December 2012 - galaxy-user - lists.galaxyproject.org

NGS with Arabidopsis thaliana built-in-index
by Tom Smith 03 Dec '12

03 Dec '12

Hi all, I've been having trouble running my Arabidopsis thaliana NGS pipeline in galaxy. Specifically, tophat alignment to the built-in-index worked fine (visual assessment in IGV) but I couldn't get cufflinks/Cuffduiff to run using the same annotation.gtf file I'd used in the alignment. Error message = Error running cufflinks. return code = -11 cufflinks: /lib64/libz.so.1. Cufflinks/cuffdiff would run without the annotation file and give a differential expression output but without the annotation file the gene_id was meaningless (XLOC_000001 etc) and all I had was a locus for a region with differential expression. After a lot of frustration I re ran the alignment using a custom built genome and annotation file from Illumina: http://cufflinks.cbcb.umd.edu/igenomes.html and hey presto, cufflinks/cuffdiff work fine. I did try altering using both chr1 and 1 for chromosome name as a discord between the chromosome naming seemed to frequently be a problem. Apart from this, what other reasons could there be for the built-in-index not working with annotation.gtf files? Is this an issue with the built-in-index (Mouse-ear Cress (Arabidopsis thaliana): Arabidopsis_thaliana_TAIR10)? Cheers, Tom SmithUniversity of York, UK

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how to download onto a server?
by Loraine, Ann 03 Dec '12

03 Dec '12

Hi, I would like to transfer results files (e.g., accepted_hits.bam) from my Galaxy history onto a server — not my local computer. How do I do that? Best, Ann ------------------------------- Ann Loraine, Ph.D. Associate Professor Department of Bioinformatics and Genomics University of North Carolina at Charlotte North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 aloraine(a)uncc.edu http://www.transvar.org http://www.bioviz.org http://www.uncc.edu

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Boxplot error.
by 柴田弘紀 03 Dec '12

03 Dec '12

Hello, I'm pretty new for Galaxy. I am running a local Galaxy server on Mac. I tried to draw a boxplot from summary statistics created from groomed fastq data. Then I got error message as follows: An error occurred running this job: gnuplot> set term png size 2048,768 ^ line 0: unknown or ambiguous terminal type; type just 'set terminal' for a list line 0: warning: Too many axis ticks requested (>1e+02) Error running gnuplot. I believe gnuplot was appropriately installed using MacPorts (confrimed it starts when I type "gnuplot" on terminal). I also installed libpng by Macports and now "png" is listed when I type "set terminal" in gnuplot for a list. How can I help it??? Thank you very much. Hiroki

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dataset not visible
by Ilse Vandecandelaere 01 Dec '12

01 Dec '12

Dear, I am working on the free public server of Galaxy for almost a week. When I opened the galaxy server this morning, my datasets were not visible. I have tried show hidden datasets or show deleted datasets, but nothing changed. How can I make my datasets visible? Thanks, Kind regards, Ilse --------------------------------------------------------------- [cid:image001.png@01CDCE11.0DF442D0] http://www.ugent.be/fw/en/research/pharmaceutical-analysis/pmicro http://www.sociomicrobiology.ugent.be/ -----------------------------------------------------------------

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History Pane empty?
by jason gagliano 01 Dec '12

01 Dec '12

Hi I just had a quick question. My History pane to the right of my Galaxy account on the web suddenly was empty when I logged in. I noticed that I can still find all my datasets under "Saved History" or "Saved Datasets" but nothing will show up now in the history pane. This is true even when I upload a new data set. Any thoughts on the problem and a solution? Thanks Jason P.S. I have read all I could find on the topic in the help sections before asking this question. But I could not find anything that worked for me (like simply deleting cookies). I am relating this to say that I am trying to be a good citizen by reading first and then asking questions :0)

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