- galaxy-user - lists.galaxyproject.org

How to implement the button "send query to galaxy" in UCSC Main tool
by Zhe Chen 01 Oct '10

01 Oct '10

Hi, Can u tell me how to implement the "send query to galaxy" button on page http://genome.ucsc.edu/cgi-bin/hgTables ? which is the tool in (Get Data)->(UCSC Main tool), on page 2. Thanks

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Getting data from NCBI
by Peter Young 01 Oct '10

01 Oct '10

The Get Data | Get Microbial Data tool is nice, but is limited to a subset of the older genomes among those that are currently available. It should surely be possible to get any accession directly from NCBI, but I don't see a tool to do that. The best I can do is to download a file to my computer and then upload it again to Galaxy. Am I missing something obvious? On a related point, I don't see GenBank listed as a format for conversion. Thanks Peter -- Prof J P W Young Department of Biology (Area 3) University of York Wentworth Way Heslington York YO10 5DD jpy1(a)york.ac.uk tel: +44 1904 328630(direct), 328500(department) fax: +44 1904 328505(department) http://bioltfws1.york.ac.uk/biostaff/staffdetail.php?id=jpwy http://www.york.ac.uk/depts/biol/staff/jpwy/jpwy.htm Email disclaimer: http://www.york.ac.uk/docs/disclaimer/email.htm

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Using output as parameter in workflow
by Lance Parsons 01 Oct '10

01 Oct '10

I have a user who is trying to use the output of summary statistics as input to the next step in a workflow. e.g. using "median + 2*stddev" as the threshold cutoff in the next step, which is "pileup-to-interval". Is that possible in galaxy workflow? The current workaround is to create two separate workflows and input the parameter manually, but that is less than ideal. Any suggestions would be appreciated. -- Lance Parsons - Software Developer/Data Analyst 134 Carl Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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options for history description using tool config
by Bossers, Alex 01 Oct '10

01 Oct '10

If you configure your tool using the xml config file it displays by default the tool action on data nr in the history description. This is useful but there are option to get more descriptive info in there. Default for the sequence length example: .. <outputs> <data name="output" format="tabular"/> </outputs> .. Gives: 2: Compute sequence length on data 1 This can be altered to have something like a description having the tool settings: .. <outputs> <data name="output" format="tabular" label="SEQLEN of ${query_type.value_label}" /> </outputs> .. Where you can reuse a specific selected value from the form entered by the user. Is there any documentation on this? The default tool_conf xml wiki has no specific info on this. I also noticed the use of .metadata in datasets to specify columns in that data... The specific I want to have for some of my tools is that the history line shows the tool description and the sequence name chosen. If I do: .. <outputs> <data name="output" format="tabular" label="SEQLEN of ${input1}" /> </outputs> .. I do get the sequence FILE name but with the complete not so informative path. Showing the descriptive fasta header would be even nicer.... Thanks Alex

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Fetch Taxonomic Representation on dataset is blank
by Ameena Nalim 27 Sep '10

27 Sep '10

Hello All I ran a metagenomic analysis on a large dataset, larger than any of the others that I have run successfully. Joining two megablast queries resulted in 370, 163, 941 lines in tabular format. I then ran Fetch taxonomic representation on the data It ran with no error messages however when it was done approximately 3 days later, it was a empty file. Why does this happen? The previous dataset with 16,017,326 lines ran successfully If I redo it, how do I know that three days from now, it will not come back empty again? any suggestions? thanks Ameena

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Re: [galaxy-user] integrating Galaxy with a relational data warehouse?
by Yury Bukhman 27 Sep '10

27 Sep '10

Thanks again for your comments. The points about huge file sizes and their "write once" nature are convincing. Are the indexes you are talking about already implemented in Galaxy? Is this how it supports its database-like join and subset operations? What about summarized downstream data types, such as gene intensities, p values from statistical tests etc? Those would seem to be relatively low-volume and less immutable. Suppose, as a simple example, I have a gene expression experiment with several samples (be that arrays or RNA-Seq runs), assigned to 2 treatments. I want to set up a workflow that would first summarize the data to get an expression value for each gene (or exon, or transcribed region) in each run, and then do t tests to discover those that are differentially expressed between the treatments. I'll need to support a project that would perform similarly designed experiments over and over again, e.g. with different cell lines and/or treatments. Although the raw data may remain as flat files in a Galaxy data library, wouldn't it make sense to store the summarized data and t test p values in a relational database? Thanks. Yury On 09/01/10, James Taylor <james(a)jamestaylor.org> wrote: > Exactly. In addition, most relational database are optimized for data that can change, but the access pattern for our raw data is write once. We can implement more efficient storage formats and indexes outside the database for this purpose. > > On Aug 31, 2010, at 5:17 PM, Hiram Clawson wrote: > > > Good afternoon Yury: > > > > Typical file sizes are currently running in the 10s and 100s of Gb for most work flows these days. > > It isn't practical to try and stuff such large single entities into a database. > > It is much more simple to compute indexes into the file and store the indexes in > > the database. We do this all the time at the UCSC genome browser. > > > > --Hiram > > > > Yury Bukhman wrote: > >> Thank you, James, for your reply. I wonder if you could elaborate ... > > _______________________________________________ > > galaxy-user mailing list > > galaxy-user(a)lists.bx.psu.edu > > http://lists.bx.psu.edu/listinfo/galaxy-user > > -- jt > > James Taylor > Assistant Professor > Department of Biology > Department of Mathematics & Computer Science > Emory University -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman(a)glbrc.wisc.edu

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stuck
by Hsu, Amy (NIH/NIAID) [E] 27 Sep '10

27 Sep '10

I'm sure this is a silly question, but I have been stuck since yesterday. I have some whole genome sequencing data - What was given to me is an enormous XL file with all the single base changes identified in 4 people. I don't want to track down all the changes, yet I've noticed some of them labeled as "novel" are in fact SNPs - particularly if I use build 130. I imported just chr, start, end using same base number for start/end from part of my file (chr 1) and then pulled down all the SNPs from UCSC for Chr. 1. What I would like to do is label the lines in my file that are snps. I have tried intersect, join, subtract, all to no avail. What am I doing wrong? Any help would be appreciated. thanks - Amy Hsu

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galaxy user PAGES
by Bossers, Alex 27 Sep '10

27 Sep '10

Hi All, Our local instance of galaxy is working fine (galaxy_dist version). I tried enabling PAGES by including enable_pages = True in the universe_wsgi.ini file first in the beta section which gave me problems. Searching the wiki and user forum indicates the enable statement should be in the [app::main] section, so I did. No luck either and same error as below. I do get a SAVED PAGES option (instead of PAGES option as described in the wiki) under USER menu where I can create pages and see them listed. But when I select edit contents I only get an empty box at the top left of the page editor and a script error (below attached) on ie8. Do I miss some prerequisite for PAGES to work correctly? Or is this an ie8 generic problem since I just checked in firefox and it seems to work. IE8 is unfortunate our embedded/default company web browser. Any help appreciated. Alex ---------Script error of the page --------------- Errordetails webpagina Gebruikersagent: Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 6.1; WOW64; Trident/4.0; SLCC2; .NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0; .NET4.0C; InfoPath.3) Tijdstempel: Mon, 27 Sep 2010 08:00:35 UTC Message: Id, string or number expected Line: 100 Char: 5 Code: 0 URI: http://galaxy01:8080/page/edit_content?id=f2db41e1fa331b3e Message: Id, string or number expected Line: 761 Char: 13 Code: 0 URI: http://galaxy01:8080/page/edit_content?id=f2db41e1fa331b3e

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Scaling - what should happen with universe_wsgi.ini
by Jelle Scholtalbers 22 Sep '10

22 Sep '10

Hi, Recently I followed the guide on http://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling. So I created two ini files, one for the web apps and 1 for the runner. Now is my question, what purpose does the universe_wsgi.ini serve. As I found out yesterday is that this ini is still used by the manage_db.sh script.. I never updated this universe_wgsi.ini file, although I moved to another database. So this script updated the wrong database.. error on my side I guess, but should I really keep 3 universe_wsgi files? And if so, what should be in which, as I now have most of the parameters in all three ini files.. Cheers, Jelle

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Galaxy 'active' users
by Erick Antezana 22 Sep '10

22 Sep '10

Hi, is there a way to check whether my Galaxy instance is being used (logged in/working)? (another way than "tail-ing" the paster.log file). thanks, Erick

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