[Gmod-ajax] JBrowse 1.6.0 released, includes feature descriptions and more!

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[Gmod-ajax] JBrowse 1.6.0 released, includes feature descriptions and more!

Robert Buels-2
Hello all,

I’m very pleased to announce the release of JBrowse 1.6.0! This release
is not quite as major as the previous two releases, but there are still
some nice things added.

See http://jbrowse.org/install/ for links to the download files.

As usual, this release comes in two flavors: the “minimal” release
(JBrowse-1.6.0-min.zip – 2.8M) that includes only the software and
documentation necessary to format your own data and run the browser, and
the “full” release (JBrowse-1.6.0-min.zip- 27.2M) that includes the
developers’ test suite, more sample data files, and developer documentation.

Here is the full list of improvements in 1.6.0:

* Added description capabilities to HTML-based features, similar to
GBrowse’s descriptions. If zoomed in far enough (as defined by
`style.descriptionScale`), adds a second line of text below the
feature’s label that shows the content’s of the featur’s Note or
description attribute (issue #67).

* Give prepare-refseqs.pl the capability to load reference sequences
from embedded FASTA sections in GFF3 files (issue #128).

* Configuration files can now recursively include eachother, and
tracks sections are merged intelligently.

* Made sequence tracks not disappear when zoomed out too far to see
base pairs. Instead, sequence tracks simply display lines
suggesting that DNA would be visible at higher
magnification. (issue #124).

* Double-clicking track labels in the simple track selector now turns
the track on (issue #123).

* Fixed bug in BigWig tracks that use the “scale”: “log” option: did
not render properly when the wiggle data included 0′s. This was due
to the fact that the origin was being mapped to Infinity. Thanks to
the Mockler Lab for the fix! (issue #127).

* Fixed bug in NCList binary search code in which zero-length
features at node boundaries would not be found (fix by Ed Lee).

* Fixed bug in which dragging the scroll bar on the simple track
selector can sometimes cause a drag-and-drop to erroneously begin
(issue #89).

* Fixed some bugs in the layout of HTML-based features in which
features in different blocks would overlap in some circumstances.
Under the hood, replaced the contour-based layout engine with a
simpler, not-much-slower implementation that is more correct in the
general case (issue #122).

* Fixed a bug with vertical centering of strand arrows and other
sub-elements of HTML-based features.

--

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org


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[Gmod-ajax] JBrowse 1.6.0 - Chrome compatibility

Mariette
Hi everyone,

it looks like the new version of jbrowse is not compatible with Chrome,
am I the only one to observe this ?
The web page is blank with chrome where jbrowse is displayed with firefox.

Jerome

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Re: JBrowse 1.6.0 - Chrome compatibility

Fahlgren, Noah
Works for me. I upgraded from 1.5.

Noah

Sent from my iPhone

On Aug 27, 2012, at 7:22 AM, "Mariette" <[hidden email]> wrote:

> Hi everyone,
>
> it looks like the new version of jbrowse is not compatible with Chrome,
> am I the only one to observe this ?
> The web page is blank with chrome where jbrowse is displayed with firefox.
>
> Jerome
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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Re: JBrowse 1.6.0 - Chrome compatibility

Scott Cain
In reply to this post by Mariette
Hi Jerome,

It works for me with both the somewhat out of date Chrome instance I
did have and the newly updated one I have now on Mac OS X 10.5.8.  Do
you have a tool that blocks javascript?

Scott


On Mon, Aug 27, 2012 at 8:21 AM, Mariette <[hidden email]> wrote:

> Hi everyone,
>
> it looks like the new version of jbrowse is not compatible with Chrome,
> am I the only one to observe this ?
> The web page is blank with chrome where jbrowse is displayed with firefox.
>
> Jerome
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> 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

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Re: JBrowse 1.6.0 - Chrome compatibility

Robert Buels-2
In reply to this post by Mariette
What version of Chrome is exhibiting the problem?

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 08/27/2012 08:21 AM, Mariette wrote:

> Hi everyone,
>
> it looks like the new version of jbrowse is not compatible with Chrome,
> am I the only one to observe this ?
> The web page is blank with chrome where jbrowse is displayed with firefox.
>
> Jerome
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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