Development News Brief

February 10, 2014

All News Briefs
Distribution Summary 2014_02_10



# 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_2014.02.10


# Upgrades
# Tool Migrations

Galaxy Tool Migrations

This release includes additional tools that have been migrated from the Galaxy distribution to the Tool Shed.

As in prior releases, Galaxy tool migration framework has been enhanced so that tool entries in the tool_conf.xml file for tools that were migrated out of the Galaxy distribution are now automatically eliminated during the migration process.

  • It is no longer necessary to manually edit the tool_conf.xml file to eliminate entries for migrated tools.
  • A back-up copy of the original tool_conf.xml file is made.
  • Associated files, such as location sample files (".loc"), are also removed from the distribution.
  • The list of migrated tools can be found here: migrated 009

# Tools & Data
  1. GenomeSpace: Improved import when initiated from within Galaxy. https://trello.com/c/maFhnXpN
  2. DataProviders: See http://wiki.galaxyproject.org[/DataProviders](/archive/dev-news-briefs/2014-02-10/DataProviders/) https://trello.com/c/Qic2fVPE
  3. Cuffdiff: A read_group.info dataset is now included in the output. https://trello.com/c/FdUYdbIn

# Visualizations
  1. Phyloviz: Saving as visualization corrected. https://trello.com/c/dzBmbyqF
  2. Scatterplot: Improvements to large data loading. https://trello.com/c/8or6FdE2
  3. Trackster:
  • Standalone web application(s) for visualizations. https://trello.com/c/i0yW8IgQ
  • Correct issue where attempting to set a custom build that has not finished processing resulted in unrecoverable infinite recursion. https://trello.com/c/AWyQSQ8F

  • CSS styling improvements include:

    • overlaying track header on track data to compress track height; this enables more data to be viewed simultaneously
    • grayscale drawing for mapped reads so that variation can easily be seen
    • using colors to denote track state (e.g. pending, error, etc.)

Trackster


# Workflows
  1. Implement default parameters. https://trello.com/c/SRxD991Y
  2. Allow overriding parameters when running a workflow. https://trello.com/c[/ZbPzTpAl](/archive/dev-news-briefs/2014-02-10/ZbPzTpAl/)
  3. API should have a way of querying published workflows and using/importing them. https://trello.com/c/LDm3dQvB

# UI
  1. Moved history panel (history.mako; base_panels.mako) from iframe implementation to base_panels DOM. Correct implementation issues. https://trello.com/c/a67ciYUI https://trello.com/c/UejOR6q2
  2. Multiple upgrades to history panel. https://trello.com/c[/P487gwJh](/archive/dev-news-briefs/2014-02-10/P487gwJh/)
  3. Refactor grids.js into a Backbone view. https://trello.com/c/Mwrvm0ia
  4. Moved tag UI/model into api/backbone.js (includes histories & others). https://trello.com/c/V288lfw3
  5. Data Libraries Beta (existing; enhancements in progress). https://trello.com/c/hLL9G2nf
  6. Interface update to use font-awesome 4.0. https://trello.com/c/BC8uYRv8
  7. In upload tool sort FTP files by default. https://trello.com/c/lLllt80V
  8. Masthead update: create a backbone-based masterhead class. https://trello.com/c[/VqigSrt](/archive/dev-news-briefs/2014-02-10/VqigSrt/)P
  9. General UI: provide a backbone class for the modal dialog box. https://trello.com/c/bk11oSS2
  10. Clearer visualization and workflow UI cues and usage/error messages for anonymous users (e.g. login required). https://trello.com/c/pgt8UzgU https://trello.com/c/yW6x44xp

# API
  1. Resolved behavior of fetching tool when provided id differed between API and UI. https://trello.com/c/he1Tm4kK
  2. Resolved API histories/set_as_current bad method signature. https://trello.com/c/knnIWf5Y
  3. Support repeat and conditional in tool execution API. https://trello.com/c/iZ9TBhog
  4. New master admin API key, managed through admin panel. https://trello.com/c/pHByKw22 https://trello.com/c/421tElw3
  5. Allow BaseAuth request to retrieve API key. https://trello.com/c/g5N4ZezT
  6. Add API functionality for creating users using stock Galaxy auth and assigning users API keys. https://trello.com/c/RGuTBsJy
  7. Introduce new generation of API decorator with tested methods in histories API. https://trello.com/c/pIsyZmST
  8. If master_api_key set, allow it to run_as if any user can run_as. https://trello.com/c/OoHNhCNb
  9. Fix for optional input handling in provenance API. Jim Johnson. https://trello.com/c/JPVR5SFt

# Core
  1. Refactor Tool testing framework to use API. https://trello.com/c[/MsJctFem](/archive/dev-news-briefs/2014-02-10/MsJctFem/) https://trello.com/c/wL21d2do
  2. Basic composite datatypes now work as test outputs. https://trello.com/c[/Vedel3J4](/archive/dev-news-briefs/2014-02-10/Vedel3J4/)
  3. Allow overriding composite type main file in archives. Peter Cock. https://trello.com/c/8XeDQEaG
  4. Disambiguated conditional parameters now supported in functional tests. https://trello.com/c/zSTrfDOB
  5. Requirements tags need to be specified for each implicit datatype converter with dependencies. https://trello.com/c/b2zg3dfP
  6. Improve Libraries security for data downloads. https://trello.com/c/bWPbQzhV
  7. Update tools to use GALAXY_SLOTS. https://trello.com/c/qq3Ryr6J
  8. Detect jobs that hit the DRM walltime and provide clear feedback to the user. https://trello.com/c[/BzlFmhi](/archive/dev-news-briefs/2014-02-10/BzlFmhi/)D
  9. Tool dependencies should fallback to default version. https://trello.com/c/flcNPQLR
  10. Remove references to g2.trac.bx.psu.edu. https://trello.com/c/Pl5JJKZT
  11. History import now includes option to import deleted/hidden datasets. https://trello.com/c/TgcdNEE7 https://trello.com/c/FS8t1jX9
  12. Flag for archive_composite_dataset() to assume/not the primary file of a composite dataset is html. https://trello.com/c/qlrYdyzT
  13. Properly handle DRMs that remember finished jobs. https://trello.com/c/9hw0K6QZ
  14. Allow adjusting the reset password length in unvierse_wsgi.ini. https://trello.com/c/t0Ag4kXU
  15. Remove all usage of simplejson, use stdlib json. https://trello.com/c/2yhBhRC2
  16. Allow core Galaxy models and install tool dependencies to target different databases. https://trello.com/c[/V0jDd](/archive/dev-news-briefs/2014-02-10/V0jDd/)JBk
  17. Allow setting metadata remotely with the LWR. https://trello.com/c[/M3i6tlU4](/archive/dev-news-briefs/2014-02-10/M3i6tlU4/)

# Pull Requests Merged

Thanks to our Galaxy community contributors!

  1. 285 - Make to_dict method stringify non-JSONable objects. Kyle Ellrott. https://trello.com/c/fzea3Km9
  2. 296 - Adding update_time to dataset to_dict methods. Kyle Ellrott. https://trello.com/c/dEz6n55E
  3. 253 - Add API call to allow for deletion/purge of dataset in a data library. Philip Mabon. https://trello.com/c/3stOCbEi
  4. 283 - Add \<version_command> to tool configuration options. Gianmauro Cuccuru. https://trello.com/c/soOJVIdd
  5. 254 - Fixes for min/max attributes. Nicola Soranzo. https://trello.com/c/HSzlZn3t https://trello.com/c[/E19F2](/archive/dev-news-briefs/2014-02-10/E19F2/)DCl
  6. 171 - Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool. Gert Hulselmans. https://trello.com/c/1LbQtxYs https://trello.com/c/zgAT56XH
  7. 321 - Fix crash when recovering jobs of a removed tool. A. Bretaud. https://trello.com/c/Mk28MZdI
  8. 304 - Add missing requirement tags. Björn Grüning. https://trello.com/c/DMjCdlle
  9. 306 - Fix typo and reduce duplication in workflow API. Nicola Soranzo. https://trello.com/c/VW5cKDjD
  10. 303 - Fix display_application with login_required=True. Björn Grüning. https://trello.com/c/Vu4hiEZu
  11. 302 - In case of proxy-prefix configuration the $PATH_TO_IMAGES is not correctly converted. Removing the beginning Slash solves it for proxy-prefix configurations and other are not affected. Björn Grüning. https://trello.com/c/oFYlaAWo
  12. 299 - Add ProxyHandler to auto-detect system proxies. Saket Choudhary. https://trello.com/c[/WpXmyngn](/archive/dev-news-briefs/2014-02-10/WpXmyngn/)
  13. 298 - API: display and import workflows shared by other users. Nicola Soranzo. https://trello.com/c/H2yxkezA
  14. 280 - Web API: fix unhandled exception when exporting a workflow with missing tools. Simone Leo. https://trello.com/c/GFgl6Gah
  15. 284 - Log a failed chmod action when installing tool dependencies. Nicola Soranzo. https://trello.com/c/cz4ahDPi
  16. 282 - Extended Metadata for History Datasets. Kyle Ellrott. https://trello.com/c/4bUllR9w
  17. 277 - Add elements to the API to allow for the creation of pages and revisions. Kyle Ellrott. https://trello.com/c/sjdlldWg
  18. 276 - Some minor select field changes including Illumina 1.8+. yhoogstrate. https://trello.com/c/mXHHRhwG
  19. 262 - Convert other 3 tools to $GALAXY_SLOTS. Nicola Soranzo. https://trello.com/c/d2YvRM7O
  20. 257 - Adding requirement tag to the ccat wrapper and remove old ccat2 wrapper. Björn Grüning. https://trello.com/c[/EdrYaNq](/archive/dev-news-briefs/2014-02-10/EdrYaNq/)B
  21. 261 - Adding history_id selection to hda search. Kyle Ellrott. https://trello.com/c[/B82liT7g](/archive/dev-news-briefs/2014-02-10/B82liT7g/)
  22. 266 - Adding Pages and PageRevisions to the search API. Kyle Ellrott. https://trello.com/c/5xsd5kNX https://trello.com/c/ch2COcm3
  23. 271 - Fixes for MOSAIK tool. Nicola Soranzo. https://trello.com/c/tcYDdJT6
  24. 267 - Fix for permission issues in drmaa_external_runner.py. Frederik Delaere. https://trello.com/c/BCirrf32
  25. 264 - Fix API workflow show for workflows created with history Extract Workflow. Nicola Soranzo and Simone Leo. https://trello.com/c/osi9S11K
  26. 247 - Fixed bug in Trackster alert message, reporting dbkey as blank when it cannot load chroms. Simon Guest. https://trello.com/c/lBB172Ac
  27. 245 - Adding parent_library_id field to the LibraryDataset 'to_dict' call. Kyle Ellrott. https://trello.com/c[/ZzK2ZwGz](/archive/dev-news-briefs/2014-02-10/ZzK2ZwGz/)
  28. 244 - add '[' and ']' to mapped strings and advanced filters. Björn Grüning. https://trello.com/c/n3Hv0CzW
  29. 242 - Fix routing to tools API when id has slashes in name. Kyle Ellrott. https://trello.com/c[/DmOinKwh](/archive/dev-news-briefs/2014-02-10/DmOinKwh/)
  30. 239 - Add name column to FASTA header in extract_genomic_context tool. Björn Grüning. https://trello.com/c/g2q9gKv0
  31. 243 - Add output_name to tool API response. Kyle Ellrott. https://trello.com/c/9OuLgGnN
  32. 241 - Fix missing import in search.py. Kyle Ellrott. https://trello.com/c/teXGjfJ2
  33. 249 - Tool Shed: Allow more actions after setup_r_environment. Björn Grüning. https://trello.com/c/LZhF6trH
  34. 252 - Tool Shed: Implement setup_perl_environment. Björn Grüning. https://trello.com/c/Sld7OZPL
  35. 248 - Tool Shed: Add more env vars to the standard env.sh file and allow more actions after setup_ruby_environment. Björn Grüning. https://trello.com/c/2amdMp4N
  36. 250 - Tool Shed: Add additional ENV vars from parent repository to child repository. Björn Grüning. https://trello.com/c/7ilpGljG

# Fixes
  1. Fix function to unshare a history that has been shared with you. https://trello.com/c/wqQua5V4
  2. Fix internal server error while loading Admin/quotas. https://trello.com/c/XFHzPmlK
  3. Fix Page buttons for included histories. https://trello.com/c/BiAQqDGN
  4. Fix tabular data not displaying in main panel. https://trello.com/c/it0oXXeT
  5. Fix transitory issue where action button clicks resulted in 2 http requests in Firefox. https://trello.com/c/WQL7EUlB
  6. Fix the server error thrown when sorting the forms grid. https://trello.com/c[/AnLyZo6x](/archive/dev-news-briefs/2014-02-10/AnLyZo6x/)
  7. Fix error from updating an installed data manager tool, when managing local data. https://trello.com/c/4dgIdWMp
  8. Fix history options menu broken in IE 9. https://trello.com/c/ii2Zh8na
  9. Fix to add new error message when GMAJ applet doesn't load (when Java not enabled in browser). https://trello.com/c/XTF1iwVN
  10. Fix for when loading api/tools/ didn't provide list of tools. https://trello.com/c[/Dv3Eyl](/archive/dev-news-briefs/2014-02-10/Dv3Eyl/)DP
  11. Fix to keep migration process from repeatedly asking you to migrate the tools - even after you have ignored the request once (if separate tool shed install database is used). https://trello.com/c[/Q7N5k6z](/archive/dev-news-briefs/2014-02-10/Q7N5k6z/)C
  12. Fix bug in Chrome where upload & login breaks due to multi-instance cookie. https://trello.com/c/9ZHao10X
  13. Fix base_panels.mako, ajaxSubmit and uncalled callbacks with added 'print' statements. https://trello.com/c/ZBpn7PtZ
  14. Fix to disallow shared workflows from being inappropriately deletable. https://trello.com/c[/EdKsl](/archive/dev-news-briefs/2014-02-10/EdKsl/)JDn

# Tool Shed

Tool Shed

Tool Migration Framework

Also see above: New Tool Migrations

  1. Tags corrected: 11 tools migrated to Tool Shed contained spurious 'version=1.0.0' attribute. https://trello.com/c/2GklJHZi
  2. Implemented the ability to easily migrate a set of repositories from a tool shed to another tool shed. https://trello.com/c/J0MKjYZt

Repositories

  1. New Tool Shed repo categories. https://trello.com/c/niCdaARH
  2. Enable easier tool upgrade process. https://trello.com/c/ct8YoJbf
  3. Add the ability for a repository owner to grant administrative privileges on their repository in the tool shed to other users. https://trello.com/c/guOeL1sF
  4. Correct installing new ruby dependencies with sourcing parent env.sh files. https://trello.com/c/Skcie86c
  5. Multi-select email alerts functional again. https://trello.com/c/ek558LLb
  6. Eliminate the recently introduced restriction on uninstalling repositories that are dependencies of other installed repositories. https://trello.com/c/4sGGB0SV
  7. Attempting to create a new tool panel section when installing tool shed repositories via the Galaxy API no longer fails. https://trello.com/c/0olcmogN
  8. Enhance setting repository metadata in the tool shed. https://trello.com/c/NhiygNQx
  9. "Latest revision" links now display all repositories. https://trello.com/c/kP4qm8RE
  10. Enhance the Galaxy repository uninstallation process. https://trello.com/c/SqdKVl2e
  11. Enhanced check prevents a new repository from being created with the same name as a deleted repository. https://trello.com/c/fUuUNRwt
  12. Tool shed listings confirmed to include last updated date and other ways for the viewer to determine currency of the wrapper. https://trello.com/c/qyknuE7L https://trello.com/c[/IwwSjI3m](/archive/dev-news-briefs/2014-02-10/IwwSjI3m/)
  13. Display message on Manage / View repository page in the tool shed if repository has repository dependencies that are deprecated. https://trello.com/c/EZuWhamr
  14. Dev Team owned repo updates

Install and Test Framework

  1. Several automated test framework fixes. https://trello.com/c/QWgsgll8
  2. Tool Shed now tests installation of packages. https://trello.com/c/HVGrShnC
  3. Captured "Tests that passed successfully" missing in "Automated tool test results" (Tool Shed regression). https://trello.com/c/ATclFLVH
  4. Allow storing tool test results in the install and test framework. https://trello.com/c/8vEp2fXv
  5. New functional test script covers capsule containing 2 repositories defining circular dependencies. https://trello.com/c/WOlpbijA
  6. Enhanced the install and test script to not use the framework to uninstall repositories that have been tested. https://trello.com/c/5fdwINOw
  7. Eliminate deleted repositories from automated tests. https://trello.com/c/uNOpaByz
  8. Improve form submission in the install and test framework's install method. https://trello.com/c/NVTlYc0t
  9. Added functional tests to check the datatypes registry's handling of tool shed repository datatypes and sniffers. https://trello.com/c/3GxawYIl
  10. New process cleans up empty tool dependency installation paths in the main and test tool dependency S3 buckets used for the repository installation and testing framework. https://trello.com/c/diCzpR7Q
  11. New functional tests for exporting and importing repository capsules. https://trello.com/c/ddPfpQcE
  12. New Functional tests for validating tool dependency definitions. https://trello.com/c/SAYhd2hx
  13. Enhance cron script for checking repositories for functional tests. https://trello.com/c/mYflXtiR
  14. Functional tests for missing env.sh files re. complex repository dependencies. https://trello.com/c/hePIlUtK

Fixes

  1. Fix grid message persistence. https://trello.com/c/im9XsLan
  2. Resolved bug in install and test framework linked to SAMtools dependency. https://trello.com/c/sN2iLCCn
  3. Fix to remove ghost folder in an old repository. https://trello.com/c/aQKWw8sn
  4. Fix admin view manage roles grid where negative values caused server errors. https://trello.com/c/oVdyX9AK
  5. Fix admin view manage roles grid where search caused server error. https://trello.com/c/BYyj6zJf
  6. Remove temporary directories created by the tool shed code. https://trello.com/c/A2YUuCs2
  7. Restore files from test-data/ that were incorrectly removed during a tool migration. https://trello.com/c/nx5Q1JSw
  8. Images now displayed in "Installed tool shed repositories" page when using proxy-prefix. https://trello.com/c/iMQoElrE


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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.

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