- galaxy-dev - lists.galaxyproject.org

Impersonate a User
by greg 11 Dec '12

11 Dec '12

Hi guys, I tried the impersonate a user feature, but I don't know how to stop impersonating a user? I tried going back to the impersonate a user feature and selecting myself but it's not clear if it changed anything, and I no longer see the History items I had before I did the impersonation. Thanks, Greg

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Mutation/SNP detection RNA-Seq
by suzan katie 11 Dec '12

11 Dec '12

Hi, I am trying to look mutations/SNPs in RNA-Seq data. Can anyone suggest me a workflow in Galaxy on how to detect SNPs and mutations Thanks in advance Suz

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problem with uploading data
by Banday, Abdul 11 Dec '12

11 Dec '12

Hi Nate, I loaded the file named s_6_1_sequence.txt.gz (Illumni file) under the login name abdul.banday(a)uconn.edu<mailto:abdul.banday@uconn.edu> as FTP.<ftp://ftp.R> Whenever I am trying to load it as history so that I can run it for analysis, the file upload is showing error and massage comes as data cannot be uncompressed. I have been trying to contact you guys from five days now. In one email you told me as soon as you have ftp transfer let me know. Could you check my file and see what is the problem. Thanking in anticipation. Postdoc at Uconn Rouf Banday

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Impossible to add a (new) tool in a workflow (in edition mode)
by Sarah Maman 11 Dec '12

11 Dec '12

Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the "tools" windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman

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About the output
by Chenhao 11 Dec '12

11 Dec '12

I made a galaxy tool which is just create a txt file. When I use this tool , I wish to let it show the detail of the txt. In the xml file I use : <output> <data name="test" format="txt"><output/> But it does not work, when I click the "eye" button in galaxy, a download dialog appear, but it is just a empty file. Could somebody tell me what should I do , I want show the txt detail in the galaxy.

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Public Tool Shed Error
by Adam Carr (NBI) 11 Dec '12

11 Dec '12

Hi, I have been using the tool shed recently and come across a problem. When a searching for valid tools within the Public Tool Shed, it seems that if the search should return nothing found, it is instead displaying a Server Error page instead. For example: http://toolshed.g2.bx.psu.edu/repository/find_tools?tool_name=wibble Is currently returning an HTTP status code of 500 Internal Server Error. [cid:image001.png@01CDD78F.1E47CE90] --- Adam Carr Linux Support & Developmnent E adam.carr(a)nbi.ac.uk T +44 1603 450161 W jic.ac.uk ifr.ac.uk tgac.ac.uk tsl.ac.uk NBI Partnership Ltd Norwich Research Park Norwich NR4 7UH The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory

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Displayed versions of tools in Galaxy
by Clare Sloggett 11 Dec '12

11 Dec '12

Hi guys, I wasn't sure if I should send this one to galaxy-user. I have just confused myself about the versions of tools displayed within Galaxy. If I select the TopHat tool, the tool UI says "Tophat for Illumina (version 1.5.0)". After I have run the job, the step panel in the History window says "Info: TopHat v1.4.1" If I select the Cufflinks tool, the tool UI says "Cufflinks (version 0.0.5)" After running the job, the step panel says "Info: cufflinks v1.3.0". Looking at the xml files, it does look like the version displayed before running is the wrapper and the version displayed on the resulting dataset is that of the command-line tool. <tool id="tophat" name="Tophat for Illumina" version="1.5.0">  <tool id="cufflinks" name="Cufflinks" version="0.0.5">  So looking at the XML it's very clear, but from the versions displayed in Galaxy I was completely confused, particularly since the two tophat version numbers happened to be similar (1.4.1 and 1.5.0). Maybe we should change it so that when Galaxy says "version" it is always explicit about whether it's "wrapper version" or just "version"? It also seems like there's no way for a user to discover the command-line tool version without actually running the tool (or is there)? Is this because Galaxy itself does not know this information? All this came about because I'm trying to specify to users which versions of tools my exported Workflow was built with, and I'm not sure how to do it without confusing them. Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

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Trying to Run MegaBlast
by greg 11 Dec '12

11 Dec '12

I have a fresh install on our cluster. I'm trying to test out the Megablast tool. The problem is that nothing is listed under "against target database". Where do I get the target databases and how do I tell galaxy about them? Thanks, Greg Here's what the tool looks like: Megablast (version 1.2.0) Compare these sequences: against target database: using word size: Size of best perfect match (-word_size) report hits above this identity (-perc_identity): no cutoff if 0 set expectation value cutoff (-evalue): Filter out low complexity regions? (-dust):

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Galaxy doesn't detect the file when we add dataset to a library under Manage data libraries
by Sachit Adhikari 11 Dec '12

11 Dec '12

Hello Everyone, We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select "Copy file into Galaxy" under "Copy data into Galaxy?" option and does not detect it when we select "Link to files ..." Is this a known issue? If it is, is there any workaround to solve the issue? Thanks Regards, Sachit

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Installation issue on EC2
by Fabiano Lucchese 11 Dec '12

11 Dec '12

Hi, all. I've been trying to deploy a CloudMan/Galaxy cluster on EC2 for a couple of days now and have been facing all kinds of unexpected weirdness's. I found out that the web-based form that automatically creates the EC2 instance uses an image that doesn`t seem to be officially supported (or at least encouraged) by the Galaxy team, so I decided to launch the instance by hand following the instructions from here: http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted Up to the point before accessing Galaxy, everything looks ok, but the service never starts. Instead, it shows up at the CloudMan Admin page as "Error" and nothing happens if I try to Stop/Start or Restart it.There's no log either. The Postgres service displays an immutable "Starting" status, while its log provides the following message: FATAL: database files are incompatible with server DETAIL: The data directory was initialized by PostgreSQL version 9.1, which is not compatible with this version 8.4.7. It does look like a messed up installation, which is quite surprising as this is supposed to be the recommended working image. Does anybody have any clue on what might be going on? Thanks in advance. F.

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