galaxy-user March 2014

galaxy-user@lists.galaxyproject.org

32 participants
34 discussions

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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question history
by Liesbeth Van Rompay 01 Apr '14

01 Apr '14

Hi, Although I am occupying 91% of my space on the Galaxy platform, since Galaxy was out, I cannot access my history anymore. No error message appears. What can I do? Best regards, Liesbeth

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Job of format conversion waiting for over 5 days
by Eduardo Fox 31 Mar '14

31 Mar '14

Hello, Please I would like to know if it would be normal of a job to be queued for several days? It is a SAM to BAM conversion, and it has been waiting for over 5 days to run. I understand that the SAM file is pretty large but other similar conversions I made on the server recently were done within few minutes. Thanks! -- Eduardo G. P. Fox http://eduardofox.blogspot.com.br/ http://www.mendeley.com/profiles/eduardo-fox/

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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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error while running Intogen.
by do kadya 28 Mar '14

28 Mar '14

Respected Sir / Ma'am, I was running Intogen using galaxy, I changes parameters name and then this error came. Can you please tell what is the meaning of this error ? Traceback (most recent call last): File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 123, in prepare_job job_wrapper.prepare() File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/__init__.py", line 702, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/tools/__init__.py", line 2639, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/ganit/galaxy_work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1395998029_86_91764.py", line 100, in respond NotFound: cannot find 'fimpact'

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Globus World 2014
by Ravi K Madduri 28 Mar '14

28 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 27 Mar '14

27 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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galaxy-user March 2014