- galaxy-user - lists.galaxyproject.org

Can't seem to stop or restart the Galaxy in server
by Sachit Adhikari 19 Oct '12

19 Oct '12

Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks

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using our own reference genome ?
by Didier Zoccola 19 Oct '12

19 Oct '12

Hi everyone, I am Didier Zoccola and i am marine biologist working on corals. I would like to do a illumina mapping from RNA-seq coming from environmental conditions. For that, i would like to use Bowtie but i have not a reference genome. We have done a de novo transcriptome using trinity assembly. I have filter by quality all my data. One possible thing is to download all the manipulated sequences on my computer and use Bowtie on my machine but it will take long time because my computer is not appropriate for this. An other thing is to download my reference transcriptome on your server. Is it possible? If not, what is the characteristics of the "ideal" computer to do the job locally ? thank you in advance Best regards Didier Zoccola ------------------------------------------ Centre Scientifique de Monaco avenue Saint Martin 98000 Monaco ☎ +377 97 77 08 73 zoccola(a)centrescientifique.mc http:// www.centrescientifique.mc

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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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