*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/
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*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/*.
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