galaxy-user September 2010

galaxy-user@lists.galaxyproject.org

43 participants
36 discussions

PCA -- princomp or prcomp
by zod 14 Sep '10

14 Sep '10

Hi, Is it possible to add the R's 'prcomp' function to the PCA tool? Or just switch the tool to use 'prcomp' instead of 'princomp'? Thanks, David

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subscription
by Inbar Plaschkes 14 Sep '10

14 Sep '10

inbar.plaschkes(a)gmail.com -- ______________________________________________________________ Inbar Plaschkes Bioinformatics Core Facility National Institute for Biotechnology in the Negev Building 51, room 314 Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Email: inbar.plaschkes(a)gmail.com Tel: 08-6479034 054-7915931 Fax: 08-6472983 http://bioinfo.bgu.ac.il

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Error after upgrade
by Farhat Habib 13 Sep '10

13 Sep '10

Dear All, After upgrading using hg pull -u -r f09915c8da94 then, hg diff after which it asked me to upgrade db which I did using, sh manage_db.sh upgrade Galaxy fails to start on my local install. galaxy.model.custom_types DEBUG 2010-09-13 11:41:18,475 pysqlite>=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): File "/home/farhat/galaxy-central/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/farhat/galaxy-central/lib/galaxy/app.py", line 42, in __init__ self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) File "/home/farhat/galaxy-central/lib/galaxy/tools/data/__init__.py", line 22, in __init__ self.add_from_config_file( config_filename ) File "/home/farhat/galaxy-central/lib/galaxy/tools/data/__init__.py", line 31, in add_from_config_file tree = util.parse_xml( config_filename ) File "/home/farhat/galaxy-central/lib/galaxy/util/__init__.py", line 101, in parse_xml tree = ElementTree.parse(fname) File "/home/farhat/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/farhat/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tool_data_table_conf.xml' Any help with rectifying this? Yours, -Farhat

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local instance of galaxy installation problems
by Abhay Krishna 12 Sep '10

12 Sep '10

Any clue, why i can not see galaxy on local host error when i run the shell script is socket.error: [Errno 98] Address already in use and browser when i access local host shows following error XML Parsing Error: syntax error Location: http://localhost:8080/ Line Number 1, Column 1:Bad Request ^ Abhay CABIMER www.cabimer.es

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join mailing list
by akshay kakumanu 11 Sep '10

11 Sep '10

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how to set up a microarray analysis workflow in Galaxy?
by Yury Bukhman 09 Sep '10

09 Sep '10

Hi, I am new to Galaxy. My co-workers have installed a Galaxy server locally and written wrappers for a couple of command-line programs. Now I would like to implement a microarray data analysis workflow using R and Bioconductor. I imagine, it would have the following steps: 1) A user uploads a set of files that constitute a microarray experiment, e.g. a bunch of Affymetrix CEL files and a spreadsheet of information that describes experimental conditions (to be imported into the phenoData slot of a Bioconductor ExpressionSet object) 2) An R script is run to parse/normalize/summarize the data and generate and ExpressionSet object. This object is stored as a file. 3) Another R script takes the ExpressionSet as its input and does some downstream analysis using appropriate Bioconductor packages I have the following questions. My apologies if they are trivial, as I am a novice here: 1) How do I enable a non-administrative user upload a dataset that consists of multiple files, for the first step of my workflow? 2) Will Galaxy store an .RData file? 3) Are there any other issues that I should know about before I plunge into this? Thanks Yury -- 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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September 8, 2010 Galaxy Development News Brief
by Jennifer Jackson 08 Sep '10

08 Sep '10

September 8, 2010 Galaxy Development News Brief http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_… Here are the highlights of what you will get if you perform the following upgrade: hg pull -u -r f09915c8da94 What's New New Multiple Sample Tracking Features * UI enhancements: checkboxes to select samples & select field to specify operations. * State change mechanism added for multiple samples and removed for individual samples in the sample_events page. * Enhanced sample searching implemented. Uses sample name, barcode and dataset name with menu items in masthead and admin menu. o Example of usage: new wild-card searches. New Custom Sorting in Grid Framework * Enhance grid framework to enable custom column sorting (default sorting unchanged). * Sort criteria are now mapped to a column, and the column defines the sorting to be done on the grid query. o Examples of usage: (a) case-insensitive sorting of text fields and (b) case-insensitive sorting for user names in published-item grids. New Data Format Conversion Tools * NGS: SAM Tools => BAM-to-SAM converts BAM format to SAM format * Convert Formats => Wig to bigWig converter New GFF Format Filtering Tools * Filter and Sort => GFF => Extract features from GFF file, Filter GFF file by attribute using simple expressions, Filter GFF file by feature count using simple expressions. * New Filter GFF file by feature count filters a GFF file using conditions based on transcripts' features counts. o Example of usage: filter for transcripts that have a minimum number of exons or transcripts that have 3' UTRs. Updated & Improved Data Libraries * Added support for the AddressField, CheckboxField, SelectField and WorkflowField form field types (in addition to the previously supported TextArea and TextField) to data library templates. * Inherited template fields now also inherit any field contents from the immediate "parent" of the current item (folder or dataset). * The information in our data library templates wiki at http:bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibraryTemplates has been updated to reflect the new features and behavior. Sample Tracking: Email notifications * Notification of specific sample state changes. * Changes made to barcode scan AMQP handler to update sample state to also send email when required. * Notification to multiple recipients. * Request events history records notifications. * UI enhancements: o "edit request" page to allow users to change notification configurations. o "request" page to show the request type state, user & notification details. Jobs & related * Improved handling of metadata to optimize job processing. Includes a new user prompt to set metadata manually or retry auto-detection externally when using 'set_metadata_externally = True' . * Enhance wig datatype to only use first 100 data lines to determine column type metadata if dataset filesize exceeds max_optional_metadata_filesize as configured in datatypes_conf.xml. * Add 'NullToolOutputActionOption' to tool output dataset actions. This action option is used implicitly when no ToolOutputActionOption(s) have been defined. o Example of usage: a metadata value can be set to a static value on a per Tool Output basis. Installation and Management * Added support for installing Galaxy on systems without direct access to the Internet. Updated Galaxy Installation wiki (see section "How to get eggs: If your Galaxy server does not have Internet access" http:bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs. * When viewing library dataset information as an administrator, add a field that displays the path to the actual disk file that underlies the dataset. Trackster * Each track now has an Overview checkbox that will set the initial chromosome-wide view. * Visualizations that users own or are shared with can now be cloned. * New go-to feature allows users to redirect quickly to a specified chromosome or position. o Example of usage: "chr1:1-100,000,000". * Drag-zoom activated when a chromosomal position is clicked on. * Line tracks display mode can also now be activated inline. * Changing display mode from "Auto" now fetches additional detail data and displays features. Displays error messages in canvas elements if present. This also limits the number of features displayed per tile. General Improvements * Slight makeover to Galaxy tabs: (a) added published item links to 'Shared Data' tab; (b) standardized personal item lists as 'Saved XXXs'; and (c) added defaults action for Visualization tab. * Minor grid refactoring. * Don't re-sort BAM files on upload if already sorted (adapted from Brad Chapman patch). * Use image_path for Workflows and now display modal instead of relative paths. -- Galaxy Project Team http:usegalaxy.org http:bitbucket.org/galaxy/galaxy-central This project is supported in part by NSF, NHGRI, and the Huck Institutes of the Life Sciences, and The Institute for CyberScience at Penn State.

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Multiple blast search
by Wong, Chloe 08 Sep '10

08 Sep '10

Hi, I am new to Galaxy and would like to say thanks for the very useful introduction video. I would like to map ~26,000 sequence on the human genome and I think I could possibly use Galaxy to do it. I managed to get data from the UCSC as the reference genome and have also loaded up my file containing the sequence that I would like to map. However I am unsure how I could align the two files. I thought maybe I could use the 'fetch alignment' tool to perform a blast search but don't think it worked. Can you please let me know if it's possible to use Galaxy for this job? and if so, can you give me some ideas/example of how I can achieve this? Thanks very much for your help in advance! Chloe Chloe Wong PhD Student MRC SGDP Research Centre, Insitute of Psychiatry, King's College London, De Crespigny Park, Denmark Hill, London SE5 8AF Tel: +44(0)20 7848 5410

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Fwd: [galaxy-lab] Question about Branch Lengths Estimation
by Guruprasad Ananda 07 Sep '10

07 Sep '10

Hi Melissa, So looks like you'll have to use 'N' as a masking character instead of #. You can either rerun quality masking on your alignments or do the following to convert your #s to Ns in your masked fasta files. 1. Convert fasta to tabular 2. Use 'Text manipulation -> Compute' tool on the tabular file from step(1) to convert #s to Ns, using the following expression: c2.replace(chr(35),"N") 3. Convert output of step(2) to Fasta using 'Convert formats -> Tabular-to-FASTA' tool with c1 as title column and c3 as sequence column. Thanks, Guru. Begin forwarded message: > From: Guruprasad Ananda <gua110(a)bx.psu.edu> > Date: September 7, 2010 4:07:54 PM EDT > To: Sergei L Kosakovsky Pond <spond(a)ucsd.edu> > Cc: "Melissa A. Wilson Sayres" <mwilsonsayres(a)gmail.com>, Galaxy Lab <galaxy-lab(a)bx.psu.edu> > Subject: Re: [galaxy-lab] Question about Branch Lengths Estimation > > Thanks Sergei! Melissa's alignments have been masked by quality scores. Will it work if she used N as a masking character instead of #? > > Guru. > > On Sep 7, 2010, at 4:04 PM, Sergei L Kosakovsky Pond wrote: > >> Hi Guru, >> >> The alignment you attached contains '#' inside sequence strings. >> HyPhy will skip those, creating misaligned sequences of differing lengths. >> The error you see happens if the first sequence is shorter than others. >> >> There are two solutions: >> >> 1). Replace '#' with characters that HyPhy understands (e.g. '-') >> 2). Tell HyPhy to accept '#' as a valid token. >> I think this option can only work with NEXUS input files, because '#' is a sequence delimiter in the MEGA format, which HyPhy tries to autodetect... >> >> Sergei >> >>> Hi Sergei, >>> >>> Melissa is trying to use HYPHY branch lengths estimator on Galaxy on 4-way primate alignments. HYPHY is however producing the following error: >>> >>> Error: >>> Internal Error in ' >>> Write2Site' - index is too high (using compact representation) >>> Call stack >>> 2 : Read Data Set ds from file PROMPT_FOR_FILE >>> 1 : ExecuteAFile from file "/tmp/tmpX5jYY7" using basepath /tmp/. reading input from _genomeScreenOptions >>> >>> >>> >>> Is this because her sequence lengths are pretty big? Is there a limi on sequence lengths? >>> Here is a sample input file that causes this problem, in case you wanted a test case: >>> http://bx.psu.edu/~gua110/Galaxy165-%5bchr22_HCOM_fasta%5d.fasta >>> Tree = ((hg18,panTro2),ponAbe2),rheMac2) >>> >>> Thanks, >>> Guru. >>> >>> >>> Begin forwarded message: >>> >>>> From: "Melissa A. Wilson Sayres" <mwilsonsayres(a)gmail.com> >>>> Date: September 7, 2010 2:58:44 PM EDT >>>> To: Guruprasad Ananda <gua110(a)bx.psu.edu> >>>> Cc: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> >>>> Subject: Re: Question about Branch Lengths Estimation >>>> >>>> Hi Guru, >>>> >>>> It worked with most of the HC-files (just one failed: chr1_HC_fasta), but hasn't worked with any of the four-way alignments, using either of these trees: >>>> >>>> (((hg18,panTro2),ponAbe2),rheMac2) >>>> >>>> nor >>>> >>>> ((((hg18),panTro2),ponAbe2),rheMac2) >>>> >>>> I tested chr1 and chr2. >>>> >>>> Ideas? >>>> >>>> Thanks! >>>> Melissa >>>> >>>> On Tue, Sep 7, 2010 at 1:27 PM, Melissa A. Wilson Sayres <mwilsonsayres(a)gmail.com> wrote: >>>> Thanks Guru!! >>>> >>>> It seems I just have a knack for finding these little quirks. :) >>>> >>>> I really appreciate you figuring this out! >>>> >>>> Best, >>>> Melissa >>>> >>>> >>>> On Tue, Sep 7, 2010 at 11:48 AM, Guruprasad Ananda <gua110(a)bx.psu.edu> wrote: >>>> Hi Melissa, >>>> >>>> This seems to be the case with pairwise alignments only. 3-way and above work well with the regular Newick tree definitions. For instance, for a 4-way alignment, you could use: ((hg17,panTro1),(mm5,rn3)) >>>> I'll update the tool help with this info. >>>> >>>> Thanks, >>>> Guru. >>>> >>>> On Sep 7, 2010, at 11:40 AM, Melissa A. Wilson Sayres wrote: >>>> >>>>> Hi Guru, >>>>> >>>>> Thanks for getting back to me so quickly! >>>>> >>>>> I'll give that a try and let you know how it goes. If this is the >>>>> problem, perhaps the instructions could be updated under the took >>>>> because the current directions give a different formatting of the >>>>> tree. It is a little counter- intuitive to have to put parentheses >>>>> around one species. Do you think it will be the same for four species? >>>>> (That I put parentheses around just hg18) >>>>> >>>>> Thanks again!! >>>>> >>>>> Best, >>>>> Melissa >>>>> >>>>> >>>>> On Tuesday, September 7, 2010, Guruprasad Ananda <gua110(a)bx.psu.edu> wrote: >>>>>> Hi Melissa, >>>>>> Looks like Hyphy doesn't like the way you specified your phylogenetic tree. I tried running the tool on your test dataset with the tree defined as ((hg18),panTro2) and it ran just fine! Please give it a shot and let me know if the problem persists.You can find a working example of the same here:http://main.g2.bx.psu.edu/u/guru/h/imported-melissa-test-history (see history item #8) >>>>>> Thanks,Guru. >>>>>> On Sep 3, 2010, at 5:21 PM, Melissa A. Wilson Sayres wrote: >>>>>> Hi there, >>>>>> I am trying to use the tool Branch Lengths Estimation under the Evolution heading. >>>>>> I have a pairwise alignment - (hg18,panTro2), but when I try to run the tool, using the HKY85 model on my FASTA formatted alignment, I get nothing in the output. >>>>>> >>>>>> >>>>>> It doesn't give an error, but instead gives: >>>>>> >>>>>> >>>>>> 143: Branch Lengths on data 120 >>>>>> empty, format: tabular, database:hg18Info: Single Alignment Analyses >>>>>> >>>>>> Any ideas? >>>>>> Thanks!!Melissa >>>>>> -- >>>>>> Melissa A. Wilson Sayres >>>>>> NSF Graduate Research Fellow, Bioinformatics & Genomics >>>>>> 306 Wartik Lab >>>>>> University Park, PA 16802 >>>>>> maw397(a)psu.edu >>>>>> >>>>>> It is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring. -- Carl Sagan >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> galaxy-user mailing list >>>>>> galaxy-user(a)lists.bx.psu.edu >>>>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>>>> >>>>>> >>>>> >>>>> -- >>>>> Melissa A. Wilson Sayres >>>>> NSF Graduate Research Fellow, Bioinformatics & Genomics >>>>> 306 Wartik Lab >>>>> University Park, PA 16802 >>>>> maw397(a)psu.edu >>>>> >>>>> It is far better to grasp the Universe as it really is than to persist >>>>> in delusion, however satisfying and reassuring. -- Carl Sagan >>>>> >>>> >>>> >>>> >>>> >>>> -- >>>> Melissa A. Wilson Sayres >>>> NSF Graduate Research Fellow, Bioinformatics & Genomics >>>> 306 Wartik Lab >>>> University Park, PA 16802 >>>> maw397(a)psu.edu >>>> >>>> It is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring. -- Carl Sagan >>>> >>>> >>>> >>>> -- >>>> Melissa A. Wilson Sayres >>>> NSF Graduate Research Fellow, Bioinformatics & Genomics >>>> 306 Wartik Lab >>>> University Park, PA 16802 >>>> maw397(a)psu.edu >>>> >>>> It is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring. -- Carl Sagan >>> >> >> /-------------------------------------------------------------------------------------------------/ >> Ignorance more frequently begets confidence than does knowledge >> >> Charles Darwin >> >> /-------------------------------------------------------------------------------------------------/ >> >> Sergei L. Kosakovsky Pond, Ph.D. >> >> Assistant Adjunct Professor >> Division of Infectious Diseases >> Division of Biomedical Informatics >> School of Medicine >> University of California San Diego >> >> Theodore Gildred Facitlity >> 220 Dickinson St Suite A >> San Diego, CA 92103 >> USA >> >> Phone: +1 619 543 8898 >> Fax : +1 619 543 5066 >> Web : http://www.hyphy.org/sergei/ >> >> HyPhy Page: http://www.hyphy.org/ >> Adaptive Evolution Server: http://www.datamonkey.org/ >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > _______________________________________________ > galaxy-lab mailing list > galaxy-lab(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-lab

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Question about Branch Lengths Estimation
by Melissa A. Wilson Sayres 07 Sep '10

07 Sep '10

Hi there, I am trying to use the tool Branch Lengths Estimation under the Evolution heading. I have a pairwise alignment - (hg18,panTro2), but when I try to run the tool, using the HKY85 model on my FASTA formatted alignment, I get nothing in the output. It doesn't give an error, but instead gives: 143: Branch Lengths on data 120 <http://main.g2.bx.psu.edu/history> empty, format: tabular, database:hg18 Info: Single Alignment Analyses Any ideas? Thanks!! Melissa -- Melissa A. Wilson Sayres NSF Graduate Research Fellow, Bioinformatics & Genomics 306 Wartik Lab University Park, PA 16802 maw397(a)psu.edu It is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring. -- Carl Sagan

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galaxy-user September 2010