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

------------

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

------------

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

------------

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

------------

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
Use Galaxy!        http://usegalaxy.org
GalaxyProject      http://galaxyproject.org


Join us at Twitter
#usegalaxy
http://twitter.com/#!/search/galaxyproject

------------
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to