Upcoming jbrowse release

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Upcoming jbrowse release

Diesh, Colin M.
Hello,
We are past due to release JBrowse version 1.11.4 according to our release schedule. If anyone would like to test out the new version, you get it from https://github.com/GMOD/jbrowse/archive/jbrowse-1.11.4-test.zip

I would appreciate review and/or testing of issues at hand.

Please see these open issues and test them out:
https://github.com/GMOD/jbrowse/issues?milestone=41&page=1&state=open
Several features, such as the gtf parser, the clear highlight button, and the collapse track list button are available on the jbrowse-1.11.4 test branch.

And closed ones:
https://github.com/GMOD/jbrowse/issues?milestone=41&state=closed
Please review these for completeness and/or conflicts with existing installations.

Any commentary and review of these issues, or unit testing that can be done, is much appreciated. 

Thanks,
-Colin
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Re: Upcoming jbrowse release

Diesh, Colin M.
Note: This is not an official release. TESTING only.
Official release is upcoming...

-Colin

On Apr 24, 2014, at 2:27 PM, Diesh, Colin M. <[hidden email]> wrote:

Hello,
We are past due to release JBrowse version 1.11.4 according to our release schedule. If anyone would like to test out the new version, you get it from https://github.com/GMOD/jbrowse/archive/jbrowse-1.11.4-test.zip

I would appreciate review and/or testing of issues at hand.

Please see these open issues and test them out:
https://github.com/GMOD/jbrowse/issues?milestone=41&page=1&state=open
Several features, such as the gtf parser, the clear highlight button, and the collapse track list button are available on the jbrowse-1.11.4 test branch.

And closed ones:
https://github.com/GMOD/jbrowse/issues?milestone=41&state=closed
Please review these for completeness and/or conflicts with existing installations.

Any commentary and review of these issues, or unit testing that can be done, is much appreciated. 

Thanks,
-Colin

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Re: Upcoming jbrowse release

Diesh, Colin M.
Hi all,
We have made some additional changes to jbrowse since my last email

These include:

- Fixed BioPerl error from setup.sh (important because any setup.sh that pulls latest BioPerl, even with older jbrowse will throw an error)

- Fixed dijit dialog scrolling bug, chrome 31/osx 10.9 using by disabling scrollbar on <body> tag https://github.com/GMOD/jbrowse/issues/386

- Fixed a small regression from my last email so that coverage histograms are correctly colored for canvas features tracks

- Changed the color of the ’T’ base in the SNPCoverage/Alignments2 track to red (mailing list issue due to Long Le)

- Fixed the ‘one pixel gap’ that can occur on Safari browser 
—— This is a long standing bug that may have been ‘introduced' in jbrowse 1.10.5 https://github.com/GMOD/jbrowse/issues/341

- Adjusted build machinery so that JBrowse builds fully on mac osx


Problems that still exist:

- Multiple Perl Tests fail using perl 5.18 due to hash order randomization introduced in this version of perl.
- Two selenium tests seem to fail on my computer always due to race conditions. I have manually checked the Xpath multiple times and there is no problem afaik
- New problem with ‘one pixel gap’ appearing on high-res screens on chrome. Normal resolution Chrome displays is not affected. 


A new release will be prepared soon. If there are concerns about the outstanding problems please let me know.
-Colin


On Apr 24, 2014, at 2:35 PM, Colin D <[hidden email]> wrote:

Note: This is not an official release. TESTING only.
Official release is upcoming...

-Colin

On Apr 24, 2014, at 2:27 PM, Diesh, Colin M. <[hidden email]> wrote:

Hello,
We are past due to release JBrowse version 1.11.4 according to our release schedule. If anyone would like to test out the new version, you get it from https://github.com/GMOD/jbrowse/archive/jbrowse-1.11.4-test.zip

I would appreciate review and/or testing of issues at hand.

Please see these open issues and test them out:
https://github.com/GMOD/jbrowse/issues?milestone=41&page=1&state=open
Several features, such as the gtf parser, the clear highlight button, and the collapse track list button are available on the jbrowse-1.11.4 test branch.

And closed ones:
https://github.com/GMOD/jbrowse/issues?milestone=41&state=closed
Please review these for completeness and/or conflicts with existing installations.

Any commentary and review of these issues, or unit testing that can be done, is much appreciated. 

Thanks,
-Colin


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Re: Upcoming jbrowse release

Diesh, Colin M.
Hi all,

We have made some final changes to make this release go as smoothly as possible. One important change is that high-dpi mode is configurable, and it is disabled it by default. I think this will help if there are any unforeseen problems with this implementation and it will allow the feature to be ‘beta tested’ by users that are outgoing enough to enable it!

Please let me know if there are any additional ideas or concerns

-Colin


On May 6, 2014, at 4:15 PM, Colin D <[hidden email]> wrote:

Hi all,
We have made some additional changes to jbrowse since my last email

These include:

- Fixed BioPerl error from setup.sh (important because any setup.sh that pulls latest BioPerl, even with older jbrowse will throw an error)

- Fixed dijit dialog scrolling bug, chrome 31/osx 10.9 using by disabling scrollbar on <body> tag https://github.com/GMOD/jbrowse/issues/386

- Fixed a small regression from my last email so that coverage histograms are correctly colored for canvas features tracks

- Changed the color of the ’T’ base in the SNPCoverage/Alignments2 track to red (mailing list issue due to Long Le)

- Fixed the ‘one pixel gap’ that can occur on Safari browser 
—— This is a long standing bug that may have been ‘introduced' in jbrowse 1.10.5 https://github.com/GMOD/jbrowse/issues/341

- Adjusted build machinery so that JBrowse builds fully on mac osx


Problems that still exist:

- Multiple Perl Tests fail using perl 5.18 due to hash order randomization introduced in this version of perl.
- Two selenium tests seem to fail on my computer always due to race conditions. I have manually checked the Xpath multiple times and there is no problem afaik
- New problem with ‘one pixel gap’ appearing on high-res screens on chrome. Normal resolution Chrome displays is not affected. 


A new release will be prepared soon. If there are concerns about the outstanding problems please let me know.
-Colin


On Apr 24, 2014, at 2:35 PM, Colin D <[hidden email]> wrote:

Note: This is not an official release. TESTING only.
Official release is upcoming...

-Colin

On Apr 24, 2014, at 2:27 PM, Diesh, Colin M. <[hidden email]> wrote:

Hello,
We are past due to release JBrowse version 1.11.4 according to our release schedule. If anyone would like to test out the new version, you get it from https://github.com/GMOD/jbrowse/archive/jbrowse-1.11.4-test.zip

I would appreciate review and/or testing of issues at hand.

Please see these open issues and test them out:
https://github.com/GMOD/jbrowse/issues?milestone=41&page=1&state=open
Several features, such as the gtf parser, the clear highlight button, and the collapse track list button are available on the jbrowse-1.11.4 test branch.

And closed ones:
https://github.com/GMOD/jbrowse/issues?milestone=41&state=closed
Please review these for completeness and/or conflicts with existing installations.

Any commentary and review of these issues, or unit testing that can be done, is much appreciated. 

Thanks,
-Colin