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== The Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release (not this one). Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised "Migrating tools" section of the Galaxy tool shed wiki to understand how this process will work. ==
== The Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release (not this one). Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised "Migrating tools" section of the Galaxy tool shed wiki to understand how this process will work: ==
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'''In 2012, the Galaxy development team will begin the process of migrating the tools that are currently available in the Galaxy distribution to the [[http://toolshed.g2.bx.psu.edu/|Galaxy Main tool shed]]. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. [[Tool Shed#Migrating_tools_from_the_Galaxy_distribution_to_the_Galaxy_Main_tool_shed|Read more...]]''' In 2012, the Galaxy development team will begin the process of '''migrating the tools that are currently available in the Galaxy distribution to the [[http://toolshed.g2.bx.psu.edu/|Galaxy Main tool shed]]'''. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. [[Tool Shed#Migrating_tools_from_the_Galaxy_distribution_to_the_Galaxy_Main_tool_shed|Read more...]]


March 12, 2012 Galaxy Development News Brief

Get Galaxy

getgalaxy

new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist

upgrade: % hg pull -u -r 40f1816d6857



Important Changes to Tool Organization

The Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release (not this one). Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised "Migrating tools" section of the Galaxy tool shed wiki to understand how this process will work:

tool shed

Migrating tools from the Galaxy distribution to the Galaxy Main tool shed

In 2012, the Galaxy development team will begin the process of migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more...


New Tool Architecture

XML configuration files used to populate your Galaxy tool panel

In the past, the file named by your tool_config_file configuration setting in your universe_wsgi.ini file was the only file used to populate your Galaxy tool panel. The default name for this file is tool_conf.xml. Since this was the only file involved in populating your Galaxy tool panel, it defined the items (tools, workflows, sections and labels) that would be displayed and the way in which they would be arranged. Read more...

Managing the layout of your Galaxy tool panel

The 3 or more files described in the previous section (tool_conf.xml, one or more shed_tool_conf.xml files, and migrated_tools_conf.xml) are all used to load tool panel items (tools, sections, labels and workflows). A new file named integrated_tool_panel.xml has been introduced to define the arrangement for displaying these loaded items in your Galaxy tool panel. Read more...

Galaxy Tool Versions

When included in the Galaxy distribution, tools are defined by "id" and "version", among other attributes. For example, the filter tool has id="Filter1" and version="1.1.0". When installed from a tool shed, the tool's id becomes it's "guid" attribute from the tool shed. If it is migrated from the Galaxy distribution to the tool shed, the filter tool will have the guid: "toolshed.g2.bx.psu.edu/repos/devteam/filter/Filter1/1.1.0". To provide backward compatibility for Galaxy workflows and the rerun button in a Galaxy history item, a mapping between the tool's old id and version and it's new id (guid) is provided by building a chain of relationships between tool versions. This happens automatically for every tool that is loaded into your Galaxy instance. Read more...


New & Updated Tools

Many tools have been recently upgraded. Please review Admin/Config/Tool Dependencies and Admin/Config/Tool Dependencies for these and other recently updated Tool Dependencies. Please see Galaxy's Main Tool Shed for additional new tools.

  • RNA-Seq Tools

    • Added CuffMerge version 1.0.0

      • Requires helper script: gtf_to_sam version 1.3.0

    • Updates for Cufflinks/compare/merge/diff tools

      • Modified default parameter values on tool form
      • Improved error message when bias correction/sequence data cannot be used
  • Updates for TopHat

    • Remove maximum value for TopHat parameter initial_read_mismatches

  • Added RViewer external display application

  • Updated IGV external display application, so that displays using vcf_bgzip will now maintain vcf headers

Galaxy Track Browser (GTB)

Trackster

  • New:

    • Enable visualization of ENCODE peak tracks (see graphic below)

    • Dynamic filtering of read tracks using quality scores
    • Enable toggling between groups of individual tracks and composite tracks
    • Enable Composite Tracks to be saved and restored
    • Make track min and max values editable inline
    • Save and restore track/group filters and tool state
  • Bug fixes:

    • Clear reference track when changing chromosomes
    • To only show differences if reference data is available
    • Use sum rather than mean for data aggregation in BBIDataProvider
    • Indicate changes when config values are changed or items are reordered or grouped
    • Move 'more rows' icon from tile level to track level

Trackster visualization of ENCODE and Composite Track data using dynamic filters

trackster-encode


Workflows

        Syntax:
            #{inputs_file_variable | option 1 | option n}
            where:
                 input_file_variable = is the name of a module input variable
                 |  = the delimiter for added options. Optional if no options.
                 options = basename, upper, lower
                 basename = keep all of the file name except the extension
                            (everything before the final ".")
                 upper = force the file name to upper case
                 lower = force the file name to lower case
        Example:
            #{input1 | basename | upper}

User Interface (UI)

Data and Libraries

CloudMan

CloudMan

Source

galaxy-cental, galaxy-dist

Bug Fixes

bugs

Announcements

News

March 2012 Galaxy Update

GCC2012 Update

2012 Galaxy Community Conference

Training Day

Galaxy is Hiring!

Galaxy wants YOU
The Galaxy Team Wants You!
Want to work on one of the fastest growing open source bioinformatics projects around? The Galaxy Project, a highly successful high throughput data analysis platform for Life Sciences with over 15,000 users worldwide, is hiring. Read more...


About Galaxy

GalaxyProject.org

The GalaxyTeam is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.

Galaxy is supported in part by NSF, NHGRI, the Huck Institutes of the Life Sciences, and The Institute for CyberScience at Penn State, and Emory University.

Join us at Twitter @galaxyproject or just read our tweets Galaxy on Twitter


Jennifer Jackson, Galaxy Team. Posted to DevNewsBriefs on <<XXXXX>>