- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Update on Qiime in Galaxy?
by Oksana Korol 19 May '16

19 May '16

Hey Bjoern, I've just started learning qiime, so probably not the best person to write tests / do clean up at the moment. Galaxy tool would have made my life much easier, by way of figuring out this beast :). Oksana Hi Oksana, > > afaik a few more tests would be nice: > > https://github.com/galaxyproject/tools-iuc/pull/431 > > But it looks more a less good. > If you want to do the final cleanup, this PR is probably ready to merge. > > > Thanks! > Bjoern > > P.S. CC Bérénice as she was working on it as well > >

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Update on Qiime in Galaxy?
by Oksana Korol 19 May '16

19 May '16

Hi galaxy tool development team and community, In the recent metagenomics hackathon it looks like there has been lots of good work done on qiime. What is the status on the tools in qiime branch of iuc repo: https://github.com/galaxyproject/tools-iuc/tree/qiime/tools/qiime? I can see that the package the tools depend on ( package_python_2_7_qiime_1_9_1) is already available on main toolshed. What is the plan for making the wrappers, that depend on this package, available on main toolshed as well? Thanks a bunch! -- :: Oksana Korol

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The Galaxy release 16.04 is out !!!
by Jennifer Hillman-Jackson 18 May '16

18 May '16

Dear Community, *The Galaxy Committers team <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organiz…> is pleased to announce the April 2016 (v 16.04 <https://docs.galaxyproject.org/en/master/releases/16.04_announce.html>) release of Galaxy.* Please note that Python 2.6 is no longer supported as of this release. See the 16.01 release announcement <https://wiki.galaxyproject.org/News/2016_01_GalaxyRelease> for details. *Highlights* [image: Inline image 1] - *New* % git clone -b master https://github.com/galaxyproject/galaxy.git - *Update to latest stable release* % git checkout master && pull --ff-only origin master - *Update to this exact version* % hg update latest_16.04 See the Admin <http://usegalaxy.org> wiki for additional details regarding the source code locations. *Thanks for using Galaxy!* The Galaxy team <https://wiki.galaxyproject.org/GalaxyTeam> -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org

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Removing stale references from a history
by Scott Szakonyi 18 May '16

18 May '16

Hello, Due to some problems on our servers, one of our users has file references that are no longer valid in one of his histories. He's requested that I remove them, but I don't see any particular way to do so through the interface. Is there any way to achieve this? I've poked around in the database but don't see any obvious link between the history and data files. Thanks in advance, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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LDAP not working release 16_01
by Mohamed Kassam 18 May '16

18 May '16

Dear all, I updated my galaxy this mornig to the release 16_01. But now my LDAP connection is nort working I have this error galaxy.auth.providers.ldap_ad DEBUG 2016-05-17 15:23:38,681 LDAP authenticate: could not load ldap module Do you have any idea, I checked the auth_conf.xml and it is still the same as the previous one. Mohamed

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Ordering dropdown Database/Build
by Scott Szakonyi 17 May '16

17 May '16

Hello, As we're indexing files through the data manager (bwa), we're noticing that they're appearing at the bottom of the dropdown, and are not ordered nicely like the default members of the list. Is there any way to order all the members of this dropdown? I've tried pushing back into the code but haven't had any luck finding out how that list is generated so far. Screenshot follows: [image: Inline image 1] Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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galaxy.masthead.js change
by Mohamed Kassam 17 May '16

17 May '16

Dear all, I would like to know which file replaced the galaxy.masthead.js file. Because I was putting in the banner the name and the logo of our local galaxy. Best regards, Mohamed

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Any tool that uses Composite Datatypes
by Ziphozakhe Mashologu 16 May '16

16 May '16

Hi All I am creating a database (neo4j) composite datatype in galaxy. The database has files flat files within a directory. Is there a tool anyone can point me to, that defines, uses/produces a composite datatype as output to use as an example? You assistance will be highly appreciated. Zipho

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GCC2016 Deadlines this Friday & Conference schedule
by Dave Clements 16 May '16

16 May '16

Hello all, This is just a reminder that* there are some key deadlines this Friday, May 20:* - Early registration ends <https://gcc2016.iu.edu/registration/index.php>. After Friday registration rates go up by over 40%. - Poster abstracts <https://gcc2016.iu.edu/abstracts/index.php> are due. - Demo abstracts <https://gcc2016.iu.edu/abstracts/index.php> are due. These are new this year and can complement a poster abstract or stand on their own. If you are wondering what's happening at GCC2016, the training and conference schedules <https://gcc16.sched.org/> are now online, featuring 21 accepted talks <https://gcc16.sched.org/overview/type/Conference> and 31 training sessions <https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any>. And, thanks to Jetstream <http://jetstream-cloud.org/> IU's newest National Science Foundation-funded project (and in which Galaxy is a partner), and the National Center for Genome Analysis Support <http://ncgas.org/> at IU are sponsoring an opening reception on Monday evening <http://sched.co/72bN> at the IU Cyberinfrastructure Building. The first ever GCC opening reception will feature local wine/beer, morsels from local eateries, and demonstrations of the 15 million+ pixel IQ-Wall, IU's Data Center, Science on a Sphere, and other IU-centric IT. Hope to see you there, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Cufflinks version
by Gaye Saginc 16 May '16

16 May '16

Hi, Which Cufflinks version is used in Galaxy? On top of the Cufflinks page it is stated " *Cufflinks*transcript assembly and FPKM (RPKM) estimates for RNA-Seq data (Galaxy Version 2.2.1.0) ". Is this the version of Galaxy or the Cufflinks tool? Thank you! Gaye

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