May 2013 - galaxy-user - lists.galaxyproject.org

Unable to use FASTQ tool on Main over several days
by Eduardo Fox 24 May '13

24 May '13

Please, I have been unable to use any of the tools under FASTQ Tools for the last 4 days. I keep getting an error message with codes, for instance GURU MEDITATION: #376b73ae417d41f3a7c2088770e13b8f. Is this part of the platform down for some reason? Best wishes and thanks, E. Fox

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Problem to download mercurial egg
by Marc DELOGER 24 May '13

24 May '13

Hello, I tried to download several times the several egg on these following mirrors but the download is always blocked near 50%...I asked several different people and they all have the same problem : http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4… <http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4…> http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-… <http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-…> Thank you in advance, Marc DELOGER

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(no subject)
by Ianiri, Giuseppe 20 May '13

20 May '13

Hi, I have worked so far on the free web-based version of Galaxy; now I have installed Bio-Linux 7, and there is Galaxy in there as well. However, I cannot access to my data (stored on the web version of Galaxy) using Galaxy on Bio Linux. If it is possible, does anyone know how to do it? Thanks, Giuseppe Ianiri

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changing parameters in tophat
by Colaneri, Alejandro Cesar 20 May '13

20 May '13

I want to run tophat with the parameter "--no-novel-juncs genome" Where do I find the options to add this parameter? Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625

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GCC2013 Early Registration ends this Friday, 24 May
by Dave Clements 20 May '13

20 May '13

Hello all, Early registration <http://bit.ly/GCC2013Reg> for the 2013 Galaxy Community Conference (GCC2013) <http://bit.ly/gcc2013> ends this Friday, 24 May. Early registration saves *up to 75% off regular registration costs*, and is downright affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + main meeting <http://wiki.galaxyproject.org/Events/GCC2013/Program>) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynote, and lightning talks, all about high-throughput biology and the tools that support it. The conference also includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> with in-depth topic coverage of twelve different topics in 15 sessions across 5 tracks. An early program is available<http://wiki.galaxyproject.org/Events/GCC2013/Program> featuring 25 oral presentations, lightning talks and poster sessions, and the just added Birds-of-a-Feather <http://wiki.galaxyproject.org/Events/GCC2013/BoF> gatherings. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then this conference is for you. Thanks, GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> ! -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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User -> Custom Builds fail on public server
by Michael Axtell 17 May '13

17 May '13

Hello. For the last several days the Custom Builds dialog has failed on the public server (main.g2.bx.psu.edu) Specifically, User -> Custom Builds returns the 'Internal Server Error' message, and other paths to the custom builds tools similarly have been failing for me. Advice? Thanks! Mike -- Michael J. Axtell, Ph.D. Associate Professor Dept. of Biology Penn State University http://axtell-lab-psu.weebly.com

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Raw counts from Galaxy
by Els Willems 17 May '13

17 May '13

Dear all, I would like to analyse some RNA-Seq I obtained in the chicken. I am implemented the Tophat-Cufflinks pipeline in Galaxy, but I would like to obtain a raw count of the number of mappings per transcript. I have not found a way to do this in Galaxy, is this possible? Thank you very much. Regards, Els --- Ir. Els Willems KU Leuven Department of Biosystems Division Livestock - Nutrition - Quality Laboratory of Livestock Physiology Kasteelpark Arenberg 30 bus 2456 B - 3001 Heverlee T (+32) 016 32 17 29 F (+32) 016 32 19 94

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failed Tophat processing steps
by Nikolay N. 17 May '13

17 May '13

Hi, I submitted a sample for Tophat processing on the main Galaxy instance and it seems to me that that the processing of that sample has failed. The corresponding sections in the history are in red (see attached screenshot). How can I find out what has happened? I don't see any error message. Shall I simple re-submit these processing steps hoping that next time they won't fail? many thanks, Nikolay

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Duplicate Accounts on Main
by Dave Clements 17 May '13

17 May '13

Hello all, The terms of use <https://main.g2.bx.psu.edu/static/terms.html> for the Galaxy Project's free Galaxy server, http://usegalaxy.org (a.k.a. Main<http://wiki.galaxyproject.org/Main>) specify Your access to the Service is provided under the condition that you abide by any published quotas on data storage, job submissions, or any other limitations placed on the public Service. *Attempts to subvert these limits by creating multiple accounts or through any other method may result in termination of all associated accounts.* In the past we have dealt with multiple accounts on an ad-hoc basis. Moving forward we are using an automated system to detect, disable, and eventually delete duplicate accounts. If the automated system determines that your account is a duplicate, your account will be disabled and you will receive an email asking you if this is the account you wish to keep. If it is, please follow the directions in the email and your access to that account will be restored. If your account is suspended and you believe that you are not in violation of Main's terms of use, then please contact terms_and_conditions(a)galaxyproject.org. Thanks, The Galaxy Team -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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receiving an email when a processing step finishes
by Nikolay N. 17 May '13

17 May '13

Hi, I am using the main galaxy instance and have submitted several processing steps that seem to have been scheduled for execution. Is there a way to get an email notification when such a processing step finishes? many thanks, Nick

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