May 2013 - galaxy-user - lists.galaxyproject.org

Dataset does not appear in a drop-down menu of a tool
by Nikolay N. 16 May '13

16 May '13

Hi, I just started using the main galaxy instance. I uploaded via FTP and imported several FASTQ files. They all appear in the list of my "saved datasets" (see attached screenshot). However, when I click on any of the tools in the left panel (e.g. "FASTQ Summary Statistics") I get in the middle panel the info for the tool but the dropdown menu listing the available FASTQ files is empty (see attached screenshot). What do I need to do to be able to perform analysis on the FASTQ files that I uploaded? many thanks, Nikolay

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Question on galaxy data visualization
by Sun, Wenping [USA] 14 May '13

14 May '13

Dear galaxy group, I have question on the data visualization from output of galaxy pipeline. Is there any ideogram tool inside of galaxy? Regards, Kathryn

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problem uploading txt data
by Chunyu Liu 14 May '13

14 May '13

hi, I had an odd problem today, seems not a problem before: I am trying to upload a simple tab-delimited text file into galaxy, but it kept telling me: empty format: txt, database: hg19 The uploaded binary file contains inappropriate content Also, showed filesize as 0 bytes. I tried Unix format, DOS format. It is a very small data, only 348 bytes. 4 rows, as attached. What is WRONG? Thanks! Chunyu

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Jobs delay
by Benjamin Leblanc 14 May '13

14 May '13

Hello, I am new user to galaxy and I was wondering if there is a way to estimate the average delay before execution of currently submitted jobs in galaxy? Best regards, -- Benjamin Leblanc, Ph.D. - K. Helin group BRIC - University of Copenhagen Ole Maaløes Vej 5, building 4, 4th floor DK-2200 Copenhagen N, Denmark Office phone: +45 35 32 55 37 Email: benjamin.leblanc(a)bric.ku.dk

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Query not starting
by Neel Aluru 13 May '13

13 May '13

Hello, I am having problem with starting my query. For days it is showing "Job waiting to run". Is the system backed up and there is a long queue? or is there a problem with my query? Normally if there is any problem it shows an error message. I am within the usage limits. I am trying to map my SOLiD data set to custom reference genome (fasta format). I converted the SOLiD output to fastq. Then I am using Map with Bowtie for SOLiD. Everything went fine quickly except the last step, which waiting for over 6 days now. Any help or suggestions appreciated. Thank you, Neel Neel Aluru Assistant Scientist Biology Department Redfield Building 3-04 Woods Hole Oceanographic Institution 45, Water Street Woods Hole, MA naluru(a)whoi.edu 508-289-3607 http://www.whoi.edu/page.do?pid=109916

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A new version of the Genomic HyperBrowser has been released!
by Sveinung Gundersen 13 May '13

13 May '13

Dear Galaxy users, We are happy to announce the release of version 1.6 of the Genomic HyperBrowser, a analysis web server built on top of Galaxy. This release is a companion to an article recently published in Nucleic Acids Research, to be included with the 2013 Webserver issue: Sandve, Geir K., et al. "The Genomic HyperBrowser: an analysis web server for genome-scale data." Nucleic acids research (2013) (http://nar.oxfordjournals.org/content/early/2013/04/29/nar.gkt342.full) To quote the abstract of the article: "The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome." In this article, an overview of most of the 42 tools and 83 analyses included with the Genomic HyperBrowser is presented (for the first time) in table form. The Genomic HyperBrowser will also be presented in the 2013 Galaxy Community Conference (http://wiki.galaxyproject.org/Events/GCC2013) in the Training day workshop titled "Statistical Genome Analysis with Galaxy", and also in a regular talk. The focus of this release has been on new and revamped tools: 1. A set of new tools has been added: - Visualize track elements relative to anchor regions - Create high-resolution map of track distribution along genome - Create high-resolution map of multiple track distributions along genome - Extract segments where value is greater/less than threshold 2. A new hypothesis test for 3D-colocalization of genomic elements has been added (along with a tool for easier access to the analysis). This hypothesis tests checks whether the elements of a genomic track is positioned on the DNA (in interphase) closer in 3D than expected by chance. The methodology has been published in a separate article: Paulsen, Jonas, et al. "Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements." Nucleic acids research (2013). (http://nar.oxfordjournals.org/content/early/2013/04/08/nar.gkt227.full) Included with this analysis are readily preprocessed Hi-C datasets for the cell lines GM06990, GM12878, hESC, K562, and RWPE1 for human (hg19), in addition to cell lines cortex and mEsc for mouse (mm9), all available in several resolutions. 3. The usability of tools has been improved: - The structure of the HyperBrowser tools has been rearranged, and renamed for easier understanding and use - Help text and usage examples (using Galaxy Pages with embedded histories) has been added to most tools 4. Numerous bug fixes and improvements have been made, including the fixing of several memory leaks. We hope you will find the Genomic HyperBrowser and new additions useful. Please let us know if you experience any problems, need help with your analysis, or have ideas for new functionality! For the HyperBrowser team, Sveinung Gundersen -- Sveinung Gundersen, PhD Student, Bioinformatics, Dept. of Tumor Biology, Inst. for Cancer Research, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway

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Map with BWA for Illumina is hung
by Casey,Richard 13 May '13

13 May '13

Hi, when we try using Map with BWA for Illumina on the public server, it never starts running and sits in a queued state forever. We have jobs that have been queued for more than 5 days. Any ideas on why these jobs never start? ------------------------------------------- Richard Casey, PhD CSU 970-492-4127 970-980-5975 richard.casey(a)colostate.edu<mailto:richard.casey@colostate.edu>

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How to analyze the Encode RNA-seq data from UCSC genome browser with Galazy
by Santagostino Marco 11 May '13

11 May '13

Dear Sir/Madam, I am new at Galaxy. I need to define if a set loci ( about 700) is transcribed, i.e. these loci overlap with those reported in the Encode RNA-seq data. The track contains several tables, can you please suggest me how to proceed? do I need to download all the tables from UCSC table browser and then upload/send them to Galaxy? Is there a way to refer only to the Encode RNA-seq track without downloading the whole table set? I have the coordinates of each one of my loci, from those I can obtain the sequences. I intended to use the Public Galaxy Main Instance. Thank you, Marco Santagostino -- Marco Santagostino, PhD Laboratorio di Biologia Molecolare e Cellulare Dipartimento di Biologia e Biotecnologie, University of Pavia Ferrata street, 9 - 27100 Pavia, Italy Tel.: +39 0382 985540 Fax: +39 0382 528496 e-mail: marco.santagostino(a)unipv.it

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nebula problem
by Gema Sanz Santos 09 May '13

09 May '13

Hello, I'm using Nebula and when I try to use the annotation tools (genomic annotation and gene annotation in NGS annotation menu) I got always this error despite of the bed file that I use: An error occurred running this job:Unable to run this job due to a cluster error I also got this error message for everything that I try, even upload data sets (which I can not upload anymore) Could you indicate me how to solve this? Regards, Gema

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Filter Fastq
by Casey,Richard 09 May '13

09 May '13

Hi, We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run? ---------------------------- Richard

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