- 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<tel:801-422-9307> Fax: 801-422-0008<tel:801-422-0008> USA

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Over disk quota
by GANDRILLON OLIVIER 26 Oct '11

26 Oct '11

Hello I just received the following message while using Galaxy through the web "You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota." I deleted a couple of files but it didn't helped. I checked the FAQ and could not get the answer. Thank's for your help Olivier

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sample for video for example 3 in ngs analyses in galaxy
by Linda McMahan 26 Oct '11

26 Oct '11

Hi, I am watching the video 'Example 3<http://screencast.g2.bx.psu.edu/galaxy/quickie12_illumina_pe/flow.html> - mapping paired-end Illumina run and visualizing results at UCSC Browser', and would like to try out the exercise. I don't have paired-end Illumina fastq sample, Could you provide me the sample mentioned in the video or point me to the location where I can get a small human paired-end Illumina fastq sample to try out the exercise in example 3. Thanks, Linda McMahan

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Names for genes in RNA-Seq analysis
by GANDRILLON OLIVIER 26 Oct '11

26 Oct '11

Hello I am using Galaxy to analyse RNA-seq libraries made from chicken cells. I just groomed my sequences, passed them through TopHat and then Cufflinks. This worked well and in the end I get a list of genes and their respective FPKM values. My only problem is that the names of the genes do not appears in the listing, they are simply reference as "CUFF.1, CUFF.2, " etc… Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer). Sincerely Olivier ----- New mail adress: olivier.gandrillon(a)univ-lyon1.fr Dr Olivier Gandrillon Centre de Génétique et de Physiologie Moléculaires et Cellulaires UMR CNRS 5534 Université Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Raphaël Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 Web adress : Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html "Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il inventait chaque jour? Précisément parce que c'était des mensonges et précisément parce qu'ils étaient une insulte à la perception. Le peuple était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire l'évidence. Les gens portaient un regard médusé sur un Goebbels déchaîné. Ils voyaient en transparence son souhait énorme de nier le nain boiteux" Tobie Nathan, in "Qui a tué Arlozoroff"

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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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