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

cluster install
by Joshua Udall 26 Oct '11

26 Oct '11

Dear Galaxy - We would like to install and instance of Galaxy on our campus cluster. The install process looks very straight forward, but tying it in with our authentication system for the current, functioning cluster may not be as simple. It appears that galaxy is easy to install if there are limited users on a local machine or on a cluster where galaxy is the main use of the cluster (so it handles all the user accounts). Where would I direct our IT admin group to get more assistance with customizing the authentication process with our existing, function cluster? -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA

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reducing size on disk to comply with quotas
by Patrick Kenneth Gonzales 26 Oct '11

26 Oct '11

Hi, I am currently using 636gb of storage and would like to reduce it. I have deleted (from disk) most of the datasets in my history. All I've kept are the Bam files which are around 2.7gb each . Unfortunately, the "size on Disk" reads 448.5gb in my saved histories window. It is my understanding that permanently deleted datasets are not considered in quotas. Also, I don't have any copies of these datasets. Where is the 448.5gb of data coming from and how can I get rid of the phantom gb's while keeping the bam files? Thanks, Patrick

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Cistrome
by Albena Pramatarova, Dr 26 Oct '11

26 Oct '11

Hi What is the procedure for getting a username and password key to use the Aspera tool? Thank you for your help. Albena

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October 25, 2011 Galaxy Development News Brief
by Jennifer Jackson 26 Oct '11

26 Oct '11

October 25, 2011 Galaxy Development News Brief This release: http://galaxyproject.org/wiki/News%20Briefs/2011_10_25 Release history: http://galaxyproject.org/wiki/News%20Briefs Source: http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 338ead4737ba Highlights: Galaxy is Hiring! Main Data and Job Quotas UI Updates Trackster (GTB) at BioVis Python 2.4 -> 2.7 Official SICER, Trinity, SAMtools rmdup All: What's New Galaxy Main User Interface (UI) Trackster (Galaxy Track Browser) Python and OS Support Galaxy Tool Shed Updated & Improved Tools Quotas and Data Management Source API Scripts Bug Fixes Thanks for using Galaxy!

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FASTQ Quality Trimmer for PE Illumina?
by Kuehn, Joanna S [V MPM] 26 Oct '11

26 Oct '11

Hello, I was wondering, can Galaxy's FASTQ Quality Trimmer tool be used on Illumina paired-end data? Would the forward and reverse read files need to be processed separately and be un-joinable afterwards for filtering? Thank you, Joanna

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Sequences are not currently available for the specified build
by Mark Silby 26 Oct '11

26 Oct '11

Hi all, We are just beginning to analyze RNA-seq data and hope to make use of the Galaxy tools. We are not using a commonly studied organism such as human. Rather, our data are from the bacterium Pseudomonas fluorescens Pf0-1. The genome for P. fluorescens Pf0-1 appears in the "database/build" menu, and we have selected this in the .sam file attributes. When we run the sam to bam conversion, we get the error "Sequences are not currently available for the specified build." Is this something that can be corrected easily? Many thanks for your help. Mark Silby

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Extract genomic DNA-strand information is not recognized
by Sarah 25 Oct '11

25 Oct '11

Hello, I am trying to extract sequences from a FASTA file containing genomic information. The coordinates are in a tab-delimited format, which is recognized as BED format by Galaxy (meaning that the 6th column is correctly interpreted as 6. Strand). However, upon running "Fetch sequences" , Extract Genomic DNA only the +-strand information is included in the output FASTA file and I receive the following ERROR message: 1,431 sequences format: fasta, database: ? Info: 1476 warnings, 1st is: Invalid interval, start '1616' > end '1177'. Skipped 1476 invalid lines, 1st is #2, "scaffold00001 1616 1177 Fom - 1" Is this a bug? How can I can adjust my input data files to get the --strand sequences as well? I have seen a similar problem in an earlier posting and there it was suggested to manually adjust the strand information column 5, but this did not work for me neither. Many thanks for your all help!!!!! Sarah

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Allelic RNA-seq!
by Jennifer Jackson 25 Oct '11

25 Oct '11

Hello Di, I am posting to the mailing list (as you intended?). Regards, Jen Galaxy team On 10/25/11 1:51 PM, Di Nguyen wrote: > Hi Jen, > > May I ask you and the community this question: > > I am sequencing the transcriptome of a hybrid mouse (BL6 x spretus). The > reference BL6 is available but Mus spretus' is not, even though the SNPs > table for spretus is available. How do I use Galaxy to identify > species-specific transcripts? > > Please accept my utmost appreciation, > > Di > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Re: [galaxy-user] Reducing overall data footprint
by Jennifer Jackson 25 Oct '11

25 Oct '11

Hi Bryn, Removing unneeded data is the best solution if using Main. One example would be saving back (locally) the original FASTQ input, then deleting it permanently from your history, rather than leaving both the raw data and the Groomed data on the server. This can actually help quite a bit if your datasets are large. See this wiki for help about Delete vs Delete Permanently: http://galaxyproject.org/wiki/Learn/Managing%20Datasets#Actions Another option is to move to a local or cloud instance: http://getgalaxy.org I am posting back to the mailing list along with a clearer subject line, to help others who may have a similar question. Best, Jen Galaxy team On 10/25/11 10:54 AM, Bryn Gaertner wrote: > Hi Jennifer, > > I am trying to run cufflinks, which I don't > think should be too hard (it's on C. elegans). Do you have any > suggestions for reducing the amount of memory I'm sucking? > > Thanks! > Bryn -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Re: [galaxy-user] data sizes & delete vs delete permanently
by Jennifer Jackson 25 Oct '11

25 Oct '11

Hi Richard, How to know overall size: Your total size is in the very upper right corner, in a lavender box. This is also noted when using the link "User -> Preferences" from the top menu bar. The size of an individual history is noted in the right history panel, located underneath the "Options" pull-down menu. How to delete permanently: Please see the wiki about Managing Datasets at: http://galaxyproject.org/wiki/Learn/Managing Datasets#Actions Specifically, the section about Delete vs Delete Permanently, although tips for moving data around are throughout the document. In short: if you just delete, the data is recoverable (by you), and it still counts as part of your quota. If you delete permanently, then it is not recoverable (by anyone, including admins), and is removed from your quota. It is probably worth the time to copy/export/save back anything to may miss when first testing out the "delete permanently" functions for individual datasets and complete histories. Hopefully this helps. I am posting back to galaxy-user(a)bx.psu.edu for others that may need similar help. All of this is in the wiki, but more detail (graphics, etc.) is planned for in the near-term to clarify the functions further. Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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