[Gmod-ajax] JBrowse 1.7.4 released

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[Gmod-ajax] JBrowse 1.7.4 released

Robert Buels-2
Hi all,

JBrowse 1.7.4 has been released, containing fixes for some more issues
found in the 1.7.3 release and earlier.  In particular, several bad bugs
have been fixed in support for Safari, Opera, and Internet Explorer.

It can be downloaded from http://jbrowse.org/jbrowse-1-7-4-bugfix-release/.

Changes in this release:

1.7.4     2012-12-06 18:20:55 America/New_York

  * Fixed a bug preventing loading of JBrowse in some browsers.  Thanks
    to Steffi Geisen for pointing this out.

  * Fixed a bug in the BigWig data backend that prevented some BigWig
    files with large numbers of reference sequences from displaying.
    Thanks to Gregg Helt for providing sample data to help isolate
    this.

  * Fixed a bug in the BigWig data backend that prevented BigWig files
    rendering in Safari.  Thanks to Gregor Rot for his help in isolating
    this.

  * Worked around a bug in Safari 6 (and probably earlier) in which
    HTTP byte-range requests are erroneously cached.  Thanks to Gregor
    Rot for pointing out the Safari problems.

  * Fixed some minor styling bugs in the facet menus of the faceted
    track selector.

  * Fixed blurry edges of location trapezoid in Firefox (Eric
    Derohanian).


Happy browsing.  ;-)


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


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Re: JBrowse 1.7.4 released

Robert Buels-2
Hi all,

There was a problem with the release zip files I originally posted on
jbrowse.org.  The software that builds the release zipfiles had a
problem and I didn't notice, and it made corrupted files.

If you have already downloaded 1.7.4, please download the zip file again
to get the working one.  Sorry for the inconvenience!  Many thanks to
Gregor Rot for noticing.


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


On 12/06/2012 06:34 PM, Robert Buels wrote:

> Hi all,
>
> JBrowse 1.7.4 has been released, containing fixes for some more issues
> found in the 1.7.3 release and earlier. In particular, several bad bugs
> have been fixed in support for Safari, Opera, and Internet Explorer.
>
> It can be downloaded from http://jbrowse.org/jbrowse-1-7-4-bugfix-release/.
>
> Changes in this release:
>
> 1.7.4 2012-12-06 18:20:55 America/New_York
>
> * Fixed a bug preventing loading of JBrowse in some browsers. Thanks
> to Steffi Geisen for pointing this out.
>
> * Fixed a bug in the BigWig data backend that prevented some BigWig
> files with large numbers of reference sequences from displaying.
> Thanks to Gregg Helt for providing sample data to help isolate
> this.
>
> * Fixed a bug in the BigWig data backend that prevented BigWig files
> rendering in Safari. Thanks to Gregor Rot for his help in isolating
> this.
>
> * Worked around a bug in Safari 6 (and probably earlier) in which
> HTTP byte-range requests are erroneously cached. Thanks to Gregor
> Rot for pointing out the Safari problems.
>
> * Fixed some minor styling bugs in the facet menus of the faceted
> track selector.
>
> * Fixed blurry edges of location trapezoid in Firefox (Eric
> Derohanian).
>
>
> Happy browsing. ;-)
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>

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Re: JBrowse 1.7.4 released

Gregor Rot-2
Hi Robert,

i checked 1.7.4 in Safari 6.0.2 and it seems the BigWig tracks are
displayed nicely now.

Thanks,
Gregor

On Thu, Dec 6, 2012 at 10:18 PM, Robert Buels <[hidden email]> wrote:

> Hi all,
>
> There was a problem with the release zip files I originally posted on
> jbrowse.org.  The software that builds the release zipfiles had a
> problem and I didn't notice, and it made corrupted files.
>
> If you have already downloaded 1.7.4, please download the zip file again
> to get the working one.  Sorry for the inconvenience!  Many thanks to
> Gregor Rot for noticing.
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
>
> On 12/06/2012 06:34 PM, Robert Buels wrote:
>> Hi all,
>>
>> JBrowse 1.7.4 has been released, containing fixes for some more issues
>> found in the 1.7.3 release and earlier. In particular, several bad bugs
>> have been fixed in support for Safari, Opera, and Internet Explorer.
>>
>> It can be downloaded from http://jbrowse.org/jbrowse-1-7-4-bugfix-release/.
>>
>> Changes in this release:
>>
>> 1.7.4 2012-12-06 18:20:55 America/New_York
>>
>> * Fixed a bug preventing loading of JBrowse in some browsers. Thanks
>> to Steffi Geisen for pointing this out.
>>
>> * Fixed a bug in the BigWig data backend that prevented some BigWig
>> files with large numbers of reference sequences from displaying.
>> Thanks to Gregg Helt for providing sample data to help isolate
>> this.
>>
>> * Fixed a bug in the BigWig data backend that prevented BigWig files
>> rendering in Safari. Thanks to Gregor Rot for his help in isolating
>> this.
>>
>> * Worked around a bug in Safari 6 (and probably earlier) in which
>> HTTP byte-range requests are erroneously cached. Thanks to Gregor
>> Rot for pointing out the Safari problems.
>>
>> * Fixed some minor styling bugs in the facet menus of the faceted
>> track selector.
>>
>> * Fixed blurry edges of location trapezoid in Firefox (Eric
>> Derohanian).
>>
>>
>> Happy browsing. ;-)
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>
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--
Gregor Rot
Bioinformatics Laboratory
Faculty of computer and information science
SI-1000 Ljubljana
Slovenia
http://www.biolab.si/en/gregor-rot

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Re: JBrowse 1.7.4 released

userName
Hi Robert,

in Internet Explorer 9 it works nearly perfect, only the bigwig tracks are not displayed. They keep showing "loading" but don't load the data.

What could this be?
Thanks,
Steffi


2012/12/7 Gregor Rot <[hidden email]>
Hi Robert,

i checked 1.7.4 in Safari 6.0.2 and it seems the BigWig tracks are
displayed nicely now.

Thanks,
Gregor

On Thu, Dec 6, 2012 at 10:18 PM, Robert Buels <[hidden email]> wrote:
> Hi all,
>
> There was a problem with the release zip files I originally posted on
> jbrowse.org.  The software that builds the release zipfiles had a
> problem and I didn't notice, and it made corrupted files.
>
> If you have already downloaded 1.7.4, please download the zip file again
> to get the working one.  Sorry for the inconvenience!  Many thanks to
> Gregor Rot for noticing.
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
>
> On 12/06/2012 06:34 PM, Robert Buels wrote:
>> Hi all,
>>
>> JBrowse 1.7.4 has been released, containing fixes for some more issues
>> found in the 1.7.3 release and earlier. In particular, several bad bugs
>> have been fixed in support for Safari, Opera, and Internet Explorer.
>>
>> It can be downloaded from http://jbrowse.org/jbrowse-1-7-4-bugfix-release/.
>>
>> Changes in this release:
>>
>> 1.7.4 2012-12-06 18:20:55 America/New_York
>>
>> * Fixed a bug preventing loading of JBrowse in some browsers. Thanks
>> to Steffi Geisen for pointing this out.
>>
>> * Fixed a bug in the BigWig data backend that prevented some BigWig
>> files with large numbers of reference sequences from displaying.
>> Thanks to Gregg Helt for providing sample data to help isolate
>> this.
>>
>> * Fixed a bug in the BigWig data backend that prevented BigWig files
>> rendering in Safari. Thanks to Gregor Rot for his help in isolating
>> this.
>>
>> * Worked around a bug in Safari 6 (and probably earlier) in which
>> HTTP byte-range requests are erroneously cached. Thanks to Gregor
>> Rot for pointing out the Safari problems.
>>
>> * Fixed some minor styling bugs in the facet menus of the faceted
>> track selector.
>>
>> * Fixed blurry edges of location trapezoid in Firefox (Eric
>> Derohanian).
>>
>>
>> Happy browsing. ;-)
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
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--
Gregor Rot
Bioinformatics Laboratory
Faculty of computer and information science
SI-1000 Ljubljana
Slovenia
http://www.biolab.si/en/gregor-rot

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Re: JBrowse 1.7.4 released

Robert Buels-2
Unfortunately, Internet Explorer 10 is the lowest version of IE that
supports the JavaScript Typed Array specification, which is used by the
BigWig (and BAM) data backends.


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

On 12/13/2012 07:18 AM, Steffi Geisen wrote:

> Hi Robert,
>
> in Internet Explorer 9 it works nearly perfect, only the bigwig tracks
> are not displayed. They keep showing "loading" but don't load the data.
>
> What could this be?
> Thanks,
> Steffi
>
>
> 2012/12/7 Gregor Rot <[hidden email] <mailto:[hidden email]>>
>
>     Hi Robert,
>
>     i checked 1.7.4 in Safari 6.0.2 and it seems the BigWig tracks are
>     displayed nicely now.
>
>     Thanks,
>     Gregor
>
>     On Thu, Dec 6, 2012 at 10:18 PM, Robert Buels <[hidden email]
>     <mailto:[hidden email]>> wrote:
>      > Hi all,
>      >
>      > There was a problem with the release zip files I originally posted on
>      > jbrowse.org <http://jbrowse.org>.  The software that builds the
>     release zipfiles had a
>      > problem and I didn't notice, and it made corrupted files.
>      >
>      > If you have already downloaded 1.7.4, please download the zip
>     file again
>      > to get the working one.  Sorry for the inconvenience!  Many thanks to
>      > Gregor Rot for noticing.
>      >
>      >
>      > Robert Buels
>      > Lead Developer
>      > JBrowse - http://jbrowse.org
>      >
>      >
>      > On 12/06/2012 06:34 PM, Robert Buels wrote:
>      >> Hi all,
>      >>
>      >> JBrowse 1.7.4 has been released, containing fixes for some more
>     issues
>      >> found in the 1.7.3 release and earlier. In particular, several
>     bad bugs
>      >> have been fixed in support for Safari, Opera, and Internet Explorer.
>      >>
>      >> It can be downloaded from
>     http://jbrowse.org/jbrowse-1-7-4-bugfix-release/.
>      >>
>      >> Changes in this release:
>      >>
>      >> 1.7.4 2012-12-06 18:20:55 America/New_York
>      >>
>      >> * Fixed a bug preventing loading of JBrowse in some browsers. Thanks
>      >> to Steffi Geisen for pointing this out.
>      >>
>      >> * Fixed a bug in the BigWig data backend that prevented some BigWig
>      >> files with large numbers of reference sequences from displaying.
>      >> Thanks to Gregg Helt for providing sample data to help isolate
>      >> this.
>      >>
>      >> * Fixed a bug in the BigWig data backend that prevented BigWig files
>      >> rendering in Safari. Thanks to Gregor Rot for his help in isolating
>      >> this.
>      >>
>      >> * Worked around a bug in Safari 6 (and probably earlier) in which
>      >> HTTP byte-range requests are erroneously cached. Thanks to Gregor
>      >> Rot for pointing out the Safari problems.
>      >>
>      >> * Fixed some minor styling bugs in the facet menus of the faceted
>      >> track selector.
>      >>
>      >> * Fixed blurry edges of location trapezoid in Firefox (Eric
>      >> Derohanian).
>      >>
>      >>
>      >> Happy browsing. ;-)
>      >>
>      >>
>      >> Robert Buels
>      >> Lead Developer
>      >> JBrowse - http://jbrowse.org
>      >>
>      >
>      >
>     ------------------------------------------------------------------------------
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>      > Remotely access PCs and mobile devices and provide instant support
>      > Improve your efficiency, and focus on delivering more value-add
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>     <mailto:[hidden email]>
>      > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
>     --
>     Gregor Rot
>     Bioinformatics Laboratory
>     Faculty of computer and information science
>     SI-1000 Ljubljana
>     Slovenia
>     http://www.biolab.si/en/gregor-rot
>
>     ------------------------------------------------------------------------------
>     LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>     Remotely access PCs and mobile devices and provide instant support
>     Improve your efficiency, and focus on delivering more value-add services
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>     _______________________________________________
>     Gmod-ajax mailing list
>     [hidden email] <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

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[Gmod-ajax] JBrowse 1.7.4 BAM files

Mariette
Hi everyone,
I tryed to add BAM tracks in my jbrowse instance, to do so I added this
in the trackList.json file at the root of my data directory:

       {
          "storeClass"   :  "JBrowse/Store/SeqFeature/BAM",
          "urlTemplate"  :  "path/to/bam",
          "label"        :  "bam",
          "type"         :  "JBrowse/View/Track/Alignments",
          "key"          :  "bam",
          "style"  :  {
             "className"       :  "alignment",
             "arrowheadClass"  :  "arrowhead",
             "labelScale"      :  100
          }
       },

which works just fine, how can I generate this track using the
biodb-to-json.pl script ? I didn't figured out how to generate this from
the allowed field in the config file.

thanks,
Jérôme


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Re: JBrowse 1.7.4 BAM files

Robert Buels-2
Hi Jérôme,

You can't configure BAM or BigWig tracks from a conf file used with
biodb-to-json.pl.

However, you can put the track configuration in a "tracks" item in the
jbrowse_conf.json file in your browser's root directory, which is never
touched by any scripts.

Or, if you prefer to build your configurations with scripts, you can
have the snippet of configuration for that track in a separate file and
use bin/add-track-json.pl to add it to your data's trackList.json file.

Or, you can put track configuration in some other file entirely, and add
that file's URL to the "include" config item where the JBrowse object is
created in index.html.

Hope this helps!

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

On 12/21/2012 08:44 AM, Mariette wrote:

> Hi everyone,
> I tryed to add BAM tracks in my jbrowse instance, to do so I added this
> in the trackList.json file at the root of my data directory:
>
>         {
>            "storeClass"   :  "JBrowse/Store/SeqFeature/BAM",
>            "urlTemplate"  :  "path/to/bam",
>            "label"        :  "bam",
>            "type"         :  "JBrowse/View/Track/Alignments",
>            "key"          :  "bam",
>            "style"  :  {
>               "className"       :  "alignment",
>               "arrowheadClass"  :  "arrowhead",
>               "labelScale"      :  100
>            }
>         },
>
> which works just fine, how can I generate this track using the
> biodb-to-json.pl script ? I didn't figured out how to generate this from
> the allowed field in the config file.
>
> thanks,
> Jérôme
>
>
> ------------------------------------------------------------------------------
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