Question: September 8, 2010 Galaxy Development News Brief
0
Jennifer Hillman Jackson ♦ 25k wrote:
September 8, 2010 Galaxy Development News Brief
http://bitbucket.org/galaxy/galaxy-
central/wiki/Features/DevNewsBrief/2010_09_08
Here are the highlights of what you will get if you perform the
following upgrade:
hg pull -u -r f09915c8da94
What's New
New Multiple Sample Tracking Features
* UI enhancements: checkboxes to select samples & select field to
specify operations.
* State change mechanism added for multiple samples and removed for
individual samples in the sample_events page.
* Enhanced sample searching implemented. Uses sample name, barcode and
dataset name with menu items in masthead and admin menu.
o Example of usage: new wild-card searches.
New Custom Sorting in Grid Framework
* Enhance grid framework to enable custom column sorting (default
sorting unchanged).
* Sort criteria are now mapped to a column, and the column defines the
sorting to be done on the grid query.
o Examples of usage: (a) case-insensitive sorting of text fields and
(b) case-insensitive sorting for user names in published-item grids.
New Data Format Conversion Tools
* NGS: SAM Tools => BAM-to-SAM converts BAM format to SAM format
* Convert Formats => Wig to bigWig converter
New GFF Format Filtering Tools
* Filter and Sort => GFF => Extract features from GFF file, Filter GFF
file by attribute using simple expressions, Filter GFF file by feature
count using simple expressions.
* New Filter GFF file by feature count filters a GFF file using
conditions based on transcripts' features counts.
o Example of usage: filter for transcripts that have a minimum
number
of exons or transcripts that have 3' UTRs.
Updated & Improved
Data Libraries
* Added support for the AddressField, CheckboxField, SelectField and
WorkflowField form field types (in addition to the previously
supported
TextArea and TextField) to data library templates.
* Inherited template fields now also inherit any field contents from
the
immediate "parent" of the current item (folder or dataset).
* The information in our data library templates wiki at
http:bitbucket.org/galaxy/galaxy-
central/wiki/DataLibraries/LibraryTemplates
has been updated to reflect the new features and behavior.
Sample Tracking: Email notifications
* Notification of specific sample state changes.
* Changes made to barcode scan AMQP handler to update sample state to
also send email when required.
* Notification to multiple recipients.
* Request events history records notifications.
* UI enhancements:
o "edit request" page to allow users to change notification
configurations.
o "request" page to show the request type state, user & notification
details.
Jobs & related
* Improved handling of metadata to optimize job processing. Includes a
new user prompt to set metadata manually or retry auto-detection
externally when using 'set_metadata_externally = True' .
* Enhance wig datatype to only use first 100 data lines to determine
column type metadata if dataset filesize exceeds
max_optional_metadata_filesize as configured in datatypes_conf.xml.
* Add 'NullToolOutputActionOption' to tool output dataset actions.
This
action option is used implicitly when no ToolOutputActionOption(s)
have
been defined.
o Example of usage: a metadata value can be set to a static value on
a
per Tool Output basis.
Installation and Management
* Added support for installing Galaxy on systems without direct access
to the Internet. Updated Galaxy Installation wiki (see section "How to
get eggs: If your Galaxy server does not have Internet access"
http:bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs.
* When viewing library dataset information as an administrator, add a
field that displays the path to the actual disk file that underlies
the
dataset.
Trackster
* Each track now has an Overview checkbox that will set the initial
chromosome-wide view.
* Visualizations that users own or are shared with can now be cloned.
* New go-to feature allows users to redirect quickly to a specified
chromosome or position.
o Example of usage: "chr1:1-100,000,000".
* Drag-zoom activated when a chromosomal position is clicked on.
* Line tracks display mode can also now be activated inline.
* Changing display mode from "Auto" now fetches additional detail data
and displays features. Displays error messages in canvas elements if
present. This also limits the number of features displayed per tile.
General Improvements
* Slight makeover to Galaxy tabs: (a) added published item links to
'Shared Data' tab; (b) standardized personal item lists as 'Saved
XXXs';
and (c) added defaults action for Visualization tab.
* Minor grid refactoring.
* Don't re-sort BAM files on upload if already sorted (adapted from
Brad
Chapman patch).
* Use image_path for Workflows and now display modal instead of
relative
paths.
--
Galaxy Project Team
http:usegalaxy.org
http:bitbucket.org/galaxy/galaxy-central
This project is supported in part by NSF, NHGRI, and the Huck
Institutes
of the Life Sciences, and The Institute for CyberScience at Penn
State.