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DevNewsBriefs/2014_08_11

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Distribution Summary 2014_08_11

http://getgalaxy.org
August 11, 2014 Galaxy Distribution News Brief



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 latest_2014.08.11


Security

<!> On July 31st, we fixed a serious security vulnerability in Galaxy and notified the community. Please upgrade immediately if you haven’t done so already: Instructions

Many thanks to Inge Alexander Raknes for reporting the issue T1eldqfK. Stay connected! We both email and tweet security alerts.

New! Citations

Wiki, Authored by Björn Grüning and Peter Cock

Tools now annotate citation information. Tools annotate citations using either DOIs or raw BibTeX - these in turn are shown as formatted citations below the help text on tool forms and may be copied to reference managers as raw BibTeX. All annotated citations in a history can also be obtained using the history options menu. kY7RCnd0

New! Docker

http://wiki.galaxyproject.org/Admin/Tools/Docker

Wiki, Authored by Eric Rasche

Added tool-to-container mechanism to package dependencies that tool developers can provide as an alternative to requirements and Galaxy's tool_dependency_dir. You can now create »Dockerized« tools, meaning tools which run within a docker container. 9lGgDlOJ

Docker integration provides even greater security with Pulsar (formerly called the LWR) to expose only the staged job directory to the running container. fUOhP58d

Improved

  1. Improved data loading efficiency in Trackster through »reference-based« compression for read tracks. qoDpckp7

  2. DRMAA Python version in eggs.ini updated to 0.7.6. This version has better string handling and supports Python 3. Upgraded by Dan Blanchard. E6h7wold

  3. Added extension point to define site-specific parameters to aid defining job destinations. Based on contributions from Hector del Risco. H87LotF7

  4. Per-destination concurrency limits for jobs linked to destination or destination tag. Aids in avoiding queue bottlenecks or user »quota-exceeded« job rejections/failures. o40wcWaU

  5. Enhanced dynamic job destinations throw new JobNotReadyException to indicate delayed decision. xdf6ibmC

  6. Created higher-level utilities about job metrics and users to better track and manage priorities (i.e. do it yourself meta-fairshare). wDjPSAsy

  7. Setting user preferences, toolbox filters, and default permissions now accessible when using external authentication. AnUdQJqj

  8. Implemented unit testing for routes in Galaxy app. Allows for testing both how URLs are going to map to controllers and actions as well as testing what paths will be produced by url_for. TG5a8OHU

  9. Added sqlite datatype and corresponding dataprovider and followed up with improved sqlite whitelisting by using the sqlparse package. Developed by Ira Cooke. 2e0ulmi1 tNaEWcg7

  10. Deprecated use of the database_engine_option_strategy = threadlocal in SQLAlchemy. The option was removed from universe_wsgi.ini.sample. iXOD4vrg

  11. Added function to assign detected dataset input format based on input format (action similar to assignment of stand-alone output format). Designed by Michael Crusoe at the GCC2014 Hackathon. 8wf9mNLy F29Wu1ET

  12. Workflow PostJobActions function »Rename« now displays available tool inputs for #{input1}  as options (custom label or actual tool input id). Additional PostJobActions functions to be enhanced in future upgrades. 9HkqqTut

  13. Action "create new workflow" now opens directly into a workflow »Edit« view, after setting name and annotation. i8d5egqY

  14. Easier to use input mapping when running workflows. A new parameter 'inputs' can now be specified. Additionally, "inputs" is more flexible and can revert to the old behavior by specifying a new parameters. wzp0TcVq

  15. The workflows API now displays annotations in detail view. wJVEsJvI

  16. Enable stopping jobs when history is deleted via the API and update comments related to stopping jobs when a history is deleted using the API. Authored and tuned by Ilya Sytchev. GE7vF8lA PgiFQMMj Tbota8xG

  17. Option to delete, rather than hide, intermediate datasets in workflows through the use of PostJobActions. YfLGkJKe

  18. Ability to locate tools relative to the tool_conf file using a string through the template resolution of ${tool_conf_dir} . IABOzpVk

  19. New dataset collections prototype for creating a dataset collection of pairs (a list of N paired collections). More enhancements planned: manually pair datasets and permit re-ordering. CIIdaxl2

  20. Add API methods for copying dataset collections between histories. s5tJOmQC

  21. Allow using data collection steps via workflow API. Implement API test for this and upgrade test for previous commit related improved workflow run endpoint. 0MY3X3SG

  22. Rename LWR to Pulsar - eliminate older LWR cruft debris and provide deeper Galaxy integration and easier configuration. OO22czXz

  23. Non-daemon asynchronous LWR operation implemented along with other relevant upgrades. xjlJH3N4

  24. Update LWR client to allow configuration of file actions via YAML. jbEnWNB4

  25. Implemented Tool Shed checksums, including the dependent setup_python_environment changes. In collaboration with Björn Grüning. RG2Undyx c6oLfsli

  26. More MQ configuration for exception states in the LWR client. mUlMj6l9

  27. Changes to ensure the use of galaxy.util.json rather than json from the python libraries. Solution from Christopher Bare. U19dsyjl

  28. Add an empty_field validator to gtf2bedgraph.xml. Contributed by Björn Grüning. YBKeZeL3

  29. Tabular display improved for datasets having a large number of columns. Now fills viewable container window without additional UI scrolling. Display »chunk size« is now configurable. Request and Testing from Peter Cock. 28dasaLn 4IrKYxy6

  30. Because package_ncurses_5_9 fails to build on filesystems that don't support hardlinks, now enable symlinks by default. Developed by Björn Grüning. bIolgPxx

  31. Datasource Tools are using provided name on Job executed page (added in an earlier release). qjaaGcRg

  32. Added to Toolshed repository actions the ability to Uninstall an installed repository that is in an error state and to delete a repository that is in a "new" state. GbPdcxOp

  33. Decided to strip() the repository names from the Toolshed "create repository" form. NGUuuCRj

Fixed

  1. Fix collection for recent Tool Shed code cleanups. For example, repository installations with the API using ./scripts/api/install_tool_shed_respositories.py. Implemented by Björn Grüning. mdNIKjbV

  2. Fix for interpreter on version commands (when different from command interpreter). Tracked down by Will Holtz, patched by Peter Cock. d5AOLrGd

  3. Admin operation »Impersonate a user« now functions when using external authentication. zwqNwflD

  4. Public Galaxy Main’s Proxy is now serving for bigBed formatted datatypes correctly in external application visualization application (such as IGB). ZLH7Lowr

  5. URL <input> tag corrected (was missing parameters) to permit proper data_source interpretation, fixing problematic URL transfer for data upload. 88dgqGuA

  6. Fix issue where running a »dockerized« tool, without a local docker image, fails (only) the first time it is used. B4Sy7VyQ

  7. Fix PBS GALAXY_SLOTS configuration for torque environments explicitly defining num slots. ygMf67oE

  8. Fix to allow editing of workflows on the fly, for radio buttons, too. Modified by Saket Choudhary.Ww1pg6jX

  9. Fix workflow multi-run inside of conditional, repeats if tool form state updated (e.g. because conditional param updated or repeat block added). qUfwVlwT

  10. 103 is not 105 initial migration fix when using threadlocal strategy. OLA2j6FA

  11. Safari 6.1.4 issue with laying out flexboxes (associated with dataset collections), making dialog usable, is now fixed. tDlTsXPx

  12. Safari 7.0.4 caching external view application 302 redirect links is also fixed. optldnPm

  13. Added job_metrics_conf.xml to .hgignore. Contributed by Nicola Soranzo. FLet9NVs

  14. Fix »figshare« DOI handling in citations. Testing support from Michael Crusoe. LOfrzvGz

  15. Dataset Collection of »type paired« no longer producing an error while running a primary tool. New automated test created. u6WglV0H e7SFiWio

  16. Upload of tools to a Tool Shed with Dataset Collections and tests defined no longer fails. Contributed by Aaron Petkau. dHqGQadb

  17. Allow history panel UI to contain datasets and dataset collections with the same id. rpfCwB1X

  18. Other dataset collection bugs identified and remedied. 0OUxFFAO

  19. Fix for using $output.extra_files_path with nested object stores. May require additional tuning. Identified by Björn Grüning. a9PVThgp

  20. Close file handles for convert delimiters to tab tool. Contributed by Saket Choudhary. Qm263dGS

  21. Fix spelling mistakes in hopefully all of the install_*_environments. Tuned by Björn Grüning. 6XLCjlEc

  22. Fix shutil.move for converted files in upload.py. qH7yZfCf

  23. Correct Test Toolshed’s invalid certificate and other associated bugs. VeCcUAeb

  24. Missing images for "fastq_quality_boxplot" tool added to the repository and help references updated. i87tG6kl

  25. Modify url_for in history_contents.py to effort to avoid certain failures on Main. 05DiHiDE

  26. Tool form logic for displaying allow_remap option was inverted. Now corrected. WfpN4Pet

  27. Added back InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0. B6eddsCv

  28. Fix the 3xx redirect handler in the Toolshed's API methods to correctly handle PUT requests. oUC4DUJC

  29. Fix for exporting Toolshed repositories that contain package recipes that define additional packages needed only for compiling the dependent package. ClgcV0Sn

  30. Correction for malformed Toolshed URLs constructed if toolshed under subdirectory. doBBlYsY

  31. Resolved an issue where when working in the Toolshed, if you haven't updated packageopenbabel*, but you are updating an other package (osra for example) that depends on the new version of openbabel ... the package is installed twice. AZpDkXED

  32. Install and test framework was not locating the test-data directory for repositories on main Tool Shed for a short time window, but was quickly made functional. 9mLrFhTJ

  33. Toolshed now respects macros when parsing package version to produce warning. TeguDYSq

  34. Remedied a Toolshed option download_file that was altered with a change_working_dir function found to be not backwards compatible. CEg62Aky

  35. Fix Main Tool Shed installation errors (URL related) for repositories owned by devteam (multiple). uPaD4wLt sI1mnNLH

Gossip

  1. Did you read above that LWR was officially renamed to PULSAR ? We don’t normally tag our own, but there’s a rumor his initials are John Chilton, or was it Natefoo?

  2. Galaxy CHARTS were a big wow! on Twitter, and we thank you for that, but they didn’t make the last News Brief. Get caught up and make sure you don’t miss the full color Charts Wiki this time around !

  3. Docker, Docker, DOCKER .. chant (er, VOTE) in Trello and you shall likely receive.

  4. Psss… we migrated a few tools off Main, but they’re enjoying good company in the Toolshed until you need them. Find your favorite SOLiD mapping tools there: BWA & Bowtie

  5. And we heard that there is quite a bit of deploy and config going on over at the Galaxy Biostars forum. From where oh where will the advice come from next? Claiming one’s account is tricky - first you need to log into your Main account, next find a tool form, and then finally click a button in the upper right corner. Jump in…

  6. For more news, we'd like to share the prior two Updates:
    July 2014 Galaxy Update
    August 2014 Galaxy Update

Galactic Stars

{*} {*} {*} {*} {*} and big Thank-You to our community of contributors!

Upgrades

  1. Review instructions for core build: Getting the Stable Distribution

  2. Review reset for Toolshed repos: Resetting Metadata For Installed Repositories

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