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3031 discussions

Globus World 2014
by Ravi K Madduri 29 Mar '14

29 Mar '14

Dear All I wanted to send a note to folks about Globus World 2014. I apologize before hand for spamming both the developer list and the users list also but I thought this may be relevant to folks on the lists. Please let me know if you have any questions. GlobusWorld is this year’s biggest gathering of all things Globus. GlobusWorld 2014 features a Using Globus Genomics to Accelerate Analysis Tutorial, and a full half day on Globus Genomicsin the main meeting, including a keynote by Nancy Cox and these accepted talks: Globus Genomics: Enabling high-throughput cloud-based analysis and management of NGS data for Translational Genomics research at Georgetown, by Yuriy Gusev, Improving next-generation sequencing variants identification in cancer genes using Globus Genomics, by Toshio Yoshimatsu Globus Genomics: A Medical Center's Bioinformatics Core Perspective, by Anoop Mayampurath Building a Low-budget Public Resource for Large-scale Proteomic Analyses, by Rama Raghavan Globus Genomics is a Globus and Galaxy based platform for genomic analysis. GlobusWorld is being held April 15-17, in Chicago. And, GCC2014 is a Silver Sponsor of GlobusWorld. -- Ravi K Madduri MCS, Argonne National Laboratory Computation Institute, University of Chicago

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Re: [galaxy-user] Trackster Error
by Jeremy Goecks 28 Mar '14

28 Mar '14

Hi Suzanne, Thanks for sharing your history. This is a file format issue on our side. We’ll get it taken care of and let you know when it’s fixed. Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University > > > On Mar 27, 2014, at 9:27 AM, Jeremy Goecks <jgoecks(a)gwu.edu> wrote: > >> Hi Suzanne, >> >> Can you share your history with me and I’ll take a look? >> >> Thanks, >> J. >> >> -- >> Jeremy Goecks >> Assistant Professor of Computational Biology >> George Washington University >> >> >> >> On Mar 24, 2014, at 5:08 PM, Suzanne Gomes <suzanneluziagomes(a)gmail.com> wrote: >> >>> Hello, >>> >>> I am trying to look at an output from Tophat using Trackster, but I keep getting the following error: >>> >>> Could not load chroms for this dbkey: dp4 >>> >>> This is not a custom dbkey - I just selected it from the list of available ones on Trackster. >>> >>> I have database/build set to: D. pseudoobscura (dp4) (dp4) for my Tophat results. >>> >>> Any ideas why this is happening and what I can do to fix it? >>> >>> Thanks >>> >>> Suzanne >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at usegalaxy.org. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> >>> http://galaxyproject.org/search/mailinglists/ >> >

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Trackster Error
by Suzanne Gomes 27 Mar '14

27 Mar '14

Hello, I am trying to look at an output from Tophat using Trackster, but I keep getting the following error: Could not load chroms for this dbkey: dp4 This is not a custom dbkey - I just selected it from the list of available ones on Trackster. I have database/build set to: D. pseudoobscura (dp4) (dp4) for my Tophat results. Any ideas why this is happening and what I can do to fix it? Thanks Suzanne

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ftp not working
by David Matthews 27 Mar '14

27 Mar '14

Hi, I'm still not able to use ftp - keeps saying connection refused either through the command line or through cyberduck - is anyone else seeing this? Best Wishes, David. _________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews(a)bristol.ac.uk

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Question regarding storage space
by Alexandre Maia 27 Mar '14

27 Mar '14

I am using Deeptools at the main public server and was adding some files initially to test. Now I have removed all my files (hidden and unhidden) and history, but my usage is still at 38%. How can I remove all the files to have a 0%? My user name is alexandre.gaspar.maia(a)gmail.com Thanks. A

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upload data to galaxy using terminal
by do kadya 26 Mar '14

26 Mar '14

Hi, Can I upload data (mostly link the data) using terminal ? MuSiC 2 tool integration is not available in their website nor in tool shed. MuSiC 2 creates folder and files by itself, which is hard to track by Galaxy. So is there any way to link files to galaxy current work space so that I can link those distracted files which are created by MuSiC 2. ex: if you run music2 bmr calc-bmr file_of_input output is 3 files, ./file1.txt ./folder1/file2.txt ./folder2/file3.txt we can not mention that we need this output filename or save file at specific location, we can not give this option. Galaxy will not able to track this output, hence i have to do it manually. So is it possible to upload this files manually by terminal ? Waiting for positive reply. Thank You - Chetan

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GCC2014 Early Registration and Abstract Submission are now OPEN!
by Dave Clements 26 Mar '14

26 Mar '14

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/

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Output file to history
by Sebastian Luna Valero 22 Mar '14

22 Mar '14

Dear All, I am trying to add a new tool in Galaxy and I have the following problem. Let me explain a simplified example. Let's imagine that my script works from CLI as follows: python script.py --input "input-file" --pattern "output-pattern" After processing "input-file", the script writes several output files and their name is given according to "output-pattern". The number of output files depends on the content of "input-file". The output files are written to the current working directory where script.py is located. In the simplest scenario, I get only one output file in the working directory. My problem is that I would like to see the output files in Galaxy's history without modifying the CLI interface. To solve this problem, I have looked at the wiki page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number… and the email here: http://dev.list.galaxyproject.org/Multiple-output-files-do-not-appear-in-hi… However, I think that mine is a different scenario. I do not want to add new output parameters in the CLI. I would like Galaxy to bring these output files to my history without modifying the CLI options, is that possible? Many thanks in advance for your help! Best regards, Sebastian.

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Usegalaxy.org network upgrade this Saturday
by Dave Clements 19 Mar '14

19 Mar '14

Hello all, Access to all TACC resources and services, including UseGalaxy.org<https://usegalaxy.org/>, will be unavailable between 9 a.m. - 5 p.m. (US Central Time) on Saturday, March 22. TACC staff will be performing an upgrade to the networking infrastructure. During this outage, users are encouraged to use the *50+ other public Galaxy servers <https://wiki.galaxyproject.org/PublicGalaxyServers>* that won't be affected by this upgrade. We apologize for any inconvenience this may cause you. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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please unsubscribe
by Bogdan Tanasa 18 Mar '14

18 Mar '14

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