April 8, 2011 Galaxy Development News Brief
http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08
Prior releases:
https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBriefs
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2011_04_08 Highlights
Workflow API
Move Data Library Items
10 New Genomes & 29 New LiftOver
Import Workflows & Histories
ClustalW Multiple-Seq Alignments & Sequence Logos
Major Trackster Visualization Improvements
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How to get this distribution
https://bitbucket.org/galaxy/galaxy-dist/
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 50e249442c5a
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Key Upcoming Galaxy Events
May 24-26, 2011 Galaxy Community Conference, Lunteren, The Netherlands.
http:galaxy.psu.edu/gcc2011/
April 24 is the Early registration deadline (save 20%!)
http://galaxy.psu.edu/gcc2011/Register.html
April 13-14, NBIC Galaxy Hackathon, Belgium. Please submit your suggestions!
http://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project
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What's New
Workflow API
An API for executing workflows has been added.
Usage examples
/scripts/api/workflow_execute.py
/scripts/api/example_watch_folder.py.
Move Data Library Items
We have introduced a feature that enables you to move library datasets
or folders (including all folder contents) to other locations within the
same data library or to a different data library altogether.
Galaxy administrators can perform this feature on any data library item
and can move items to any data library. Users that are not Galaxy
administrators must be given the modify library item permission on an
item in order to move it, and they'll need the add library item
permission on the desired target data library folder in order for it to
be displayed in the select list of targets.
Moving a single dataset
To move a single dataset, select the Move this dataset option from the
dataset's pop-up menu.
http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08_g1_move_dataset.png
The default behavior is to move items to other locations within the same
data library, so you'll initially be presented with a list of valid
folders from which to choose for the new target location.
http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08_g2_select_folder.png
After selecting the desired folder, clicking the Move button will move
the dataset to the selected folder.
Moving a Folder
Moving a folder is very similar to moving a single dataset - just select
the Move this folder option from the folder's pop-up menu.
http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08_g3_move_folder.png
To move the folder to a different data library, after selecting the Move
this folder option, click the Choose another data library link on the
Move data library items page. The folders select list will change to a
select list of data libraries to which you are authorized to move the
item. When you select a target data library, the select list will change
again to display the list of folders in the selected data library to
which you are authorized to move the item. Clicking the Move button will
move the folder and all of it's contents to the selected target folder
within the selected target data library.
The target folders select list is filtered to included only valid
folders to which you can move the item. For example, you cannot move a
folder to one of it's own sub-folders in one step. To do this, the
sub-folder must be moved outside of it's parent, and then the parent can
be moved to the folder that it previously contained.
http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08_g4_move_folder1.png
------------
Updated & Improved
Data Content
* Genomes
o New & included in NGS Tools
+ Saccharomcyes cerevisiae:
Saccharomcyes_cerevisiae_S288C_SGD2010
+ Arabidopsis lyrata: Araly1
+ Purple Sea Urchin: strPur3 and Spur_v2.6
+ Hydra: Hydra_JCVI
+ Zebrafish: danRer7
+ Poplar: Ptrichocarpa_156
+ Chimpanzee: panTro3
+ Northern White-Cheeked Gibbon: nomLeu1
+ Korean Man AK1: Homo_sapiens_AK1
o New & not included in NGS Tools
+ Caenorhabditis remanei: caeRem2
o Existing genomes added to NGS Tools
+ hg19 Canonical female (no Y chromosome)
+ Streptococcus pneumoniae R6: 278
+ Drosophila virilis: droVir3 and droVir2
* New LiftOver Files
o caeRem2 --> caePb1, caeRem2 --> caeRem3, caeRem2 --> cb3,
caeRem2 --> ce4, caeRem2 --> priPac1, calJac3 --> hg18,
canFam2 --> monDom5, danRer6 --> danRer7, danRer7 --> fr2,
danRer7 --> gasAcu1, danRer7 --> hg19, danRer7 --> mm9,
danRer7 --> oryLat2, danRer7 --> panTro3,
danRer7 --> tetNig2, danRer7 --> xenTro2,
droVir3 --> droVir2, fr2 --> danRer7, gasAcu1 --> danRer7,
hg18 --> calJac3, hg19 --> danRer7, mm9 --> danRer7,
panTro3 --> danRer7, panTro3 --> hg19, ponAbe2 --> calJac3,
ponAbe2 --> monDom5, strPur2 --> ci2, tetNig2 --> danRer7,
xenTro2 --> danRer7
* Add Genomes to Your Instance
http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
* Current Galaxy Main Genomes
http://bitbucket.org/galaxy/galaxy-central/wiki/GenomeData
Current Tools
* Add more verbose error reporting to FASTQ Groomer tool. Provides
more information to allow users to determine what is wrong with
FASTQ files with invalid format.
* Enhance Bowtie wrapper to accept non-Sanger variant FASTQ files.
* Allow Upload Tool to function on https URLs.
* Add count GFF features tool and tests:
o Filter and Sort --> GFF --> Filter GFF file by feature
count using simple expressions.
o Tool counts the number of features in a GFF file. Note:
this is different than the number of lines because a single
GFF feature can often span multiple lines.
* Tophat v1.2.0 support:
o (a) allow indel search.
o (b) max insertion and max deletion lengths.
o (c) library type.
* Updated gff_filter_by_feature_count tool now accepts and
correctly handles all GTF, GFF, and GFF3 files.
* Changes for detecting and loading BAM data type
Samtools version 0.1.13 or newer produces an error condition when
attempting to index an unsorted BAM file. To determine if a BAM
file is sorted, we first use Samtools to check the headers. If
this does not provide a definitive answer and Samtools version
0.1.13 or newer is being used, we index the BAM file to see if it
produces the error. This process provides a more robust approach
to determining if the BAM file is sorted.
New Tools
* Multiple Alignments: ClustalW multiple sequence alignment program
for DNA or proteins.
* Motif Tools: Sequence Logo generator for FASTA data (example:
ClustalW alignment).
o Both tools originated from the Community Tool Shed (see
below).
o The Sequence Logo tool uses Weblogo3 wrapped into Galaxy to
generate a sequence logo. The input file must be a FASTA
file in your current history. It is recommended for viewing
multiple-sequence alignment output from the ClustalW tool.
Set the ClustalW output to FASTA to create the input for
this tool.
A typical output looks like this:
http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08_rgWebLogo3_test.jpg
Community Tools (Tool Shed)
* Tuning: Clarified what is being searched in the Tool Shed.
* New ClustalW wrapper (see http://www.clustal.org) for protein/dna
multiple alignments based on the Galaxy ClustalW wrapper posted
by Hans-Rudolf Hotz in an email on the developer list.
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
* New Weblogo3 wrapper (http://weblogo.berkeley.edu) that creates
sequence logos from FASTA data such as the output from a ClustalW
alignment.
Data Libraries
* Disabled problematic eager loading on data libraries. Very large
data libraries will load two to three times quicker.
* Upload Improvement with example walk-through:
Uploading data library datasets
1. Apply a corrected version of the patch from Peter Cock that flips the
"Preserve directory structure?" setting when uploading library datasets
from filesystem paths. The checkbox is now "yes" instead of the original
"no", and is checked by default.
http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08_g5_preserve.png
2. Flip the behavior of the "Copy data into Galaxy" feature when
uploading library datasets (similar to 2 above) to be more clear and
logical. Instead of a single checkbox, this is now a select list with
clearly defined options. The default setting is to copy the files into
the configured Galaxy file store.
http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08_g6_copy_files.png
3. Allow importing items from a history to replace a library dataset
with a new version. Previously, you could only replace a library dataset
with a new version by uploading a single file.
http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08_g7_replace_dataset.png
Workflows
* Users can now import copies of their own Workflows and Histories.
Trackster
* Enhancements:
o Implemented a data manager for Trackster and drawing is now
completely tracked and controlled.
o Put show_insertions and show_differences in read track
config.
o Filtering now supports:
+ (a) score columns in BED and GFF.
+ (b) GTF attributes.
o Added BED and GFF support to visual analytics framework,
and enable GOPS intersect and subtract tools to work with
visual analytics.
* Improvements:
o Insertions and deletions now shown in reads.
o Save and restore mode for feature and read tracks.
o Bug fixes for drawing feature tracks in Squish and Dense
mode.
o Menus and menu items now work correctly.
o Remove form from navigation controls so that enter key
works properly and sets the chrom/low/high.
o Enable full keyboard navigation via arrow keys.
* Bug fixes:
o Fix issues with navigation input:
+ (a) arrow keys no longer perform navigation
+ (b) invalid chromosome names are handled well.
o Fix feature track bugs so that intervals are correctly
drawn as half-open.
o Use gap to correctly position read connector in Pack mode.
o Fix read id bug in Trackster BAM data provider.
Example of Trackster visualization:
Track of reads mapped using Tophat (spliced) including the transcript
assembled from those reads.
http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08_j1_trackster.png
User Interface (UI)
* SGD Yeast genome added as a Gbrowse display site.
* IGV added as an external display application. This is not enabled
on Galaxy main, but is available for local instances.
CloudMan
* FTP data upload enabled.
http://bitbucket.org/galaxy/galaxy-central/wiki/cloud
Source
* Improvements in reliability and speed regarding manipulation of
instance data volumes.
* The value set in 'new_file_path' in universe_wsgi.ini will now be
used for creation of all temporary files. This obviates the need
for setting $TEMP when running data source tools on the cluster.
* Datatypes:
o Add a 'subclass' flag to datatype definitions in
datatypes_conf.xml that allows dynamic creation of a
subclass.
o Allow composite datatype datasets to be populated in the
Upload tool from files that were uploaded to the Galaxy FTP
server.
* Tool configuration enhancements:
o Allow DataToolParameter to be filtered on attributes other
than dbkey (dynamic options).
o Allow FromParamToolOutputActionOption and
ParamValueToolOutputActionOptionFilter to access attributes
of parameter values.
Tool Test Framework
* Specifying 'ftype="bam"' as a parameter on a test's <output> tag
will now cause the test framework to use 'samtools view' to
convert the file to SAM. This should make it easier to debug why
the test tool output differs from your baseline test output.
Test framework enhancements:
* Allow toolbox tests to upload a file found located in
subdirectories.
* Fix a bug occurring on the determination of uploaded dataset name
during the handling of the removal of .gzip or .zip extension
from the uploaded filenames.
* When using re_match comparison method in functional tests and
line counts do not match, print out first 40 lines of the history
file.
Admin Menu
* Add a checkbox to the Create Group page that if checked will
create a new Role with the same name. This provides a similar
feature the the existing checkbox on the Create Role page.
* However, the behavior is now changed such that new associations
are created when the checkbox is checked, whereas before, only
the Group or Role objects with the same name were created, but
not associated with anything.
Bug Fixes
* Following the login link from the Logout page no longer redirects
you to the Logout page once you have logged in.
* The peek setting method, set_peek(), should now function
consistently across datatypes descending from Text, particularly
with respect to line count estimation.
* Apply patch from Ry4an Brase to correct "NoneType preference on
the jobs view" issue.
* Don't alter the contents of a file while uploading to a data
library if using one of the Upload files from file system paths
or Upload a directory of files options in conjunction with the
Link to files without copying into Galaxy option. This partially
resolves the issue where a supposedly sorted BAM file was being
resorted upon upload to a data library when using this option. A
better implementation of determining whether a BAM file has been
sorted (so that it does not get resorted) remains to be done.
* Extract Genomic DNA tool:
o Do not fix strand for GFF input.
o Handle non-GFF files when interpret features is true.
* Set default value for Cuffdiff's minimum alignment count
parameter to reflect v0.9.3.
* Enhance GFF reader to handle headers and comments and fix bug so
that new feature starts when transcript_id or gene_id changes.
* Suppress most logging for Cufflinks and Cuffdiff as the logging
can generate output that is incompatible with UTF-8 format used
by database.
* Set message type to error when history deletion fails due to
sharing.
* Show masthead links to Published Visualizations and Published
Pages only if Tracks or Pages are enabled.
* Shared visualizations work again.
* Fix bug in recently used tool submenu.
* Change default value for Tophat coverage search to true.
------------
About Galaxy
The Galaxy team is a part of BX at Penn State, and the Biology and
Mathematics and Computer Science departments at Emory University.
http://www.bx.psu.edu/|BX/
http://www.psu.edu/
http://www.emory.edu/
http://www.biology.emory.edu/
http://www.mathcs.emory.edu/
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.
http://www.nsf.gov/
http://www.genome.gov/
http://www.huck.psu.edu/
http://www.ics.psu.edu/
http://www.emory.edu/
Source http://bitbucket.org/galaxy/galaxy-central
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GalaxyProject http://galaxyproject.org
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------------
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