- 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 30 Nov '12

30 Nov '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 30 Nov '12

30 Nov '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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Re: [galaxy-user] Analysis in queue but not running
by Dave Clements 30 Nov '12

30 Nov '12

Hi Lew, CC'ing the galaxy-user list because I am assuming that your question is about the free public server ("Main") @ usegalaxy.org / main.g2.bx.psu.edu. If you have any future questions about Main, please post them to Galaxy-User so that others can see the question and respond. If I am reading the qstat output correctly, there are currently ~140+ jobs in the NGS queue, which means that Main is currently under very heavy load. The best thing to do is let the jobs sit in the queue. Killing and restarting them bumps them to the end of the queue. We are currently discussing a number of options for letting users know in situations like this, that while the job is not currently running, it is in the queue, and is moving forward. Thanks, Dave C PS: and the number of jobs in the queue has dropped by 2 since I started typing this email. On Fri, Nov 30, 2012 at 10:05 AM, Lewis Bowman <lbowman(a)mailbox.sc.edu>wrote: > I have tried repeatedly to run Cuffdiff using cuffmerge output (38) and > cufflinks output (25 and 29). In every case the job does not begin to run > and status says"Job is waiting to run." Has Galaxy been down for the last > several days? I am unsure what to do since I have received no error > message. Thanks for you help. > > Lew Bowman > > -- > Lewis H. Bowman > Department of Biological Sciences > University of South Carolina > Columbia, SC 29208 > PH: 803-777-5157 > FAX: 803-777-4002 > EMAIL: lbowman(a)mailbox.sc.edu > > -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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December 2012 Galaxy Update
by Dave Clements 30 Nov '12

30 Nov '12

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Cuffdiff tracking file does not report all genes and trancrips from reference annotation?
by Wei Liao 30 Nov '12

30 Nov '12

Hi, Galaxy user. I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local instance to check differential expressed genes in my samples. I have 3 normals and 6 cancers samples, I did the following: - After tophat for each samples, run cufflink with refseq annotation which has 25266 genes and 43091 transcripts - cuffmerge all cufflink outputs contains 58112 lines - run cuffdiff with 3 normals as triplicate and compare to each cancer sample. Suprisingly, I fould out that the tanscripts tracking file, gene tracking, CDS tracking only has 2000 genes and 4000 transcripts. So the cufflink only compare 2000 genes and 4000 transcripts between samples. The question I want to ask here is that *why are the rest of the genes and transcripts not being tested and included in the tracking files?* Do you know what cause this kind of problem? Thanks, Wei -- Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 North Hills, CA 91343 818-891-7711 ext 7645

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User's information
by Sachit Adhikari 30 Nov '12

30 Nov '12

Where are the user's information stored in Galaxy? I can't find the information in universe_wsgi. Regards, Sachit

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"Metadata is being auto-detected" stuck in continuous loop
by Redvers Richard 29 Nov '12

29 Nov '12

Greetings, Recently on the Main Galaxy site, on numerous occasions, when trying to convert a tabular dataset datatype to an interval format, Galaxy attempts to detect Metadata - but continues unabated in this loop for days on end, both with Biomart datasets and my personal custom datasets, with no end in sight. Copying the dataset to a new history seems to fix this, but surely there must be a better workaround than constantly shuffling things into new histories when converting to interval format? Any advice would be greatly appreciated. Regards, Rick Richard P. Redvers, PhD Metastasis Research Laboratory Cancer Cell Biology Program Peter MacCallum Cancer Centre p: +61-3-9656-3713 (Office) +61-3-9656-1285 (Lab) f: +61-3-9656-1114 w: http://www.petermac-research.org/ Mailing Address: Courier Address: Locked Bag #1 2 St Andrew's Place A'Beckett St East Melbourne East Melbourne Victoria, 3002 Victoria, 8006 AUSTRALIA This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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