March 2016 - galaxy-dev - lists.galaxyproject.org

Alternative methods for external authentication
by Amelia Ireland 01 Mar '16

01 Mar '16

I'd like to set up a galaxy instance to use a custom external authentication system. The documentation has examples of using LDAP and Apache-based authentication, but I wondered if there was a more general method for hooking up a login system. Thanks! Amelia Ireland Integrated Microbial Genomics

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Missing modules after upgrade to 16.01
by C. Ch. 01 Mar '16

01 Mar '16

Hi, I've upgraded to 16.01 and have error messages indicating missing modules. This produces problems while setting the metadata. The processes run, the results are there but the history entry is in red. How can I trigger the installation of all the modules that galaxy needs with the new pip based mechanism? Thanks for the help!Cristian

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Python 2.6 Support
by Dannon Baker 01 Mar '16

01 Mar '16

We're currently discussing when we should stop supporting Python2.6 and it'd be useful to know how much this might impact local Galaxy administrators. Does anyone on the list have strong feelings or concerns about this and want to weigh in? Here's the issue on GitHub for more information and discussion: https://github.com/galaxyproject/galaxy/issues/1596 Thanks! Dannon

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March 2016 Galaxy News: GCC2016 deadlines this month, GSOC 2016, RAD-Seq Hack …
by Dave Clements 01 Mar '16

01 Mar '16

Hello all, The *March 2016 Galactic News <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03>* is hot off the presses: - *GCC2016 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#GCC2016>* news: - *Oral presentation abstracts due March 20 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#GCC2016_Abstract_Submi…>.* If you are doing work in data-intensive biology then you are strongly encourage to present your work at the conference. Oral presentations, poster presentations, and the new Visualization Showcase & Software Demos are all opportunities to share your work. - Register early <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#GCC2016_Early_Registra…> and save up to 40% off regular registration costs. Early bird prices start at less than $45 / day for post-docs and students. - Apply for a GCC2016 Scholarship <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Scholarships:_Internat…> . *Applications from international applicants are due March 20.* - The 2016 GMOD Meeting <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#GMOD_Meeting.2C_June_3…> will be held immediately following GCC2016, also at Indiana University. - And, we have a returning sponsor: Please welcome *BioTeam <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Sponsors>* to GCC2016. - *March 7-8: Online IUC Contribution Fest - RADSeq Tools and Workflows <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#March_7-8:_Online_IUC_…>* - *Galaxy in Google Summer of Code <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Galaxy_in_Google_Summe…>* - Twelve other upcoming events <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Upcoming_Events> - 54 new publications, including 4 highlighted pubs <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#New_Papers> - New jobs <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Who.27s_Hiring> - New releases <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Releases>, including the new CloudBridge <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#CloudBridge_0.1.0> and two important security announcements <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Security_Announcements> - Two new Galaxy servers <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#New_Public_Galaxy_Serv…> - New ToolShed Contributions <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#ToolShed_Contributions> Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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tmp directory
by Raphenya, Amogelang 01 Mar '16

01 Mar '16

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GATK problems with data manager
by Scott Szakonyi 01 Mar '16

01 Mar '16

Hi all, Sorry to be repetitive, but this issue is really blocking our efforts to develop the workflow that we need in our instance of Galaxy. If anyone has any familiarity with the issue described below, please let me know. I really need to get this solved. One of my co-administrators is having some issues with data indexed/processed with data managers in GATK. His email to me: Currently there is no way to load a genome into versions of GATK above version 1.4. No version seems to be able to load a reference from history and only version 1.4 seems to work with the available picard-gatk data manager. We need to be able to work with these later versions of GATK, 3.4 on the Galaxy tool shed is the latest. Thanks! Scott -- 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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novoalign in Galaxy
by Peter van Heusden 01 Mar '16

01 Mar '16

Hi there We're busy integrating novoalign in our local Galaxy - there doesn't seem to be a tool around for this, but I recall some people saying they were using (single threaded) novoalign with Galaxy. Does anyone know if tool XML has already been written? If not, we'll just have to write it. Peter

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Downgrade tool upload tool
by Makis Ladoukakis 01 Mar '16

01 Mar '16

Hello everyone, I was wondering whether it's possible to downgrade the upload tool to the previous version(1.1.4). I copied the upload.py and upload.xml scripts from a previous galaxy version to the tools/data_source/ directory and reloaded the tool as admin but it hasn't changed even when I restarted the server. Do I have to change something else in addition? Thank you, Makis

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