[galaxy-user] 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/UseGalaxyRsync>server 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/DataToolParameter>set 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. -- Jennifer Hillman-Jackson http://galaxyproject.org