October 2011 - galaxy-user - lists.galaxyproject.org

fastq groomer
by arabidopsis 02 Nov '11

02 Nov '11

Hi all, Fastq groomer has Solexa or Illumina 1.3+ as an input quality format. I asked at the sequencing facility about their machine and output and they said their format was Illumina 1.8+ (the newest). I tried to convert my fastq file into Sanger by fastq groomer, using Illumina 1.3+ as an input option and got all reads with quality of around 10... Does it mean that Galaxy cannot be used on a dataset with 1.8+ encoding or something else was wrong? Thanks, Slon

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get data through FTP site
by Benoit HENNUY 02 Nov '11

02 Nov '11

Hello, I uploaded (on Oct, 25) data through FTP site and I was not able to retreiven them to include them in a history. I suppose that the files should appeared in the FTP list under the Get data page. THese data are named "P2 fastq .gz" files that I wold like to use in RNA Seq workflow. Thank you to help me to be able to use these data. Best regards, Benoit HENNUY GIGA Genomics University of Liege Belgium

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Re: [galaxy-user] Names for genes in RNA-Seq analysis
by Michael Gooch 02 Nov '11

02 Nov '11

Regarding the GTF files for cuffllinks, how do I obtain one for all human mRNA that actualy contains gene names rather than accession numbers. I went to the UCSC table browser but their files contain accession numbers that I dont know how to decode en-masse.

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Genome database/builds missing?
by Daniel N. Hupalo 02 Nov '11

02 Nov '11

I've been using galaxy to analyze maf files and today the drop down list for database/builds for genomes has lost most of the genomes once listed. I no longer see any bacteria or plants on the list, specifically TAIR9 arabidopsis is no longer on the drop down list when it was just yesterday. Did something change? Thanks - Dan

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Dataset not appearing as available input to SAM analyses
by James Nelson 02 Nov '11

02 Nov '11

Hi, I'm trying to use the SAM/Filter pileup analysis on some pileup output files I've uploaded. But when I click the analysis link, these output files don't appear in the Select dataset dropdown menu; instead only one file, the output from FASTQ Summary Statistics which is obviously not pileup output, is shown. Thanks Clare Nelson

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RNA-seq with Staphylococcus aureus strain Newman
by Joe J Harrison 02 Nov '11

02 Nov '11

Hello, Would you please add Staphylococcus aureus strain Newman to your database? Workflows to analyze data for genomes available through your database are really simple - but I must admit that I've been struggling with trying to get this to work for a genome (and in particular with the annotation) that I've uploaded myself. Thanks for the help and the continued support! Joe ---- Joe J. Harrison Senior Fellow Department of Microbiology University of Washington

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Amazon AMI
by Daniel Muehlschlegel 31 Oct '11

31 Oct '11

Hi, I installed the Amazon Galaxy CloudMan today but am not able to load any of the Galaxy AMIs. The AMI on the user galaxy webpage does not exist, but 3 AMIs do. I tried the 2 most current ones and they don't load: It looks like everything is fine on the Amazon side: Thanks for your help, Danny

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Upcoming Galaxy Events
by Dave Clements 31 Oct '11

31 Oct '11

Hello all There are several Galaxy related events going on at Cold Spring Harbor Laboratory in November, but if you aren't already registered for those it is now too late to get in. However, there are several deadlines in November and events in the coming months. See the Events<http://wiki.g2.bx.psu.edu/Events>page ( http://wiki.g2.bx.psu.edu/Events) for a full listing of upcoming events. If you have a Galaxy related event please send it to outreach(a)galaxyproject.organd we will help you get the word out. Date Topic/Event Venue/Location Contact November 2-5 Best practices for variant discovery through Galaxy: Oscillating evolution within dual coding genes <http://meetings.cshl.edu/meetings/info11.shtml> Genome Informatics 2011 <http://meetings.cshl.edu/meetings/info11.shtml>, Cold Spring Harbor, New York, United States Dan Blankenberg <http://wiki.g2.bx.psu.edu/dan> November 8-21 Advanced Sequencing Technologies & Applications Course<http://meetings.cshl.edu/courses/c-seqtech11.shtml> Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> November 9-15 Compuational & Comparative Genomics Course<http://meetings.cshl.edu/courses/c-ecg11.shtml> Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 8-21 2012 2012 Workshop on Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kruml…> Features Galaxy and much more. *Application deadline is November 1.* Český Krumlov, Czech Republic James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 14-18 2012 Galaxy Session @ GMOD Workshop PAG 2012 <http://www.intlpag.org/>, San Diego, California, United States Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> January 17 2012 Reproducible workflows for next generation sequencing analysis<http://www.nowgen.org.uk/facilities/events/event.php?id=30> Nowgen <http://www.nowgen.org.uk/>, University of Manchester<http://www.manchester.ac.uk/>, United Kingdom Tom Hancocks <training(a)nowgen.org.uk> Thanks, Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Queuepool limit problem
by Cinto Queky 31 Oct '11

31 Oct '11

Hi All, We encountered queuepool limit problem after running the workflows for a few times. We have tried to increase these 2 parameters: database_engine_option_pool_size and database_engine_option_max_overflow to 20 and 40 respectively. Are there other parameters that we can change? Thanks,Cinto

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Problem launching cloud instance
by Clare Sloggett 30 Oct '11

30 Oct '11

Hi all, I wasn't sure whether to send this to galaxy-dev or galaxy-user. I'm having a problem launching a Galaxy instance on Amazon. I have done this in the past with no problems. I suspect I'm doing something trivial wrong but can't work out what! The problem is that after starting the instance, when I go to http://public-dns-url/cloud and the "Initial Cluster Configuration" window pops up, the initial storage size text box is disabled. That is, the text box after the first radio box ("Galaxy Cluster") is greyed out. So, I can't enter a size for the storage and if I just proceed without doing so, it (I think) causes CloudMan to fail. I thought I was probably just having browser issues but I get the same problem repeatedly in Chrome and Firefox. When I inspect the element, I see <input disabled="true" ... name="g_pss"...> so I think it really is disabled. This seems like a weird problem so I suspect it's me, but I can't work it out. Any help would be appreciated! Thanks, Clare -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759

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