[Gmod-ajax] JBrowse 1.2 release

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[Gmod-ajax] JBrowse 1.2 release

Mitch Skinner
JBrowse 1.2 is released, and now I'll be catching up on my email
backlog, including a number of gmod-ajax messages.

The code is available here (with minified javascript, which speeds up
initial page loads):

http://jbrowse.org/releases/jbrowse-1.2.zip

or from github (without the minified JS):

https://github.com/jbrowse/jbrowse/tree/1.2-release

Release notes:

version 1.2, Febrary 2011

These notes document changes since release 1.1 in September 2010.

Most of the work in this release went into making JBrowse handle large
amounts of feature data better.  Before, the amount of memory used
when processing BAM files was more than 10 times the size of the file;
now, the amount of memory required is fixed.

Other new features in this release:

- Import of UCSC database dumps.  A ucsc-to-json.pl script is now
   provided for taking database dumps from UCSC and creating a JBrowse
   instance using them.  The "genePred" and "bed" track types are
   currently supported; "psl" tracks are not yet supported.

- Touch.  Juan Aguilar's code for using JBrowse on an iOS device
   (iPhone, iPod touch, iPad) is now integrated.  As of the current
   release, users wanting to use JBrowse on those devices have to
   navigate to a separate HTML page (touch.html) rather than the
   default index.html; i.e. the code does not currently detect
   touchscreen devices automatically.

- Bug fixes. A number of bugs have also been fixed, including one that
   restricted the placement of the "data" directory, and a bug in
   wiggle rendering that caused spurious peaks or troughs at tile
   boundaries.

Known issues/limitations with this release:

- Some additional CPAN modules are now required:

     PerlIO::gzip
     Heap::Simple
     Devel::Size

- No JSON-level backward compatibility. If you are upgrading from an
   older version of JBrowse, you will have to regenerate all the JSON
   files on your server. This means wiping your jbrowse/data directory
   and re-running all server scripts (flatfile-to-json, biodb-to-json,
   wig-to-json, etc.) to regenerate your data from the original
   FASTA/GFF/BED/WIG files. We apologize for the inconvenience of this,
   but it is inevitable sometimes; we do aim to minimize the number of
   releases which are backwardly-incompatible in this way.



------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
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Re: JBrowse 1.2 release

Bernd Jagla
Hi Mitch,

just installed it without much of a problem (only thing being that I
don't know how to update with git or how to set up my MAC to use the
http_proxy system variable..., but downloading and installing worked
without any glitch).

I have imported a sorted bam file and it worked. Unfortunately I am
missing a scale for the histogram view of the bam files. Also, in the
most zoomed-out view the bars seem to be off or I don't understand how
these values are calculated (I would probably want to have a max value
rather than a mean...) Is there a way to change this?

Great work, will send feedback as it comes...

Best,

Bernd

On 2/17/2011 10:16 AM, Mitch Skinner wrote:

> JBrowse 1.2 is released, and now I'll be catching up on my email
> backlog, including a number of gmod-ajax messages.
>
> The code is available here (with minified javascript, which speeds up
> initial page loads):
>
> http://jbrowse.org/releases/jbrowse-1.2.zip
>
> or from github (without the minified JS):
>
> https://github.com/jbrowse/jbrowse/tree/1.2-release
>
> Release notes:
>
> version 1.2, Febrary 2011
>
> These notes document changes since release 1.1 in September 2010.
>
> Most of the work in this release went into making JBrowse handle large
> amounts of feature data better.  Before, the amount of memory used
> when processing BAM files was more than 10 times the size of the file;
> now, the amount of memory required is fixed.
>
> Other new features in this release:
>
> - Import of UCSC database dumps.  A ucsc-to-json.pl script is now
>     provided for taking database dumps from UCSC and creating a JBrowse
>     instance using them.  The "genePred" and "bed" track types are
>     currently supported; "psl" tracks are not yet supported.
>
> - Touch.  Juan Aguilar's code for using JBrowse on an iOS device
>     (iPhone, iPod touch, iPad) is now integrated.  As of the current
>     release, users wanting to use JBrowse on those devices have to
>     navigate to a separate HTML page (touch.html) rather than the
>     default index.html; i.e. the code does not currently detect
>     touchscreen devices automatically.
>
> - Bug fixes. A number of bugs have also been fixed, including one that
>     restricted the placement of the "data" directory, and a bug in
>     wiggle rendering that caused spurious peaks or troughs at tile
>     boundaries.
>
> Known issues/limitations with this release:
>
> - Some additional CPAN modules are now required:
>
>       PerlIO::gzip
>       Heap::Simple
>       Devel::Size
>
> - No JSON-level backward compatibility. If you are upgrading from an
>     older version of JBrowse, you will have to regenerate all the JSON
>     files on your server. This means wiping your jbrowse/data directory
>     and re-running all server scripts (flatfile-to-json, biodb-to-json,
>     wig-to-json, etc.) to regenerate your data from the original
>     FASTA/GFF/BED/WIG files. We apologize for the inconvenience of this,
>     but it is inevitable sometimes; we do aim to minimize the number of
>     releases which are backwardly-incompatible in this way.
>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>


------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax