- galaxy-user - lists.galaxyproject.org

hello Newbie questions about galaxy and clustering
by leconte 19 Apr '13

19 Apr '13

hello I have installed an galaxy instance for purpose testing on a 8 CPU server without problem all run perfectly. I have made some galaxy xml wrapper to understant how galaxy calls program and other little things. Now I want to install a Galaxy server with a cluster configuration. Before I have tested HTCondor but I have no Idea how I can mix Galaxy and HTCondor. The perfect thing was somebody have already tested this type of condor. But I can satisfy myself with any other cluster type. What I don't understant in fact ( maybe my worst problem ) where lie all parts of this puzzle. I explain. I know that I need Galaxy. I know too I need a cluster ( in my case HTCondor ) I understand I need something between these 2 parts ... I think something like PBS or SGE but it's not totaly clear for me I'm search on galaxy mailling list archive ... but I just found 2 mails in 2008 :( has anybody made this conf or have a configuration ? greetings PS : sorry for my poor english :)

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Fwd: [Gmod-announce] 2013 GMOD Summer School: Apply now!
by Dave Clements 17 Apr '13

17 Apr '13

Hello all, The 2013 GMOD Summer School is now accepting applications. Galaxy will again be included in the topics covered. And Amelia says: Applications are competitive, so we encourage you to apply well before the > deadline, June 10th. So, if you are interested, act soon. Dave C ---------- Forwarded message ---------- From: Amelia Ireland <amelia.ireland(a)gmod.org> Date: Wed, Apr 17, 2013 at 11:15 AM Subject: [Gmod-announce] 2013 GMOD Summer School: Apply now! To: gmod-announce <gmod-announce(a)lists.sourceforge.net>, gmod-devel(a)lists.sourceforge.net We are now accepting applications for the 2013 GMOD Summer School, to be held NESCent, Durham, North Carolina from July 19th to 23rd. The GMOD Summer School is the best way to learn how to install, configure, and use popular GMOD tools, including GBrowse, JBrowse, Galaxy, MAKER, Tripal, WebApollo, and Chado; courses are taught by the tool developers, and there will be evening sessions for those who want to work on their own data or troubleshoot issues with the developers. More information and online application form: http://gmod.org/wiki/2013_GMOD_Summer_School Applications are competitive, so we encourage you to apply well before the deadline, June 10th. If you have any questions, please contact help(a)gmod.org and we will be happy to answer them. -- Amelia Ireland GMOD Community Support http://gmod.org || @gmodproject ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ Gmod-announce mailing list Gmod-announce(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gmod-announce -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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fastq quality trimmer
by Tomaz Rijavec 17 Apr '13

17 Apr '13

Dear "Galaxy Team", I have a question regarding the fastq quality trimmer (by sliding window) tool. What is the script running behind it? Is it a modified version of the fastx_quality_trimmer found in the fastx tools package? Is there a standalone version of it one can set up locally and run it from the command line. Thanks for all the info you can provide. best regards, Tomaž -- Lep pozdrav / Best Regards, dr. Tomaž Rijavec -------------------------------------------------------- Inštitut za fizikalno biologijo d.o.o. / Toplarniška ulica 19, 1000 Ljubljana / T: 01 587 54 70 / www.ifb.si Institute of Physical Biology / Toplarniška ulica 19, SI-1000 Ljubljana, Slovenia / T: +3861 587 54 70 / www.ifb.si

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Put an apache password on galaxy?
by Lee Katz 16 Apr '13

16 Apr '13

Hi, I am relatively new to Galaxy. I would like to set it up as an apache password protected site. I have tried to do it, but I realize now that it has its own server built-in and that it is ineffective to set up .htaccess because it isn't reading .htaccess (or so I think). More information: Apache works (test page loads, and I can change it), and Galaxy works (I even made a new tool that is working). I have Ubuntu 12. My basic, basic need is to set up a server-level password like what .htaccess would provide. Could anyone help? Thank you. -- Lee Katz, Ph.D.

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cufflink workflow
by Ianiri, Giuseppe 16 Apr '13

16 Apr '13

Hi, I want to compare gene deferentially expressed in two conditions (1 and 2). I don't have a GTF reference annotation. In my first attempt, I mapped my Illumina reads with TopHat. Then I run Cufflink, and Cuffmerge on my Cufflink outputs for the conditions 1 and 2. At the end, I run Cuffdiff using the Cuffmerge output (1 + 2) and the TopHat output for the two samples of interest. I got genes and transcripts differentially expressed, but I was expecting a quite different output (based on the literature). Do you guys think I did anything wrong? Also, I am not sure the question makes sense, but is the Cuffmerge step essential for the comparison of my two samples? Or could I use my Cufflink outputs for samples 1 and 2 for running Cuffdiff? Regards, Giuseppe Ianiri Email: ianirig(a)umkc.edu

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Metagenome Analysis
by Mike Dyall-Smith 16 Apr '13

16 Apr '13

I have looked through the metagenome tools and looked at the tutorials, and was wondering how one could pull out reads that contain specific protein domains or COGS. Blastx is not possible (?) but megablast could get GI codes, and these could potentially be used to retrieve CDD information. I just can't see the way to do this on galaxy. Any suggestions would be greatly appreciated. Mike DS Sent from my iPhone4

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Re: [galaxy-user] FW: problem using Depth of Coverage (GATK)
by Jennifer Jackson 15 Apr '13

15 Apr '13

Hi Gema, The histogram tool has the columns labeled on the tool's form - there are a few different values that you could pull out and graph, using others as labels, but last one is the coverage for that region of the chrom. The second tool's output is a bedGraph file, the format is also defined on the tool form, with the last value being coverage, the full specification is also here: http://wiki.galaxyproject.org/Learn/Datatypes#BedGraph The tool group "Graph/Display Data" maybe of interest, or you could use a browser to visualize the bedGraph file. The resulting dataset will have links. Best, Jen Galaxy team On 4/12/13 7:20 AM, Gema Sanz Santos wrote: > Hi Jennifer, > > Thank you very much for your answer. > > I think that alternative is good for me, but how can I get the plot? > The output is a table but I don't know exactly which columns to select > for getting the histogram plot or the bed graph. > > Best, > Gema > > From: Jennifer Jackson <jen(a)bx.psu.edu <mailto:jen@bx.psu.edu>> > Date: Tuesday, April 9, 2013 10:50 PM > To: Gema Sanz Santos <ge2sasag(a)gmail.com <mailto:ge2sasag@gmail.com>> > Cc: <galaxy-user(a)lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>> > Subject: Re: [galaxy-user] problem using Depth of Coverage (GATK) > > Hello Gema, > > The tool group "GATK-Tools (beta)" is not indexed to function with the > hg19 genome. > > As an alternative on the public Main Galaxy server, please see the > tool group " BEDTools". There are two tools here that calculate > coverage using BAM data as input. > > Another alternative is to set up either a local or cloud Galaxy, > obtain the hg19 indexes from GATK, then run the analysis there. If you > wish to try this please see: > http://getgalaxy.org > http://usegalaxy.org/cloud > > Take care, > > Jen > Galaxy team > > On 4/7/13 11:41 PM, Gema Sanz wrote: >> >> Hello, I´m trying to use depth of coverage to check the coverage of >> my reads. I already have the bam files (created with sam to bam) but >> they are still not recognized by depth of coverage and I got this >> error message: >> >> "Sequences are not currently available for the specified build" >> >> I used "human (homo sapiens) hg19 full" for mapping but I can´t >> select it, it only allows b37 version. I tried to change the build in >> edit parameters to b37 and then it is recognized but I got another >> error at the end of the analysis. >> >> Any suggestions? >> >> Thank you very much in advance >> >> Gema >> >> >> >> ___________________________________________________________ >> 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/ > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Which "Library Type" should I use for single-end reads
by Du, Jianguang 15 Apr '13

15 Apr '13

Hi All, I have a very basic question about parameters for running TopHat. I have datasets of single-end reads. These datasets were generated with Illumina Genome Analyzer IIx. Which "Library Type" should I choose to run Tophat? Thanks. Best, Jianguang

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Barcode splitter on paired end reads
by Veranja Liyanapathirana 15 Apr '13

15 Apr '13

Dear Galaxy team, I am sorry for repeatedly asking this question but I would like some feed back from anyone who has used barcode splitter on paired end reads as the different alternatives I used do not give satisfactory results in terms of expected read alignments. I have a set of Illumina Miseq reads with inhouse barcodes that I need to de maultiplex. It is esstential to make sure that the read 1 and read 2 are split to the same group and in instances that this condition is not fulfilled, the reads to be discarded. I tried to 1. Join read 1 and read 2 and then run barcode splitter, followed by FASTQ splitter 2. Use barcode splitter on read 1 and read 2 separately and use FASTQ joiner on the results to exclude instances where R1 and R2 are in different reads followed 3. Use barcode splitter on R1 and R2 results and straightaway use Bowtie for illumina for mapping The results I get in the three methods are not compatible with each other. I would like to know the best method from the experience of other users on what the best method using Barcode splitter on Illumina Paired end reads, Thank you, Kind Regards, Veranja Veranja Liyanapathirana Graduate Student CUHK

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Tool for changes in bedgraph files
by Kristin Denise Kernohan 12 Apr '13

12 Apr '13

Hi everyone, I am new to Galaxy and wondering if anyone can help me with a quick question. I have two data sets which are currently in a bedgraph format. I am looking for a tool to compare between them and find unique or changed sites. Is there a tool to compare between samples and generate a list of changed sites? Thank you very much Kristin

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