Development News Brief

All News Briefs
Distribution Summary 2014_04_14

Get Galaxy

new: $ hg clone
upgrade: $ hg pull
$ hg update release_2014.04.14

# Upgrades
# Data
  1. New and updated reference genomes added to Rsync server that mirrors contents of the public Main instance
  • New/updated genomes: 115

    • includes hg38
    • note: all available in tool "Extract Genomic DNA"
  • New bowtie indexes: 60
  • New bowtie2 indexes: 115
  • New BWA indexes: 54
  • New lastz indexes: 54
  • New sam indexes: 64
  • New picard (srma) indexes: 59
  • New liftOver mappings: 163
  1. MAF hg19 100waymultiz conservation alignment sourced from UCSC
  2. Replaced: The sam index for hg_g1k_b37 was updated to use "samtools faidx" with version 0.1.18 (original from GATK 1.4 bundle used 0.1.13). The older index lead to some issues with BAM<->SAM conversion using the newer SAMTools version.

# Visualizations
  1. Framework turning
  2. Trackster:
Galaxy Galaxy
    Trackster: Prior coverage display     New deep coverage view

# Workflows
  1. Prep for dataset collections: Refactor out common logic for running workflows across controllers

# UI
  1. New/Updated Dataset Action Controls:
  1. When multiple tool versions installed, default to the latest version
  2. Better handling when one of many versions of a tool repo is uninstalled[/BmdG2201](/archive/dev-news-briefs/2014-04-14/BmdG2201/)
  3. Unify the places where histories are shown and used: UI view and in core code
  4. Configure workflow menu, improve buttons and styling
  5. Handle disabled sessionStorage/localStorage more gracefully in the history pane
  6. Remove BaseView from base-mvc
  7. Do not serve non-HTML content that may contain JavaScript in such a way that web browsers execute it
  8. There are now 2 interfaces to data libraries (the original and new Beta) and feedback is welcomed
  9. Wiki page on how to compile the css.

  1. New functions:
  1. Improved history payload and returned error consistency
  2. Check ftype attribute (if defined) on test output datasets
  3. Published histories contents now fully accessible (no permissions issue)
  4. Correct exception formats used in history & HDA

# Core
  1. Admin:
  1. Config:
  1. Jobs:
  1. LWR:
  1. Eggs:

# Pull Requests Merged

Thanks to our Galaxy community contributors!

  1. 309 - Job module for API (list and inspect jobs). Kyle Ellrott.
  2. 312 - Remove unused imports and unused variables. Fix spacing. Nicola Soranzo.
  3. 316 - Fixing non-string parameter selection for job searches. Kyle Ellrott.
  4. 317 - Web API: safer and cleaner workflow parameter passing. Simone Leo.[/JaC2](/archive/dev-news-briefs/2014-04-14/JaC2/)EBM8
  5. 318 - Adding deleted field to 'to_dict' and search selection of Workflows. Kyle Ellrott.
  6. 315 - Allow jobs to be filtered by tool_id and history_id as well as by state. The tool_id is compared with the like operator. James Johnson
  7. 322 - Added "ignore lines starting with specific characters" to group tool. Clayton Turner.
  8. 323 - API methods to access Workflow Usage. Kyle Ellrott.[/UetzHj64](/archive/dev-news-briefs/2014-04-14/UetzHj64/)
  9. 325 - Use placeholder instead of value in html5 - editor.mako. Trevor Wennblom.
  10. 326 - Specify third-party cookies must not be blocked - Trevor Wennblom.
  11. 331 - Code housekeeping: standardize whitespace in various locations. Trevor Wennblom.[/WtWdxP2n](/archive/dev-news-briefs/2014-04-14/WtWdxP2n/)
  12. 341 - Workflows API enhancements (pull request #337 corrected). Nicola Soranzo and Simone Leo.
  13. 338 - Patch to expose the actual dataset id in the LDDA and HDA to_dict calls (in addition to the instance id). Kyle Ellrott[/BrOscq](/archive/dev-news-briefs/2014-04-14/BrOscq/)TJ
  14. 339 - Strip trailing slashes in tool IDs. Björn Grüning.
  15. 334 - Optional Input Datasets Not Compatible with Parallelism Tag. Michael Li
  16. 346 - Tool panel label bug correction. Nicola Soranzo.
  17. 353 - Add BCF datatype sniffing, so BCF files are not uncompressed during upload. Nicola Soranzo.
  18. 355 - Workflow API: show also workflow owner, so a user can check it before importing. Nicola Soranzo.


  1. Fix issue with tool panel display when the tool_conf.xml has only a single entry
  2. Fix issue when multiple versions of the same tool installed results in separate entries in the tool panel
  3. Fix Published Page's JS error
  4. Fix error in Babel egg utf-8, OSX 10.7
  5. Fix failures when using unicode in History name editable_text fields
  6. Fix tool form image display for toolshed installed tools
  7. Fix to improve link format in user activation emails
  8. Fix problem with rerun of tools having DataToolParameter set as optional
  9. Fix bug in Tool Panel when installing repositories[/AiUefff](/archive/dev-news-briefs/2014-04-14/AiUefff/)C

# Tool Shed

Tool Shed


  1. Reorganization of the Tool Shed wiki is underway! See current changes[/ToolShed](/archive/dev-news-briefs/2014-04-14/ToolShed/) and what is next up
  2. Data Manager documentation specific to toolshed


  1. New Tool Shed categories
  • Genome-Wide Association Study
  • Imaging
  • RNA
  1. Add support for the new repository type: Repository suite definition
  2. Enhancements for updating a repository
  • Will now trigger the install of new dependencies
  • Handles newly defined repository dependencies included in updates to installed repositories
  1. Defined a base set of utilities that can be expected to be on systems into which tool dependencies are being installed, related to project-in-planning
  2. Dependency added to keep package_pysam_0_7_7 from failing on tool shed
  3. Update Main Tool Shed Picard repo that contained invalid tools
  4. Update FreeBayes repo so that it specifies precompiled binaries in dependency definition
  5. Update EMBOSS repo so that it downloads a precompiled platform-specific binary

Install and Test Framework

  1. Tool shed install and test framework now works with API driven tool tests
  2. Eliminate the use of fabric as the installation process for repositories
  3. Test script to provide coverage for recently discovered scenario that produced a white ghost upon Galaxy install
  4. Test script to provide coverage for recently introduced repository administration feature
  5. Test script to check toolshed dependency files for broken/invalid download URLs

Tool Shed Fixes

  1. Fix setup_r_environment broken in central repo
  2. Fix scenario where by uninstalling and reinstalling a repository that has been updated creates database entries for repositories that are persistently in the New state
  3. Fixes in automated test framework
  4. Fix bug in install and test framework related to samtools migration


Project Updates

  1. News
  2. Events
  3. Videos on Vimeo
  4. April 2014 Galaxy Update
  5. March 2014 Galaxy Update

# About

The Galaxy Team is a part of the Center for Comparative Genomics and Bioinformatics at Penn State, and the Department of Biology at Johns Hopkinis 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 Johns Hopkins University.

The public Main instance of Galaxy at utilizes infrastructure generously provided by the iPlant Collaborative at the Texas Advanced Computing Center, with support from the National Science Foundation.

Follow us on Twitter @galaxyproject or read our tweets at Galaxy on Twitter

Have a suggestion? Please see Using the Galaxy Issue Board, and be sure to up vote the issues important to YOU.