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Reference Genomes for NGS Tools - A Couple Questions
by greg 20 Dec '12

20 Dec '12

Hi all, I'm finishing up installing Galaxy on our local cluster. I'm at this step regarding setting up reference genomes: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup#Setting_Up_the_Refe… But it looks like a whole lot of manual work that needs to be done by a system administrator. I was kind of expecting this would be something end users would be able to do. I'm actually not sure we have the resources for a sys admin to install all of these reference genomes every time someone needs one. I guess here are my questions: Am I misunderstanding the process? Is there a different way that normal users can add reference genomes instead? Is there anything in the works that lets users easily add these? Is there a way to use NGS tools without installing reference genomes? Thanks, Greg

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liftOver Exception caught attempting conversion
by Nikoloas Sidiropoulos 20 Dec '12

20 Dec '12

Hi I downloaded and extracted the .chain files for liftOver and edited the .loc file. After restarting Galaxy I have the option to convert my files to the respective coordinates but when running the job I get the same error for each. "Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/tools/extract/liftOver_wrapper.py", line 81, in raise Exception, 'Exception caught attempting conversion: ' + str( e ) Exception: Exception caught attempting conversion" I also found this in the handler.log file: "galaxy.tools DEBUG 2012-12-20 11:37:09,902 Error opening galaxy.json file: [Errno 2] No such file or directory: '/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/000/98/galaxy.json' " Do you know how could this be sorted? Thanks in advance, Nikos

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Integrating generated graphics from cli tool?
by Samuel Lampa 20 Dec '12

20 Dec '12

Hi, I'm looking into integrating some R scripts into Galaxy, which create some graphics / plots. We are interested in integrating those in galaxy somehow, or otherwise presenting them to the user in an as easy way as possible. I wanted to check if there is some support for this kind of functionality there already, or if I'll need to hack something together myself? (I couldn't really find anything here on the mailing list). Many TIA! Best // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se

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Extracting bacterial seq from cordinates
by shamsher jagat 19 Dec '12

19 Dec '12

I have a bacterial genome from ncbi and woulld like to extract seq from the corresponding fasta file of bacterial genome. Since i have list of coordinates so would not be possible to extract one by one. Is there any interface within galxy that i can use. Thanks

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feature or bug with the tool shed?
by David Gene Morgan 19 Dec '12

19 Dec '12

Hi, I just installed a galaxy server and ran into something that may be a deliberate feature or a genuine bug when trying to install a package from the main tool shed. I got the Admin tab working, went to the section dealing with tool sheds and selected "Search for valid tools" in the Galaxy main too shed. I was able to find the tool I wanted (NCBI Blast+, and I found multiple revisions) but I never found anything remotely like an "Install" button. There are bare-bones instructions for a manual install of the tool, but nothing automatic. However, if I start with "Browse valid repositories" and _then_ search for "ncbi blast" (and not "ncbi blast+"), I find a single revision that has a "Preview and install" option and an "Install into local Galaxy" button. So the only question here is whether this behavior is a bug or a feature. In other words, should I be able to automatically install packages using my first approach, or does Galaxy prevent this deliberately? -- David Gene Morgan cryoEM Facility 320C Simon Hall Indiana University Bloomington 812 856 1457 (office) 812 856 3221 (EM lab) http://bio.indiana.edu/~cryo

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copying files via galaxy API
by Richard Park 19 Dec '12

19 Dec '12

Hi Everyone, Is there a way to directly copy files from galaxy with the proper file name? I'm currently using the galaxy API to download files via HTTP, but it is very slow and would like to speed up the process of copying files directly, but am having a hard time getting the proper file names. Are there any suggestions on how to copy files directly from galaxy without HTTP and with the proper filenames? # Looking up files via API $ ./display.py <api_key> http://localhost:8080/api/libraries/86cf1d3beeec9f1c/contents/32ff5cf1b96c1… Member Information ------------------ ldda_id: 32ff5cf1b96c1df7 misc_blurb: 10,028,615 lines name: H3K9me3_L3_FE_2.wig data_type: txt file_name: /galaxy-central/database/files/000/dataset_733.dat uploaded_by: rpark(a)bu.edu template_data: {} genome_build: ? model_class: LibraryDataset misc_info: uploaded txt file file_size: 48439126 metadata_data_lines: 10028615 message: id: 32ff5cf1b96c1df7 date_uploaded: 2012-12-15T01:53:08.655366 metadata_dbkey: ? # Downloading files using a URL like http://127.0.0.1:8080/datasets/a4975bc1e68708d4/display?to_ext=txt thanks, Richard

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Problems with Internet Explorer 9?
by Peter Cock 19 Dec '12

19 Dec '12

Hello all, Are there (or were there) any known problems with Galaxy under Microsoft Internet Explorer 9? One of our biologists is now having problems with our local Galaxy server, probably after updating his browser. Specifically new history entries do not seem to automatically update from queued to running to done, and also the "peep" functionality to expand/collapse a history entry had stopped working. This was on a large history of about 100 entries. We installed Firefox 10, logged into Galaxy, and it was fine with this same history. A quick test on the public Galaxy with a single history entry seemed to work in both browsers, so perhaps this is something you've already fixed in the latest Galaxy - or perhaps it depends on the size of the history. Any ideas? Has anyone else seen something similar? Thanks, Peter

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help configuring tools in Galaxy
by Tilahun Abebe 19 Dec '12

19 Dec '12

Hi, We installed a local galaxy a couple of days ago following the basic installation instruction (http://wiki.galaxyproject.org/Admin/Get%20Galaxy) The installation went well, all the tools are listed on the left. I can also upload data to Galaxy. However, an error occurs when I try to run RNA-seq analysis. I am thinking the tools are not configured properly. Can you give me tips to configure NGS tools? An example file with setup syntax will help as well. Thanks. Tilahun

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Error in TopHat
by Sachit Adhikari 19 Dec '12

19 Dec '12

This is the error I am getting while running Tophat. What's causing this? I have the default hg19 index files. Error in tophat: [Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3) ----------------------------------------------- [Tue Dec 18 10:08:33 2012] Preparing output location ./tophat_out/ [Tue Dec 18 10:08:33 2012] Checking for Bowtie index files Error: Could not find Bowtie index files /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19.* TopHat v1.3.3 TopHat v1.3.3 tophat -p 4 /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19 /opt/galaxyprod/galaxy-dist/database/files/000/dataset_45.dat

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producing HTML output with images
by Nikhil Joshi 19 Dec '12

19 Dec '12

Hi all, I am having trouble producing HTML output with images. In the past I have been able to produce HTML files with no images and it seemed to work fine. However, now I am writing a script that produces diagnostic images and I want to display all of the images on one page using HTML. I am using the "files_path" variable to create the plots in the working directory, and then I am using the "extra_files_path" variable to access the final plot from the html file. I look at the resulting HTML files and it points to the proper plot full path, and the plot DOES exist... but when I click to view the output, the plot doesn't render. It just shows an empty box with a "broken image" icon, however, the text does render. I copy the plot file, and I can view it fine by itself. I copy the plot and the html and I can view the page just fine offline, but galaxy doesn't want to render the image for some reason. What am I doing wrong? - Nik. -- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center Davis, CA

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