galaxy-user September 2010

galaxy-user@lists.galaxyproject.org

43 participants
36 discussions

Apache setup
by Andreu Alibés 07 Sep '10

07 Sep '10

Hi, Anyone has a full example of the configuration of Apache and Galaxy? (I mean, more than what is already at http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy) Thanks, Andreu -- -------------------------------------------- *Andreu Alibés, PhD **Bioinformatics Core & EMBL-CRG Systems Biology Unit Center for Genomic Regulation* C/ Dr. Aiguader 88, 08003 Barcelona, Spain Phone: +34 93 316 0202 http://sites.google.com/site/aalibes

2 1

group-based permissions
by Davide Cittaro 06 Sep '10

06 Sep '10

Hi all, I would like to give access permission on our data libraries using Groups. Apparently I can only assign permissions to Users and Roles... Is this a bug or a feature? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

3 5

Moving Histories from old to new Galaxy build
by Lucilla Luzi 03 Sep '10

03 Sep '10

Hi all. We are moving from an old version of Galaxy (build: 1349) to the current one; we know there is a big gap in between Im wondering if there is a way to move in just one unpainful step all the saved histories from the old version to the new one, or alternatively to download/save entire histories at once from the old and then reload them to the new build. Any other ideas? Thank you a lot for your help! Lucilla

3 5

Re: [galaxy-user] integrating Galaxy with a relational data warehouse?
by Yury Bukhman 01 Sep '10

01 Sep '10

Thank you, James, for your reply. I wonder if you could elaborate on why storing the bulk of the data in a relational database seems impractical, or point me to a document where this is discussed at more length. Yury On 08/31/10, James Taylor <james(a)jamestaylor.org> wrote: > Hi Yury, > > > we are planning to build a data warehouse for a research center that utilizes multiple high-throughput experimental platforms, e.g. plate-based HTS assays, microarrays of several different types, ChIP-seq, RNA-seq. We have been thinking of managing the data in a relational database. Galaxy looks attractive to us for its workflow management and data provenance features, e.g. to keep track of how raw data are analyzed to produce normalized & summarized datasets and/or final sets of statistics such as p values. We wonder how amenable would Galaxy be to integration with a relational data store. > > > > One possible scenario might be to have Galaxy import a dataset from a relational database, run a workflow, then submit the results back to the database with the associated history or link thereto. > > This is certainly a reasonable possibility. You could have a Galaxy tool for submitting data to your database. I would imagine such a tool would produce a Galaxy dataset as output with whatever unique identifier is necessary to recover exactly that data from the database for another analysis. > > > Another possibility is to forgo the relational database altogether and do all our data management within Galaxy. > > > I can only give you our experience from inside Galaxy. After initial analysis we made a decision to store all data in Galaxy as files on disk, with metadata (data about data, connections between datasets, workflows, et cetera) in a relational database. We feel this decision has worked well. For the scale of data we see, as well as the wide variety of different data types, a relational database did not, and still does not, seem practical to us. > > -- jt > > James Taylor > Assistant Professor > Department of Biology > Department of Mathematics & Computer Science > Emory University -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman(a)glbrc.wisc.edu

3 2

problems with Galaxy
by pande 01 Sep '10

01 Sep '10

Hi, I uploaded two files since morning today and the message that is being displayed is "tool is waiting to run" Can someone please let me know the reason. thanks.

2 1

HTTP Error 503: Service Unavailable
by Erick Antezana 01 Sep '10

01 Sep '10

Hi, I've tried to update my local instance but I got the following error message: HTTP Error 503: Service Unavailable is the server down? cheers, Erick

2 1

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galaxy-user September 2010