- galaxy-user - lists.galaxyproject.org

password reminder
by c.sun＠nki.nl 10 Feb '12

10 Feb '12

Dear sir or madam, I can not receive the password reminder. Could you please help me out? Thanks in advance! Best Chong

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Production environment
by David Castillo 10 Feb '12

10 Feb '12

Hello, I've just installed Galaxy in my server in order to run it locally but there's a couple of tasks I haven't been able to complete, I hope somebody could advice me on how to accomplish them: I wanted to be able to have direct access to the contents stored in my server, so when click on 'Get Data'; 'Upload File' I can get the files stored in my server instead of the files stored in my personal computer. Is this even possible? If not, what other options do I have if I want to load heavy packages (~3 GB) without having to wait much? I haven't been able to 'Edit' Workflows like in the public server, I have been able to create them, but once I try to edit them it just attempts to load the 'Workflow Editor' but it never does. How can I solve this? Do I have to configure something before attempting to do this? Thanks in advance, David ___________________________________________________________ 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/

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user/groups/roles/permissions ???
by Bernd Jagla 09 Feb '12

09 Feb '12

Hi, I am relatively new to Galaxy and couldn't find an explaination on how you envision the concepts of users/groups/roles etc... I am managing a Galaxy instance and have different groups of biologist (users), who should all are allowed to see the data from that group. Then I have a group of users who are not super users, but still should be able to see data from different groups of biologistl; they should also be able to upload data, other should not... I would like to make sure that my understanding of groups and users is the same as that of Galaxy and also would like to find explaination and possibly example of how to use "roles" and potentially other tools. Could you please point me to where in the documentation this explained? Kind regards, Bernd

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How to get reads counts from cufflins?
by Li, Jilong (MU-Student) 09 Feb '12

09 Feb '12

Hi all, I got the normalized values (FPKM) from cufflinks. And I want to get relative reads counts. How can I do that? Another question: how does cufflinks handle isoform genes while calculating the reads counts? Or what papers can help me understand this? Thank you very much! Victor

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Tophat settings
by Jack Colicchio 08 Feb '12

08 Feb '12

In the new version of tophat they allow for over 3 mismatches in the initial alignment, however your server still gives an error if you attempt to move this over 3. This is problematic for trying to map RNAseq reads where there is moderate divergence between the RNA and the reference genome. Jack

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Re: [galaxy-user] about Mapping Quality
by Kevin Silverstein 08 Feb '12

08 Feb '12

Jeremy, This is not strictly correct. Tophat/bowtie don't report mapping quality values that are as meaningful as BWA, but there is some information in the mapping quality values tophat reports. Tophat yields 4 distinct values for its mapping quality values (you can do a "unique" count on the mapping quality field of any SAM file from tophat to verify this): 255 = unique mapping 3 = maps to 2 locations in the target 2 = maps to 3 locations 1 = maps to 4-9 locations 0 = maps to 10 or more locations. Except for the 255 case, the simple rule that was encoded by the authors is the usual phred quality scale: MapQ = -10 log10(P) Where P = probability that this mapping is NOT the correct one. The authors ignore the number of mismatches in this calculation and simply assume that if it maps to 2 locations then P = 0.5, 3 locations implies P = 2/3, 4 locations => P = 3/4 etc. As you can clearly see, then MapQ = -10 log10(0.5) = 3; -10 log10(2/3) = 1.76 (rounds to 2); -10 log10(3/4) = 1.25 (rounds to 1), etc. -Kevin Date: Tue, 7 Feb 2012 17:56:34 -0500 From: Jeremy Goecks <jeremy.goecks(a)emory.edu> To: "Li, Jilong (MU-Student)" <jl482(a)mail.missouri.edu> Cc: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> Subject: Re: [galaxy-user] about Mapping Quality Message-ID: <84AF17B7-3317-43CF-92BA-C60D17A6E037(a)emory.edu> Content-Type: text/plain; charset="us-ascii" Tophat/Bowtie does not yield mapping quality, so, as per the SAM spec, that field is set to 255, indicating that quality is unavailable. http://samtools.sourceforge.net/SAM1.pdf Best, J. On Feb 7, 2012, at 5:46 PM, Li, Jilong (MU-Student) wrote: > Hi all, > > I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file, the value of some mapping quality (the 5th column) is 255. What does it mean? And I found these reads which have mapping quality 255 mapped to unique place. > > Thanks! > > Victor > ___________________________________________________________ > 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/

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ftp server
by Sebahattin Cirak 08 Feb '12

08 Feb '12

Dear All, it states that to upload fastaQ files bigger then 2Gb to use the Galaxy FTP server, but when I log in , I can not see an access to the FTP server in order to upload it, sorry it may be trivial. Please tell me , thanks Sebahattin

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April 2012 GMOD meeting registration open
by Scott Cain 08 Feb '12

08 Feb '12

Hello, I am pleased to announce that registration is open for the April 2012 GMOD meeting The cost for the meeting is $40 if you register before March 7th and $50 after. The meeting will be held April 5-6 at Georgetown University in Washington DC, right after the Biocurator meeting. I am also pleased to announce that the keynote speaker will be Deanna Church from the NCBI. In addition to the main meeting, there will be a Galaxy workshop the evening of April 5. To register for the meeting, go to: http://gmod2012.eventbrite.com/ For more information on the meeting, go to: http://gmod.org/wiki/April_2012_GMOD_Meeting If you would like to present at the meeting, or suggest a topic for discussion, please feel free to add it to the meeting page, or email me. If you register before March 7th, you will be entered in a drawing to get some GMOD swag from CafePress. Thanks and see you in April, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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Database Function
by La Chi 08 Feb '12

08 Feb '12

hi , i have created a script which calls a database function(sub_id) and this function returns multiple columns , say its return 12 columns in database , but when i created its tool(function) in galaxy , i am able to return only 1 column(username) in galaxy tool which is not desirable result for me. i want to know how can i return all column from my database function(sub_id) and print its result in separate file(bed format) which should be shown history panel , here is my code function.py file import sys, os.path, logging from galaxy import eggs import pkg_resources from galaxy.model import * from sqlalchemy import * def load_db_values(): pkg_resources.require( "psycopg2" ) engine = create_engine('postgresql://postgres:@132.100.1.1:5432/users') connection = engine.connect() result_set = connection.execute( "select * from sub_id(5,10,10)" ) db = [] for row in result_set: db += [(row ['username'],str(row[ 'userid' ]), False),] connection.close() return db def __main__(): columns = [int(x) for x in sys.argv[1].strip().split(',')] for col in columns: print col if __name__ == "__main__": __main__() function.xml file <tool id="FA" name="function" version="2.0.0"> <description>function</description> <command interpreter="python">function.py $cols </command> <code file="function.py" /> <inputs> <param name="cols" type="select" multiple="true" display="checkboxes" label="Start" help="any help" dynamic_options="load_db_values()" > <validator type="no_options" message="You must pick at least one value." /> </param> </inputs> <outputs> <data format="bed" name="out_file1" /> </outputs> </tool> function.py and function.xml files are located in galaxy-dist/tools/user tool_config <section name="Function" id="FA"> <tool file ="user/function.xml/> </section> thanks

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How can I tell what programs are used by a tool?
by Beale, Holly (NIH/NHGRI) [F] 07 Feb '12

07 Feb '12

Hi all -- I'd like to know what programs are used when I run a tool on my data. Ideally I'd also like to know what parameters are passed to command line tools. For example, I uploaded a sam file to the main galaxy server at PSU. I ran Filter Indels. I got output. What programs were used in this manipulation? samtools mpileup? GATK? FASTX toolkit? I hope I'm missing something extremely obvious. Thanks for your help. Holly

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