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

Data table named 'bowtie2_indexes' is required by tool but not configured
by Sachit Adhikari 19 Oct '12

19 Oct '12

I am getting this error in Bowtie2 and Tophat2: Data table named 'bowtie2_indexes' is required by tool but not configured Data table named 'tophat2_indexes' is required by tool but not configured. How can I solve it? Thanks

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Bowtie2 and Tophat2 for Galaxy
by Sachit Adhikari 19 Oct '12

19 Oct '12

Hello Everyone, Can someone please give me the link to download .py file and the wrapper(.xml) of Bowtie2 and Tophat2? Thanks

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galaxy MAIN data problem
by kaswath 18 Oct '12

18 Oct '12

Hello Galaxy, I have a dataset about 20.8GB to work with using the NGS analysis. I FTPd the dataset and created a workflow for the analysis and ran the job on the entire 20.8GB on Galaxy main around september 27th. I waited on about two to four days .....no output of any sort ! I had requested the results be saved in a different history. I checked , but no new history with results was created ! I reran the job again after a week or so and still no results ! I had tried running this on small dataset and it had worked earlier ! Anyhow, getting back to this proble,m I have NOT receive any error message however , my USAGE bar on the top right is at 90% !! So I went back and deleted the old copies of my history I had , even so the usage bar is still at 90%! Before I ran my workflow I had the usage bar being way less ! Please can u let me know what is happening? Why I have not received any results on my analysis yet? I really need to get this done ASAP ! Thanks so much for all your help ! Regards Kshama.

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Error installing MACS on local Galaxy
by Jerzy Dyczkowski 18 Oct '12

18 Oct '12

Hello, I cannot run MACS on the local Galaxy. When I install MACS version 1.4., it gives error something like "cannot find macs". When I install version 1.3.7.1 it gives error "/line 34, in <module> from MACS.OptValidator import opt_validate ImportError: No module named MACS.OptValidator"/ I sourced PATH to the directory with this module. Any ideas? best regards, Jerzy -- Dr Jerzy Dyczkowski Bioinformatician Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Grisebachstr. 5 D-37077 Göttingen Email: Jerzy.Dyczkowski(a)eni-g.de Phone: +49 (0)551 39-12352

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Do I need to have tool or dependencies installed in the server to run Galaxy tools?
by Sachit Adhikari 18 Oct '12

18 Oct '12

I integrated Bismark in Galaxy in my server. I downloaded Bismark from Galaxy Tool shed. I just copied the Bismark into /tools directory and added some codes in tool_conf.xml to make it visible. Do I need to install the real Bismark application in the server too? I am really confused here. Thanks

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cuffcompare input
by i b 17 Oct '12

17 Oct '12

dear forum, I have two samples, treated and untreated. When I run cuffcompare (to created the gtf file for cuffdiff) do i have to give as input the cufflinks from both samples and the reference annotation or only the treated cuffliks? I very confused. any help much appreciated. thanks, ib

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cuffdiff values different for same sample
by i b 17 Oct '12

17 Oct '12

Hello forum, I have ran cuffdiff with two samples, treated vs untreated, and had certain values as expressed in the output (isoform differential expression). When I ran it again, using a different treated sample, but SAME UNTREATED SAMPLE, the values assigned to the untreated are different. Why is this if values are calculated from a unique FPKM? This happend for other jobs where I have ran the same untreated vs other treated samples... Thanks a lot, ib

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The last column in the output file of 'Screen Motif'
by Yunyi Zhu 17 Oct '12

17 Oct '12

Hi, I was using the tool 'Screen Motif' to find a particular motif in given region of genome. I don't know what dose the last column in the output file stand for. My guess is that it's -10*log(p), is it? -- 朱云依 Yunyi Zhu 中国科学技术大学 University of Science and Technology of China

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FW: problem in data uploading
by Amit Maiti, PhD 17 Oct '12

17 Oct '12

Hi, I am a first time user in galaxy for analysis of my RNA-Seq data. I am facing problem in loading data in galaxy. 1.I successfully transfered fastq files (from Illumina) by FTP and then tried to upload by checking each files and execute. 3. Initially it was yellow (with rotating circle) and then turned pink instead of green. It seems probably there is an error in uploading. But the files disappeared from the upload page but lined up with pink (at the history) and shows that 72.4GB of the disk space are occupied. I can view the files also with 'display data with viewer'! 4.when I tried analyze with TOPHAT, it tells you have no files in history! 5. When I wanted to do the whole process again but FTP tells yours files are already exists (transferred) in the server. But since they are not at the upload page, I can not upload again each one by checking them to correct the error? 6. Could you please advice me how to solve this problem and successfully upload files that would be good for analysis. Thanks for your help, Amit K. Maiti, PhD Oklahoma medical Research foundation, Oklahoma city, ok 73104 Phone-405 271 8099 Mobile-409 256 9557

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How to merge Fastq groomer files in Galaxy?
by Fang,Xiefan 17 Oct '12

17 Oct '12

Dear Galaxy users, Does anyone know how to merge several FASTQ groomer files by using Galaxy? If not, is there any other program that can achieve this? The size of one FASTQ groomer file is around 1GB. Thank you! Best regards, Xiefan Fang, Ph.D. Postdoctoral associate Department of Pediatrics College of Medicine University of Florida Phone: 352-294-5675 Email: xiefanfang(a)ufl.edu

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