- galaxy-user - lists.galaxyproject.org

bed to bigbed conversion
by Gijs Santen 19 Jun '11

19 Jun '11

Dear users, I am only recently beginning to discover Galaxy, so please bear with me... I am trying to convert a bed to bigbed file, but the job remains 'grey', it does not start. I repeated the same conversion with the UCSC sample file (http://genome.ucsc.edu/goldenPath/help/examples/bedExample.txt) , but it still does not work. I simply uploaded the file directly from the link and then used the bed-to-bigbed conversion tool. So either I am doing something wrong or could there be an issue with this conversion on the server? Thanks for your insights, Gijs

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Galaxy server issues?
by David K Crossman 17 Jun '11

17 Jun '11

Hello! We uploaded 12 samples to Galaxy last night via FTP. This morning, I went to "Get Data" and clicked on all 12 that were under the FTP location, chose the type of file they were and reference genome and then clicked "Excecute." The 12 moved over to the History panel and after a couple of minutes went from gray to yellow. As of this moment, all 12 are still in the yellow stage (still spinning). Is this normal for that many samples (each sample is about 8GB in size) or should they already have turned green? Any info would be greatly appreciated. Thanks, David

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Galaxy Workshops @ USC June 23-24
by Dave Clements 17 Jun '11

17 Jun '11

Hello all, There will be two Galaxy workshops at the University of Southern California (USC) next week. Both are presented by Jeremy Goecks of Emory University and the Galaxy team. *Both workshops are open to the public:* *Galaxy: A web‐based workbench for interactive and reproducible analysis of high‐throughput sequencing data, Thursday, June 23, 2011* At Aresty Auditorium, Harylene J Norris Cancer Research Tower, USC Health Science Campus, 1450 Biggy Street Registration is free, but required. Register at https://uschsl.qualtrics.com/SE/?SID=SV_bDaxnZwEfrfk1BG 9:15am-Noon Introduction to Galaxy including 30 min. Q&A Session 2:00pm-5:00pm High‐throughput sequencing data analysis including 45 min. Q&A Session *Progress and Challenges in Developing a Web-based Platform for Computational Biomedical Research, Friday, June 24, 2011 * See USC ISI AI Seminar Page ( http://ai.isi.edu/index.php?module=seminars/index) for details on time and location. The recent reliance on computation in biology has created an informatics crisis for biomedical researchers: computational resources are often difficult to use, communicating techniques and experiments is challenging, and reproducibility is very limited. Galaxy is one approach for addressing these problems. Galaxy is a popular Web-based platform for performing accessible, reproducible, and transparent genomics research. Galaxy provides a collaborative environment for performing complex analyses with automatic and unobtrusive provenance tracking; these features allow transparent sharing of both the precise computational details underlying an analysis and also intent, context, and narrative. Based on experiences with Galaxy, Jeremy will discuss some open problems that might be addressed using artificial intelligence methods and techniques. Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.org/

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Extract Genomic DNA Problem
by Steve Taylor 17 Jun '11

17 Jun '11

Hi, I was trying to extract FASTA sequences using the following tab separated data for Chicken on the Galaxy Main server: chr5 47258168 47259240 chr18 1938527 1939965 chr2 101973625 101974007 chr4 75653898 75674045 chr19 4258837 4263299 chr4 39330049 39372715 chr4 9606881 9610083 chr15 7264937 7265599 chr21 6659189 6667015 chr2 351239 352821 I got the following galaxy output: ==================================== 7: Extract Genomic DNA on data 6 empty format: fasta, database: galGal3 Info: 10 warnings, 1st is: Unable to fetch the sequence from '47258168' to '1072' for build 'galGal3'. Skipped 10 invalid lines, 1st is #1, "chr5 47258168 47259240" Any ideas what I am doing wrong? Thanks, Steve

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Re: [galaxy-user] New Galaxy User
by Paul-Michael Agapow 17 Jun '11

17 Jun '11

Gaurav > 1. Is there any help file explaining directory structure and what all > configuration files used for? The Galaxy wiki is the best place to go for these things, as Louise-Amelie said. You should be able to ignore most things in the config files initially as they will "just work". You can ignore most of the directory structure as well, except perhaps the "tools" directory. > 2. I got list of all dependencies from website, Do I have to install all > tools in /usr/local/bin/ or can be installed at any custom location? Mostly, the install should (again) "just work" (install the tarball or distrib and run). I've a got a Galaxy installation checklist here: <http://www.agapow.net/science/bioinformatics/galaxy/installing-galaxy> It's a bit peculiar to my own situation, but it might give you another point-of-view. ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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Question about output CuffDiff SplicingDiff
by Felix Mayr 16 Jun '11

16 Jun '11

Hi there, Looking at the output of the SplicingDiff files of CuffDiff, me and my colleagues are preplexed about the output of the p_values and q_values. We've tried different inputs of different samples to compare but never seem to manage to get p_values smaller than 0.50 and we keep getting higher than 1 q_values (also smaller which we expect) which we think is strange too. The input files we use for the CuffDiff are the CuffCompare of a combined CuffCompare of a dataset, or the CuffCompare of just the two samples we want to analyse. For the samples input files we use the TopHat files respectively. Could you please help us get meaningful results for the SplicingDiff files or help us understand the data? The top 5 rows of our typical SplicingDiff file: test_id gene_id gene locus sample_1 sample_2 1583 TSS11905 XLOC_028193 - chr5:134910259-134914719 q1 q2 2385 TSS12870 XLOC_030892 - chr7:29976178-30008608 q1 q2 8005 TSS6887 XLOC_016656 - chr18:47803031-47807892 q1 q2 10214 TSS9761 XLOC_022527 - chr20:43128822-43138649 q1 q2 2818 TSS13383 XLOC_032450 - chr8:100899717-100905900 q1 q2 status value_1 value_2 sqrt.JS. test_stat p_value q_value 1583 OK 0 0 0.000771867 0.797878 0.501645 164.5400 2385 OK 0 0 0.001548470 0.797809 0.505482 82.8991 8005 OK 0 0 0.003288510 0.797717 0.508184 55.5615 10214 OK 0 0 0.001414180 0.797620 0.510277 41.8427 2818 OK 0 0 0.007112780 0.797416 0.513678 33.6973 Thanks in advance for your most appreciated help, Felix Mayr

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SRMA on a local galaxy instance?
by Gong, Henry 16 Jun '11

16 Jun '11

Does anyone know how to get SRMA to work properly in galaxy? I've used the pre-built 0.1.15 jar as well as a 0.1.16 jar I built from source, but the result of an SRMA re-alignment job in both instances is a python process which only takes a few percent CPU (or less, since it only seems to be outputting timestamps to the terminal). Here are my system's specs if they're important: 2.8Ghz Intel i5, 4 core; 4GB 1333MHz DDR3; 1TB HDD (430GB free). The OS is OS X 10.6.7. I've also built the required indices and placed them in path/to/galaxy-dist/hg19/srma_path/hg19.dict, hg19.fa.fai, and hg19.fa; the hg19 is a concatenated version of the various chromosome and contig files, and I've followed the sample files in adding these locations to the .loc files (both srma and picard tools). The NGS installation page seems to suggest that SRMA does work, so I'm not sure if I'm overreacting, but I'd really appreciate any advice on this, since I imagine others have had similar problems. Cheers, Henry

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galaxy cluster setup
by Robert Jackson 16 Jun '11

16 Jun '11

Does anyone have practical info on galaxy setup on a cluster? Robert C. Jackson Software Systems Specialist III The University of Texas Pan-American Computer Support Services Division of Information Technology Phone: 956-665-2455 Fax: 956-665-8777

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New Galaxy User
by gaurav thareja 16 Jun '11

16 Jun '11

Hi All, I am a new user of Galaxy. I am trying to configure galaxy on my local system. I took clone of repository(https://bitbucket.org/galaxy/galaxy-dist). But I have couple of issues while understanding code base: 1. Is there any help file explaining directory structure and what all configuration files used for? 2. I got list of all dependencies from website, Do I have to install all tools in /usr/local/bin/ or can be installed at any custom location? I have already gone through tutorial (http://gmod.org/wiki/Galaxy_Tutorial) which was quite helpful and interesting but doesn't quite talk about my doubts above. Regards Gaurav Thareja -- Regards Gaurav Thareja

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Cufflinks advice
by Michael Gooch 15 Jun '11

15 Jun '11

I attempted to run cufflinks on some RNA sequencing data. It seemed to complete without any errors, but the output files were empty. I am trying to figure out if I did something wrong or whether my data needs some additional processing before cufflinks will be able to use it. (Or whether the data is unsuitable for cufflinks.) The data is paired end reads. M. Gooch

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