[galaxy-announce] April 14, 2014 Galaxy Distribution News Brief

*April 14, 2013 Galaxy Distribution News Brief*

Distribution Summary 2014_04_14 https://wiki.galaxyproject.org/News/2014_04_14_Galaxy_Distribution

* Highlights:*

* Visualization framework updates and Trackster updates * Tool Shed updates to repos, test frameworks, and documentation * Over 100 genomes with updated content on our rsync server * UI Dataset action controls expanded and overall unification of design * API functionality additions and new job control/admin abilities * Administrator, Configuration, Job control, and Egg features and updates * 18 new community contributions added

Get Galaxy

getgalaxy http://getgalaxy.org/

*getgalaxy.org http://wiki.galaxyproject.org/Admin/Get%20Galaxy*

*galaxy-dist.readthedocs.org http://galaxy-dist.readthedocs.org/*

*bitbucket.org/galaxy/galaxy-dist http://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

*

*Review instructions for core build:Getting the Stable Distribution http://getgalaxy.org/*

*

*Review reset for Tool Shed repos:Resetting Metadata For Installed Repositories http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories*

Data

1.

New and updated reference genomes added toRsych https://wiki.galaxyproject.org/Admin/UseGalaxyRsyncserver that mirrors contents of the public Mainhttp://usegalaxy.org http://usegalaxy.org/instance

* New/updated genomes: 115 o includes hg38 o 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 2.

MAF hg19 100waymultiz conservation alignment sourced fromUCSC http://genome.ucsc.edu/

3.

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 tuninghttps://trello.com/c/kdhJ1Dit

2.

/Trackster/:

*

Sow complete read/feature across tile boundaries, in all tileshttps://trello.com/c/Q03dC1QC

*

Better handling of deep coverage regions in read trackshttps://trello.com/c/TxxzqWNx

Workflows

1.

Prep for dataset collections: Refactor out common logic for running workflows across controllershttps://trello.com/c/pdGNjllH

UI

1. New/Updated Dataset Action Controls: * Located at the top of the history pane * Ability to select: all, none, or check individual datasets * Actions: Hide, Unhide, Delete, Undelete, Permanently delete (Purge) *

https://wiki.galaxyproject.org/Learn/Managing%20Datasets#Searching_Datasets

* Additional actions pending review/implementation *

https://trello.com/c/8gLGPzxV,https://trello.com/c/mq1m6X5M,

2.

When multiple tool versions installed, default to the latest versionhttps://trello.com/c/zRBZ9nvD

3.

Better handling when one of many versions of a tool repo is uninstalledhttps://trello.com/c/BmdG2201

4.

Unify the places where histories are shown and used: UI view and in core codehttps://trello.com/c/7cN0nmKH

5.

Configure workflow menu, improve buttons and stylinghttps://trello.com/c/xFzp3lt6

6.

Handle disabled sessionStorage/localStorage more gracefully in the history panehttps://trello.com/c/V2VCxzmx

7.

RemoveBaseViewfrom base-mvchttps://trello.com/c/xUV4qvIc

8.

Do not serve non-HTML content that may containJavaScriptin such a way that web browsers execute ithttps://trello.com/c/G67ELiMI

9.

There are now 2 interfaces to data libraries (the original and new Beta) and feedback is welcomedhttps://trello.com/c/d3muKvqr

10.

Wiki page on how to compile the css.https://wiki.galaxyproject.org/Develop/CSShttps://trello.com/c/gLI6hUjN

API

1. New functions: *

Make histories importable and/or published via the API is now implimented (sharing with individual users a pending feature update)https://trello.com/c/Bcsadi1q

*

History export/importhttps://trello.com/c/qhu1KdWU

*

Ability to extract workflow from a history to workflowshttps://trello.com/c/ZTehdMZH

2.

Improved history payload and returned error consistencyhttps://trello.com/c/fWC7WgQf

3.

Checkftypeattribute (if defined) on test output datasetshttps://trello.com/c/hFFlM4gY

4.

Published histories contents now fully accessible (no permissions issue)https://trello.com/c/KME3ZRRY

5.

Correct exception formats used in history & HDAhttps://trello.com/c/bS9wY4Ri

Core

1.

Admin: History view, allow importing purged datasetshttps://trello.com/c/tbhpQdMF

2.

Admin: User list, show 'activated' and 'create_time' columnshttps://trello.com/c/C6MhEHWo

3.

Admin: Setting user quota at zero is now permitted (noZeroDivisionError http://moinmo.in/ZeroDivisionError)https://trello.com/c/38NoBtlL

4.

Admin: Admin user now has permissions to copy datasets from any history to a libraryhttps://trello.com/c/Ed91qIUC

5.

Admin: Improvements to 'Impersonate User' implementationhttps://trello.com/c/lny2me4u

6.

Config: Renametool-data/shared/ucsc/ucsc_build_sites.txttoucsc_build_sites.txt.sample

7.

Jobs: Prevent 'unicode' strings being sent to pbs library as hostnamehttps://trello.com/c/NlFXYDta

8.

Jobs: Fix Torque CLI runner to recognize complete ('C') state as 'ok'https://trello.com/c/vSO52k17

9.

Jobs: Are now cancelled if a running history item is deleted (via API).https://trello.com/c/PDmUdtbw

10.

LWR: Several updates including communication via message queue, more plannedhttps://trello.com/c/6DcXqXNt

11.

LWR: Introduce and extend along withComputeEnvironment, to eliminate string based path rewritinghttps://trello.com/c/dL0poowc

12.

Egg Update: Guppy 0.1.9+https://trello.com/c/zeSnHEav

13.

Egg Update: Boto 2.25 to facilitate launching into VPChttps://trello.com/c/QXfJQhlS

14.

Egg Addition: PyYAML 3.10 to be used initially withCloudlaunchfor parsingpersistent_data yamlhttps://trello.com/c/JMZkqBtH

15.

Lib: package_libpng_1_6_7 deprecated, replaced with package_libpng_1_6_8https://trello.com/c/Wr5U8laVhttps://trello.com/c/65DOL7PL

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/JaC2EBM8

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 Johnsonhttps://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

9.

325 - Useplaceholderinstead ofvaluein 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

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 Ellrotthttps://trello.com/c/BrOscqTJ

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 Lihttps://trello.com/c/WMgr8Xx0https://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 entryhttps://trello.com/c/6nJIhOdJ

2.

Fix issue when multiple versions of the same tool installed results in separate entries in the tool panelhttps://trello.com/c/SlNI79mR

3.

Fix Published Page's JS errorhttps://trello.com/c/yGw1DwwM

4.

Fix error in Babel egg utf-8, OSX 10.7https://trello.com/c/PUdh6SWw

5.

Fix failures when using unicode in History name editable_text fieldshttps://trello.com/c/MTdotrHR

6.

Fix tool form image display for toolshed installed toolshttps://trello.com/c/5G6jlB4B

7.

Fix to improve link format in user activation emailshttps://trello.com/c/JALX9DL3

8.

Fix problem with rerun of tools havingDataToolParameter http://moinmo.in/DataToolParameterset as optionalhttps://trello.com/c/pzHcSGzK

9.

Fix bug in Tool Panel when installing repositorieshttps://trello.com/c/AiUefffC

Tool Shed

Documentation

1.

Reorganization of the Tool Shed wiki is underway! See current changeshttps://wiki.galaxyproject.org/ToolShedand what is next uphttps://trello.com/c/Gg0jnll7

2.

Data Manager documentation specific to toolshedhttp://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_rep...

Repositories

1.

New Tool Shed categorieshttps://trello.com/c/niCdaARH

* Genome-Wide Association Study * Imaging * RNA 2.

Eliminate the use of fabric as the installation process for repositorieshttps://trello.com/c/zJoRROvv

3.

Enhancements for updating a repositoryhttps://trello.com/c/c4Y9t7db

* Will now trigger the install of new dependencies * Handles newly defined repository dependencies included in updates to installed repositories 4.

Add support for the new repository type: Repository suite definitionhttps://trello.com/c/sxXMmfLs

5.

Defined a base set of utilities that can be expected to be on systems into which tool dependencies are being installedhttps://trello.com/c/gYlRdqwr, related to project-in-planninghttps://trello.com/c/7VTlX9rD

6.

Dependency ez_setup.py added to keep package_pysam_0_7_7 from failing on tool shedhttps://trello.com/c/AkACDWix

7.

Update Main Tool Shed Picard repo that contained invalid toolshttps://trello.com/c/mxxHWxLY

8.

UpdateFreeBayesrepo so that it specifies precompiled binaries in dependency definitionhttps://trello.com/c/zYoVHKoV

9.

Update EMBOSS repo so that it downloads a precompiled platform-specific binaryhttps://trello.com/c/iW3Amhl5

Install and Test Framework

1.

Tool shed install and test framework now works with API driven tool testshttps://trello.com/c/vfr7b0VK

2.

Test script to provide coverage for recently discovered scenario that produced a white ghost upon Galaxy installhttps://trello.com/c/JICmJueB

3.

Test script to provide coverage for recently introduced repository administration featurehttps://trello.com/c/vjTrhIST

4.

Test script to check toolshed dependency files for broken/invalid download URLshttps://trello.com/c/i4GVgZwS

Tool Shed Fixes

1.

Fix setup_r_environment broken in central repohttps://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 statehttps://trello.com/c/iUDUM4Ut

3.

Fixes in automated test frameworkhttps://trello.com/c/QWgsgll8

4.

Fix bug in install and test framework related to samtools migrationhttps://trello.com/c/sN2iLCCn

Project Updates

1.

News http://wiki.galaxyproject.org/News

2.

Events http://wiki.galaxyproject.org/Events

3.

Videos on Vimeo https://vimeo.com/galaxyproject

4.

/April 2014 Galaxy Update http://wiki.galaxyproject.org/GalaxyUpdates/2014_04/

5.

/March 2014 Galaxy Update http://wiki.galaxyproject.org/GalaxyUpdates/2014_03/

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

About

*GalaxyProject.org http://galaxyproject.org/*

The*Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam*is a part of the*Center for Comparative Genomics and Bioinformatics http://www.bx.psu.edu/*at*Penn State http://www.psu.edu/*, and the*Department of Biology http://www.bio.jhu.edu/*at*Johns Hopkinis University http://www.jhu.edu/*.

*Galaxy http://usegalaxy.org/*is supported in part by*NSF http://www.nsf.gov/*,*NHGRI http://www.genome.gov/*, the*Huck Institutes of the Life Sciences http://www.huck.psu.edu/*, and*The Institute for CyberScience at Penn State http://www.ics.psu.edu/*, and*Johns Hopkins University http://www.jhu.edu/*.

The/public Main instance https://wiki.galaxyproject.org/Main/of*Galaxy*at*http://usegalaxy.org http://usegalaxy.org/*utilizes infrastructure generously provided by the*iPlant Collaborative http://www.iplantcollaborative.org/*at the*Texas Advanced Computing Center https://www.tacc.utexas.edu/*, with support from the*National Science Foundation http://www.nsf.gov/*.

Follow us on*Twitter@galaxyproject http://twitter.com/galaxyproject*or read our tweets at*Galaxy on Twitter https://wiki.galaxyproject.org/GalaxyOnTwitter*

Have a suggestion? Please see*Using the Galaxy Issue Board http://wiki.galaxyproject.org/Issues*, and be sure to up vote the issues important to YOU.