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Development News Brief

14 April 2014

All News Briefs
Distribution Summary 2014_04_14


Get Galaxy

getgalaxy    getgalaxy.org
galaxy-dist.readthedocs.org
bitbucket.org/galaxy/galaxy-dist
new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable
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 http://usegalaxy.org 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 https://trello.com/c/kdhJ1Dit
  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 https://trello.com/c/pdGNjllH

# UI
  1. New/Updated Dataset Action Controls:
  1. When multiple tool versions installed, default to the latest version https://trello.com/c/zRBZ9nvD
  2. Better handling when one of many versions of a tool repo is uninstalled https://trello.com/c[/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 https://trello.com/c/7cN0nmKH
  4. Configure workflow menu, improve buttons and styling https://trello.com/c/xFzp3lt6
  5. Handle disabled sessionStorage/localStorage more gracefully in the history pane https://trello.com/c/V2VCxzmx
  6. Remove BaseView from base-mvc https://trello.com/c/xUV4qvIc
  7. Do not serve non-HTML content that may contain JavaScript in such a way that web browsers execute it https://trello.com/c/G67ELiMI
  8. There are now 2 interfaces to data libraries (the original and new Beta) and feedback is welcomed https://trello.com/c/d3muKvqr
  9. Wiki page on how to compile the css. https://wiki.galaxyproject.org/Develop/CSS https://trello.com/c/gLI6hUjN

# API
  1. New functions:
  1. Improved history payload and returned error consistency https://trello.com/c/fWC7WgQf
  2. Check ftype attribute (if defined) on test output datasets https://trello.com/c/hFFlM4gY
  3. Published histories contents now fully accessible (no permissions issue) https://trello.com/c/KME3ZRRY
  4. Correct exception formats used in history & HDA https://trello.com/c/bS9wY4Ri

# 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. https://trello.com/c/s2Gk6QlH
  2. 312 - Remove unused imports and unused variables. Fix spacing. Nicola Soranzo. https://trello.com/c/iWaf1ak4
  3. 316 - Fixing non-string parameter selection for job searches. Kyle Ellrott. https://trello.com/c/ZXZ9lEkN
  4. 317 - Web API: safer and cleaner workflow parameter passing. Simone Leo. https://trello.com/c[/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. https://trello.com/c/lv9q67nF
  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 https://trello.com/c/dvLvPUmK
  7. 322 - Added "ignore lines starting with specific characters" to group tool. Clayton Turner. https://trello.com/c/j6TP6M7m
  8. 323 - API methods to access Workflow Usage. Kyle Ellrott. https://trello.com/c[/UetzHj64](/archive/dev-news-briefs/2014-04-14/UetzHj64/)
  9. 325 - Use placeholder instead of value in html5 - editor.mako. Trevor Wennblom. https://trello.com/c/PIZAXsOS
  10. 326 - Specify third-party cookies must not be blocked - repository.py. Trevor Wennblom. https://trello.com/c/XsAUr6wl
  11. 331 - Code housekeeping: standardize whitespace in various locations. Trevor Wennblom. https://trello.com/c[/WtWdxP2n](/archive/dev-news-briefs/2014-04-14/WtWdxP2n/)
  12. 341 - Workflows API enhancements (pull request #337 corrected). Nicola Soranzo and Simone Leo. https://trello.com/c/zizGdqy1
  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 https://trello.com/c[/BrOscq](/archive/dev-news-briefs/2014-04-14/BrOscq/)TJ
  14. 339 - Strip trailing slashes in tool IDs. Björn Grüning. https://trello.com/c/bpKNn66u
  15. 334 - Optional Input Datasets Not Compatible with Parallelism Tag. Michael Li https://trello.com/c/WMgr8Xx0 https://trello.com/c/Muw6fd8h
  16. 346 - Tool panel label bug correction. Nicola Soranzo. https://trello.com/c/8NpgYM3U
  17. 353 - Add BCF datatype sniffing, so BCF files are not uncompressed during upload. Nicola Soranzo. https://trello.com/c/FVKZhlsU
  18. 355 - Workflow API: show also workflow owner, so a user can check it before importing. Nicola Soranzo. https://trello.com/c/cMiaYcCI

Fixes

  1. Fix issue with tool panel display when the tool_conf.xml has only a single entry https://trello.com/c/6nJIhOdJ
  2. Fix issue when multiple versions of the same tool installed results in separate entries in the tool panel https://trello.com/c/SlNI79mR
  3. Fix Published Page's JS error https://trello.com/c/yGw1DwwM
  4. Fix error in Babel egg utf-8, OSX 10.7 https://trello.com/c/PUdh6SWw
  5. Fix failures when using unicode in History name editable_text fields https://trello.com/c/MTdotrHR
  6. Fix tool form image display for toolshed installed tools https://trello.com/c/5G6jlB4B
  7. Fix to improve link format in user activation emails https://trello.com/c/JALX9DL3
  8. Fix problem with rerun of tools having DataToolParameter set as optional https://trello.com/c/pzHcSGzK
  9. Fix bug in Tool Panel when installing repositories https://trello.com/c[/AiUefff](/archive/dev-news-briefs/2014-04-14/AiUefff/)C

# Tool Shed

Tool Shed

Documentation

  1. Reorganization of the Tool Shed wiki is underway! See current changes https://wiki.galaxyproject.org[/ToolShed](/archive/dev-news-briefs/2014-04-14/ToolShed/) and what is next up https://trello.com/c/Gg0jnll7
  2. Data Manager documentation specific to toolshed http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository https://trello.com/c/OPOakK4w

Repositories

  1. New Tool Shed categories https://trello.com/c/niCdaARH
  • Genome-Wide Association Study
  • Imaging
  • RNA
  1. Add support for the new repository type: Repository suite definition https://trello.com/c/sxXMmfLs
  2. Enhancements for updating a repository https://trello.com/c/c4Y9t7db
  • 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 https://trello.com/c/gYlRdqwr, related to project-in-planning https://trello.com/c/7VTlX9rD
  2. Dependency ez_setup.py added to keep package_pysam_0_7_7 from failing on tool shed https://trello.com/c/AkACDWix
  3. Update Main Tool Shed Picard repo that contained invalid tools https://trello.com/c/mxxHWxLY
  4. Update FreeBayes repo so that it specifies precompiled binaries in dependency definition https://trello.com/c/zYoVHKoV
  5. Update EMBOSS repo so that it downloads a precompiled platform-specific binary https://trello.com/c/iW3Amhl5

Install and Test Framework

  1. Tool shed install and test framework now works with API driven tool tests https://trello.com/c/vfr7b0VK
  2. Eliminate the use of fabric as the installation process for repositories https://trello.com/c/zJoRROvv
  3. Test script to provide coverage for recently discovered scenario that produced a white ghost upon Galaxy install https://trello.com/c/JICmJueB
  4. Test script to provide coverage for recently introduced repository administration feature https://trello.com/c/vjTrhIST
  5. Test script to check toolshed dependency files for broken/invalid download URLs https://trello.com/c/i4GVgZwS

Tool Shed Fixes

  1. Fix setup_r_environment broken in central repo https://trello.com/c/zyCzlgzo
  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 https://trello.com/c/iUDUM4Ut
  3. Fixes in automated test framework https://trello.com/c/QWgsgll8
  4. Fix bug in install and test framework related to samtools migration https://trello.com/c/sN2iLCCn


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# About

GalaxyProject.org

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 http://usegalaxy.org utilizes infrastructure generously provided by the iPlant Collaborative at the Texas Advanced Computing Center, with support from the National Science Foundation.

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