine.mpi-cbg.de/planmine/begin.do,  and many more.

Allow me to provide specific comments regarding the GMOD membership
criteria below.

Please do not hesitate if you have any questions.

Kind regards,

Yannick
-----

Meets a Common Need
Growing citations & userbase demonstrate this.

Useful Over Time
Usage has steadily increased since 2012. The tool wraps BLAST (we are
seeking funding to hopefully also wrap DIAMOND). We are implementing novel
visualisations to increase analysis power/researchers productivity
(including thanks to a recent GSoC).

Configurable and Extensible
All source code is open. Key configurable things are separated out.
 - e.g. can use built-tin "sinatra" web server - or go via apache or nginx
(as we do on antgenomes.org)
 - the most common customization is to add links from BLAST hits to
specific databases (e.g. genome browser or other cross-ref) - this is done
in a modular manner, using custom "links.rb" plugins that remain stable
even when the rest of sequenceserver is upgraded. E.g. see
http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse

Open Source License for All Users
GNU AGPL v3

Interoperable With Other GMOD Components
All it needs is a directory of one or more FASTA files.
There is no internal database (the directory is scanned on launch) - thus
we don't connect to Chado. We do nothing with annotations and thus don't
support GFF.
(the jbrowse page actually has a decent section on linking things up -
http://gmod.org/wiki/JBrowse_FAQ#How_can_I_link_BLAST_results_to_JBrowse )

Commitment of Support
We've been supporting this without specfic funds since 2012 and hope to be
able to continue doing so. Being part of GMOD will hopefully also help
attract funding. Mailing list is here:
 https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
The code is well documented, the site and doc page are decent -
http://www.sequenceserver.com and http://www.sequenceserver.com/doc/
Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues
We are happy to commit to continuing these efforts.
We have encouraged (and attracted) code contributions in the past and will
continue to do so.

Users and Support Mailing List(s)
 https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
 Issue tracker is here: https://github.com/wurmlab/sequenceserver/issues

Public repository
https://github.com/wurmlab/sequenceserver

-- 
------------------------------------------------------------------------
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] FW: JBrowse: override metadata display in 'About this track' box

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

I'm not sure if it is ComboTrackSelector specific but there are callbacks
called fmtMetaValue_* and fmtMetaField_* callbacks in the config

That can help customize the About popups

-Colin

On Fri, Jan 25, 2019 at 12:37 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Colin,
>
>
>
> Any thoughts on how I can get around this?  Or this metadata locked in
> once I have a reference to an external metadata CSV file?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Vaneet Lotay
> *Sent:* Tuesday, January 22, 2019 2:47 PM
> *To:* gmo...@li...
> *Subject:* JBrowse: override metadata display in 'About this track' box
>
>
>
> Hello,
>
>
>
> I am using the ComboTrackSelector plugin to have both the Hierarchical and
> Faceted track selectors active at the same time currently in my JBrowse.
> This is because I have metadata to display in the faceted track selector
> which comes from a CSV file.  What I notice is that every column of this
> same metadata is displayed in the pop up box when I click on the track
> label drop down bar and select ‘About this track’.  I’ve tried adding
> additional metadata fields or overwriting the content of some of the fields
> there because I didn’t like the format in which they are displayed but that
> doesn’t work it seems locked in to displaying the metadata from the CSV
> file referenced in the tracklist2.json file.
>
>
>
> Do you know if there’s any way I can stop it from displaying the metadata
> show in the faceted track selector and specify my own metadata fields to be
> displayed in the ‘About this track’ box possibly via the original
> tracklist.json file?
>
>
>
> 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] ways to implement cross-species links in apollo/jbrowse?

[Andrew F. <ad...@nc...>]

Hi Malcom-
thanks for pointing that out! if I ever knew JBrowse had that plugin, I 
had totallt forgotten it (though I've recently been using
the similar functionality that is present in IGV for MAF files). This 
could definitely come in handy for us.

I guess the main difference between going this route and what I was 
describing would be the requirement to generate whole-genome 
pre-computed nucleotide-level alignments; the things I was describing 
earlier were more or less just based on the idea  that genes had been 
assigned into families by some method (e.g. we typically just match 
proteins against HMMs representing some standardized set of gene 
families), and then only "aligning" at the level of the gene order and 
orientation. But integrating the two approaches would certainly be quite 
powerful, and we've been thinking about such approaches a bit recently; 
knowing that JBrowse supports this feature is definitely helpful.

thanks again

Andrew



On 1/24/19 12:21 PM, Cook, Malcolm wrote:
>
> Lurking here, but, mightn’t a perhaps useful interface to navigating 
> such syntelogs/orthologues be to (somehow) extend the mafviewer 
> <https://github.com/cmdcolin/mafviewer> plugin to allow linking to 
> precomputed multiple alignments…???
>
> *From:* apo...@li... <apo...@li...> 
> *On Behalf Of *Andrew Farmer
> *Sent:* Tuesday, January 22, 2019 12:32 AM
> *To:* ap...@li...; Michael Poeschla 
> <Mic...@ag...>; gmo...@li...
> *Subject:* Re: [apollo] ways to implement cross-species links in 
> apollo/jbrowse?
>
> **CAUTION: Non-Stowers email**
>
> Hi Michael-
> we have similar comparative genomics interests within our project 
> (which happens to deal with more or less closely related plant 
> species); and we've approached it in a couple of different ways, one 
> of which might be able to work for you too.
>
> The first way is simplest and perhaps appropriate for your case since 
> you already have precomputed orthology; we've simply injected an AJAX 
> service callout into the gene details dialog in JBrowse, and the 
> implementation of the service is responsible for providing links to 
> other resources for the gene (which in your case could be a set of 
> links to each of the orthologs).
> You can see it in action here:
> http://www.medicagohapmap2.org/jbrowse/?data=medtr%2FA17_HM341.gnm4&loc=medtr.A17_HM341.gnm4.ann2.Medtr5g089110&tracks=A17_HM341.gnm4.ann2
> (after you click on the glyph for the gene model, there might be a 
> slight pause before the links appear while the AJAX call is being 
> handled; we should probably have an indicator of sorts there)
>
> The second way is having JBrowse working in conjunction with a 
> multi-genome micro/macro synteny comparison app we've been developing 
> (the Genome Context Viewer (GCV): 
> https://github.com/legumeinfo/lis_context_viewer/wiki/Examples);
> this allows on-the-fly parameterized determination of syntelogs, which 
> can be communicated to drive JBrowse using messaging via a 
> BroadcastChannel; although we're still pretty much just exploring this 
> mechanism for effecting inter-application communication it so far 
> seems promising. But actually, even without this event-based approach, 
> the mechanism in the first option I described above can also just 
> linkout to the GCV app (as we've done among our links in that example, 
> just see the one described as "similar genomic contexts"). One 
> possible merit of this approach is that it can take you to related 
> regions of genomes via synteny even when an ortholog for the gene in 
> question appears to be missing (which is sometimes just an artifact of 
> assembly/annotation).
>
> If any of this seems to merit further discussion, I'd happy to discuss 
> further (and/or point you to someone from my group who can give more 
> implementation details).
>
> hope it helps, in any case
> Andrew
>
> On 1/21/19 9:48 AM, Michael Poeschla wrote:
>
>     Hi all,
>
>     I want to implement something with our apollo browser and was hoping that someone could point me in the right direction to get started, or let me know if a solution already exists. We have a browser loaded with closely related teleost species. I also have a table with orthologous genes between the species and their genomic locations that I want to use as the basis for a new feature, where I could click on an annotation in apollo (or jbrowse track) and then be able to click through to orthologous sites in other species. Not sure if this is a jbrowse or apollo issue so posting it to both lists per the developer's advice (thanks Nathan!).
>
>     Any advice/suggestions would be appreciated.
>
>     Thanks in advance!
>
>     Michael
>
>
>
>     This list is for the Apollo Annotation Editing Tool. Info athttp://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...@li...  <mailto:sy...@li...>  | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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