- galaxy-user - lists.galaxyproject.org

Tools xml option 'from_file'
by Henrikki Almusa 11 Nov '08

11 Nov '08

Hi, I'm trying to add blast (or megablast actually) to galaxy. To allow it to use databases, I need to tell it what there are available. That is done with file 'blastdb.loc' In page http://g2.trac.bx.psu.edu/wiki/XmlQuickReference There is little information, but where exactly should that file be? It doesn't seem to read it from tools (where the xmls are) directory or the main directory of galaxy at least. Thanks, -- Henrikki Almusa

4 4

BioMart results come back as XML
by Peter Andrews 05 Nov '08

05 Nov '08

I expected my biomart data to be in table form so that I could easily join it with some UCSC tables but instead it came back as XML. How do I manipulate it as a table? Thank you, Peter Andrews -- -------------- Peter Andrews Programmer Computational Genetics Lab Dartmouth Hitchcock Medical Center (603) 653-9963

1 0

Galaxy and Arabidopsis
by Vesselin Baev 05 Nov '08

05 Nov '08

Dear All, Is it possible (and how) for Galaxy to work with Arabidopsis genome? Vesko -- ------------------------------------------------ Dr. Vesselin Baev Research Assistant Professor University of Plovdiv Dept. Molecular Biology Bioinformatics Group Tzar Assen 24 Plovdiv 4000, BULGARIA +359 32 261 (560) +359 89 43 80 945 Skype: vebaev vebaev(a)gmail.com baev(a)uni-plovdiv.bg http://plantgene.eu/

2 1

SecurityFeatures - admin_users
by Andrew Olson 05 Nov '08

05 Nov '08

I'd like to set up admin_users on my galaxy installation. Adding this to universe_wsgi.ini has no effect. What do I need to do to get this working? Andrew

2 1

format vs datatype
by very 05 Nov '08

05 Nov '08

Does any know what's the difference between format and datatype in the xml file which has to be composed to add a tool? It would be better if anyone can list all the formats and datatypes user can pick. Thanks!

2 1

Fetch closest feature on data
by Steve Taylor 03 Nov '08

03 Nov '08

Hi, Is there a way of returning accession number or IDs using "Fetch closest feature on data" in Galaxy? When I tried this function, it returned a list of coordinates and a temporary id (the first four columns are the input data). chr16 8038 8480 16.1 0.09567793 chr16 12632 13347 16.2 0.06949871 chr16 12632 13347 16.2 0.06949871 chr16 8038 8480 16.1 0.09567793 chr16 12632 13347 16.2 0.06949871 chr16 45006 46378 16.3 0.52806085 I was expecting it to work in a similar way to the Bioconductor ACME function findClosestGene where I get the nearest RefSeq gene accession. Kind regards and thanks for any help, Steve ------------------------------------------------------------------ Medical Sciences Division Weatherall Institute of Molecular Medicine/Sir William Dunn School Oxford University

1 0

Using SGE cluster
by Henrikki Almusa 31 Oct '08

31 Oct '08

Hi, I'm trying to get SGE cluster to run some tools on galaxy. I've set the 'start_job_runners = sge' and 'default_cluster_job_runner = local:///'. I'm hoping that this setup would run tools locally, unless tool is set to run on cluster in '[galaxy:tool_runners]' section. However this seems to fail with following message: Exception: SGEJobRunner requires DRMAA_python which was not found The DRMAA python package however is installed as is libdrmaa.so.1.0. And importing the DRMAA package works in python command prompt. How should I proceed with this? Regards, -- Henrikki Almusa

2 8

set an upload size limit
by Davide Cittaro 30 Oct '08

30 Oct '08

Hi all, how can I set a size limit for data to be uploaded in galaxy? Thanks 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 */

2 1

About adding tools
by Henrikki Almusa 30 Oct '08

30 Oct '08

Hi, I'm looking at how to add tools to galaxy. Is there any info on what the tool.xml can have within it (dtd or documentation or something)? Another thing is the command line. Is it possible to use optional command line switches that don't have values. Eg. grep has option '-i' which means ingore case (and if not given it is case sensitive). Regards, -- Henrikki Almusa

2 4

passing SGE parameters
by Chris Cole 29 Oct '08

29 Oct '08

Hi, Is it possible to specify SGE parameters on a job-by-job basis? For example, say I want set off an array job or specify a parallel environment for certain jobs. Thanks, Chris

2 1