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June 2, 2014 Galaxy Distribution
by Jennifer Jackson 02 Jun '14

02 Jun '14

June 2, 2014 Galaxy Distribution <http://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution> *News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2014_06_02>**Highlights:* * Dataset Collections introduced * Changes to database build (dbkey) organization * Enhancements to Tool configuration and Workflow options * Trackster, User Interface, and Admin panel upgrades * Significant updates to Admin and Job functionality * Tool Shed repository and API additions * Data updates plus new Security features and Bug fixes * new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2014.06.02 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>* * /Thanks for using Galaxy!/ The Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam>

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June 2014 Galaxy Update Newsletter: GCC2014 registration closes in 1 week!
by Dave Clements 30 May '14

30 May '14

Hello all, The June 2014 Galaxy Update Newsletter <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06> is out! There's a lot going on in the project and the community right now. The big news for the coming month is - *GCC2014 registration closes June 6! <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#GCC2014:_June_30_-_Jul…>* - (OK, that's a lie, but after June 6, late registration rates kick in, and you really don't want to pay those.) - *GCC2014 starts June 30 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#GCC2014:_June_30_-_Jul…>!* - *The first ever GCC Hackathon starts June 28 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy_Hackathon_at_GC…>!* - After a very long and productive life, the *Galaxy-User mailing list is retiring on June 6* <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy-User_Being_Reti…>. (Don't worry. It's been replaced by Galaxy Biostar <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy-User_Being_Reti…> .) There are also at least 14 other Galaxy related events <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Other_Events> in the next two months in Thailand, Canada, France, the United States, Italy, the Netherlands, Australia, and Brazil. And, in the past month there were: - 49 new papers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#New_Papers> - One new public server (deepTools) <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#New_Public_Servers> - One new Galaxy deployment description (deepTools) <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy_Community_Hubs> - and a stunning number of ToolShed contributions <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#ToolShed_Contributions> Please let us know if you have anything to include in the July newsletter, and we will see you in Baltimore! Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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GCC2014 Early Registration closes this Friday, May 23
by Dave Clements 19 May '14

19 May '14

Hello all, This just a reminder that early registration<https://wiki.galaxyproject.org/Events/GCC2014/Register> for the 2014 Galaxy Community Conference (GCC2014)<https://wiki.galaxyproject.org/Events/GCC2014> *closes this Friday, May 23* Register early and *avoid paying 70% more for regular registration costs.* Early registration is downright affordable, with combined registration (Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main meeting) starting at $140 for post-docs and students. Registering early assures you a place at the conference and also a spot in the Training Day workshops<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay>you want to attend. And ... - The program <https://wiki.galaxyproject.org/Events/GCC2014/Program> , and abstracts <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> for all accepted talks are now available. - Registration for the GCC2014 hackathon<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon> is also open (and also has limited capacity - register for that now too<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon> ) - We are pleased to have Penguin Computing<http://www.penguincomputing.com/>as a Silver Sponsor for GCC2014 You are strongly encouraged to register this week. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Thanks a bunch, and hope to see you in Baltimore! Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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May 2014 Galaxy News Update
by Dave Clements 30 Apr '14

30 Apr '14

Hello all, The May 2014 Galaxy Update Newsletter<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05> is out! There's a lot going on in the project and the community right now. The big news in the past month is the move from the Galaxy-User mailing list to Galaxy Biostar<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Biostar> for user support. This has been running for a week now, and has been very well received. The other big news is upcoming events. *Early registration for GCC2013 closes May 23 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#GCC2014:_June_30_-_Jul…>* . Register now <https://wiki.galaxyproject.org/Events/GCC2014/Register> and save more than 70% on registration costs, and Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> registration is an additional 55% off if you register for both at the same time. We are also pleased to announce this year's keynote speaker<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Keynote_Speaker:_Steve…> and the first ever GCC Hackathon<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Hackathon_at_GC…> . There's also a Galaxy UK Tour<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#UK_May_2014_Galaxy_Tour> which is visiting Norwich and Edinburgh in May, and there are at least 17 other Galaxy related events<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Other_Events> in the next 70 days in Norway, France, *online*, Croatia, Thailand, Canada, the US, the Netherlands, and Australia As always, there are new papers<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Papers> (47 of them, including four we highlighted), new public Galaxy Servers<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Public_Servers> (Globus Genomics Proteomics<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Globus_Genomics_Proteo…> and SunLab Galaxy<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#SunLab> ), new jobs<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Who.27s_Hiring> (7 postings in 6 countries), new tools in the project ToolShed<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Project_ToolShe…> (um, *lots*), and a new public ToolShed<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Public_Tool_Sheds> (at the Dutch Techcentre for Life Sciences (DTL) <http://www.dtls.nl/dtl/>. Dave Clements and the Galaxy Team<https://wiki.galaxyproject.org/GalaxyTeam> http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Announcing the Galaxy Biostar Forum
by Jennifer Jackson 23 Apr '14

23 Apr '14

Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on usegalaxy.org, a Cloudman instance, or any other Galaxy, if you have something to say about Using Galaxy, this is the place to do it! Current integration with usegalaxy.org * We imported the whole history of galaxy-user(a)bx.psu.edu mailing list into Biostar * If you access Galaxy Biostar from usegalaxy.org (menu Help/Galaxy Biostar) you will be automatically logged in. * A Galaxy Biostar account will be created for you if it did not previously exist. To obtain this account’s password please use the password reset feature of Galaxy Biostar (https://biostar.usegalaxy.org/accounts/password/reset/) * When you have a question, search Biostar directly from any Galaxy tool page. Read more about how to get started at https://wiki.galaxyproject.org/Support/Biostar Roll-out phase * Galaxy Biostar is available at http://biostar.usegalaxy.org and will be our primary avenue for support * The galaxy-user(a)bx.psu.edu mailing list will continue to be supported during the transition but starting now please use the biostar.usegalaxy.org forum to ask all questions about using Galaxy. * Please do not double post to both Galaxy Biostar and galaxy-user(a)bx.psu.edu * Send us feedback through the forum's post "Welcome to Biostar" to tell us what you think. What’s next * Notice will be given when the galaxy-user(a)bx.psu.edu mailing list is retired. * Archives of galaxy-user(a)bx.psu.edu will remain accessible. We hope you will like the change and look forward to any feedback you may have. Thank you for using Galaxy! The Galaxy team

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Announcing the Galaxy Biostar Forum
by Jennifer Jackson 23 Apr '14

23 Apr '14

* Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org <https://biostar.usegalaxy.org/>! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on *usegalaxy.org <http://usegalaxy.org>*, a***<https://usegalaxy.org/cloud>**Cloudman <http://usegalaxy.org/cloud> *instance, or any other <https://wiki.galaxyproject.org/PublicGalaxyServers> *Galaxy <http://getgalaxy.org>*, if you have something to say about Using Galaxy, this is the place to do it! Current integration with usegalaxy.org * We imported the whole history of galaxy-user(a)bx.psu.edu mailing list into Biostar * If you access Galaxy Biostar from *usegalaxy.org* <http://usegalaxy.org> (Top*m*enu: "Help ->Galaxy Biostar")you will be automatically logged in. A Galaxy Biostar account will be created for you if it did not previously exist. To obtain this account's password please use the password reset feature of Galaxy Biostar (https://biostar.usegalaxy.org/accounts/password/reset/) * When you have a question, search Biostar directly from any Galaxy tool page. Read more about how to get startedat https://wiki.galaxyproject.org/Support/Biostar Roll-out phase * Galaxy Biostar is available at *http://biostar.usegalaxy.org*and will be our primary avenue for support * The galaxy-user(a)bx.psu.edu mailing list will continue to be supported during the transitionbut starting now please use the biostar.usegalaxy.org <http://biostar.usegalaxy.org>forumto ask all questions about using Galaxy. * Please do not double postto both Galaxy Biostar and galaxy-user(a)bx.psu.edu * Send us feedback through the forum's post *"Welcome to Biostar"* to tell us what you think. What's next * Notice will be given when the galaxy-user(a)bx.psu.edu mailing list is retired. * Archives of galaxy-user(a)bx.psu.edu will remain accessible. We hope you will like the change and look forward to any feedback you may have. Thank you for using Galaxy! *Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam>* *

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GCC2014 Poster Abstracts due April 25, THIS FRIDAY
by Dave Clements 21 Apr '14

21 Apr '14

Hello all, This is just a reminder that poster abstracts for the 2014 Galaxy Community Conference (GCC2014) *are due this Friday. * Abstracts can be submitted at https://wiki.galaxyproject.org/Events/GCC2014/Abstracts Note that posters are reviewed and accepted on a rolling basis, until all slots are full. The deadline is this Friday but sooner may be better. In other news: - We are delighted to have Steven Salzberg as the keynote speaker<https://wiki.galaxyproject.org/Events/GCC2014#Keynote_Speaker> . - Registration for the GCC2014 hackathon<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon>is now open - Early registration<https://wiki.galaxyproject.org/Events/GCC2014/Register>for the GCC2014 Training Day and Meeting<https://wiki.galaxyproject.org/Events/GCC2014/Program>are also open - Abstracts <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>for accepted talks will start showing up on the website this week. Thanks, and hope to see you in Baltimore, Dave C On Fri, Feb 14, 2014 at 1:33 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hello all, > > *We are pleased to announce that Early Registration > <https://wiki.galaxyproject.org/Events/GCC2014/Register> and Talk and > Poster Abstract Submission > <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> are now open for > the 2014 Galaxy Community Conference (GCC2014) > <https://wiki.galaxyproject.org/Events/GCC2014>.* > > GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014> will be held at > the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…>of Johns > Hopkins University <http://jhu.edu>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>, > United States, from June 30 through July 2, 2014. GCC2014<https://wiki.galaxyproject.org/Events/GCC2014>starts with a Training > Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring > four *five* parallel tracks, each with three, two and half hour long > workshops. There are 13 different topics spanning the full Galactic > spectrum of topics. Take a look!<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> > > *Early registration > <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open. > Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training > Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main > meeting) starting at $140 for post-docs and students. Registration is > capped this year at 250 participants, *and we expect to hit that limit*. > Registering early assures you a place at the conference and also a spot in > the Training Day workshops you want to attend. > > You can also book affordable conference housing at the same time you > register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics>for details on this and other housing options. > > *Abstract submission > <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral > presentations and posters is also open. Abstract submission for oral > presentations closes April 4, while poster submission closes April 25. > Poster authors will be notified of acceptance status within two weeks of > submission, while presentation authors will be notified no later than May2. > *Please consider presenting your work. If you are dealing with big > biological data, then this meeting wants to hear about your work.* > > The *GigaScience <http://www.gigasciencejournal.com/>* "Galaxy: Data > Intensive and Reproducible Research" series announced for the last > conference has published its first papers<http://www.gigasciencejournal.com/series/Galaxy>, > *and is continuing to take submissions for this year's meeting and beyond*. > BGI is also continuing to cover the article processing charges until the > end of the year, and for more information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibilit…>. > > > Thanks, and hope to see you in Baltimore! > > The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Galaxy Hackathon at GCC2014
by Dannon Baker 17 Apr '14

17 Apr '14

Galaxy has a fantastic developer community, from the very active mailing lists and #galaxyproject IRC channel to individuals who have submitted literally hundreds of pull requests and patches. We are always looking for ways to interact with existing community members and get even more people involved. To that end, we’re thrilled to officially announce the very first Galaxy Hackathon (http://bit.ly/gcc2014hack) The hackathon will be a three day event taking place at Johns Hopkins immediately preceding GCC2014 from June 28th-30th. Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or Cloudman!) with other folks? The Galaxy Hackathon will be a great opportunity to meet and work closely with other community and Galaxy Team members over the course of three days, culminating in some really great improvements and new features to show off at the Galaxy Community Conference afterward. Participation in the hackathon itself is completely free, but there's limited space so if you're interested and would like to participate please go ahead and book both your lodging and hackathon seat at http://bit.ly/gcc2014hackreg. To help organize ideas and people into more concrete projects, we've also set up a hackathon-specific Trello board that we'd love for everyone to go ahead and start using at https://trello.com/b/3YgU637b/gcc2014-hackathon. The board is public and open to commentary and voting, but to create new cards you’ll need to be added as a member so please note the instructions on the board for that. Finally, we are very happy to have Curoverse (https://curoverse.com) on board as the exclusive Peta level sponsor of the hackathon. If you know of any other group that might be interested in sponsoring at the Giga level please let us know. We hope to see you in June, and can't wait to see what we can accomplish! -Dannon Baker on behalf of the GCC2014 Hackathon Organizing Committee

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April 14, 2014 Galaxy Distribution News Brief
by Jennifer Jackson 15 Apr '14

15 Apr '14

*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/65DOL… 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… 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

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April 2014 Galaxy Update Newsletter: GCC2014 Talk Abstracts due this Friday
by Dave Clements 31 Mar '14

31 Mar '14

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