galaxy-dev November 2010

galaxy-dev@lists.galaxyproject.org

63 participants
98 discussions

ABySS genome assembler integration into Galaxy
by Richard Bruskiewich 23 Nov '10

23 Nov '10

Colleagues, Rumor has it that some developer in the Galaxy community is already integrating the ABySS genome assembler ( http://www.bcgsc.ca/platform/bioinfo/software/abyss/) into Galaxy. Does anyone have any details about this? Cheers -- *Richard Bruskiewich, PhD* Senior Scientist, Computational and Systems Biology Applications Team for Computational Genomics T.T. Chang Genetic Resources Center International Rice Research Institute

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Existing efforts to convert the QIIME pipeline to Galaxy?
by Tim te Beek 23 Nov '10

23 Nov '10

Hello all, Is anyone aware of any existing efforts to port the QIIME sequencing pipeline (http://qiime.sourceforge.net/) to Galaxy? I would like to run QIIME analyses through Galaxy to get better control of intermediate processing steps, but before I start to convert (a subset of) some 90 scripts, I'd first like to make sure this has not been done before by anyone willing to share their work. So: has anyone converted the QIIME pipeline to Galaxy before, and would they be willing to share their scripts? Best regards, Tim

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empty_field validator for multi-select column parameter
by Peter 23 Nov '10

23 Nov '10

Hi all, I have a tool where for one parameter I want the user to pick one or more columns from a tabular file. Other tools do this too, e.g. filters/uniq.xml (the Statistics "Count" tool) uses: <inputs> <param name="input" type="data" format="tabular" label="from query" help="Query missing? See TIP below"/> <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurrences of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> ... </inputs> I would like extend this by adding a validator to prevent the user trying to run my tool with no columns (in fact, I think this would be a good idea for filters/uniq.xml as well - currently the error is only spotted when the tool is run). There is a list of validators given on the wiki page, http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax I expected to be able to use the empty_field validator, but that doesn't work - is this a bug?: <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurrences of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> <validator type="empty_field" message="Pick at least one column"/> </param> I found a workaround, based on the fact that no columns is passed to the command line tools as the string 'None', using the expression validator: <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurrences of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> <validator type="expression" message="Pick at least one column">str(value)!='None'</validator> </param> Peter

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Re: [galaxy-dev] [galaxy-user] FastQ Import
by Nate Coraor 22 Nov '10

22 Nov '10

Martin Laforest wrote: > Hello, > > I'm currently trying out Galaxy and I like a lot thus far. We have our own > instance on a test server. > > I have one issue with the time it takes to import large fastq files > (s_x_sequence.txt files from the GAIIx actually). I think it may be our > set up or something. How long is it suppose to take to upload a 5 > gigabytes file? Hi Martin, I've moved this conversation over to our development list since it pertains to a local installation of Galaxy. It's difficult to say how long it should take since it's going to depend on connection speed and write performance on the server. Also, browsers may not be able to handle file uploads > 2GB. Is the dataset still in the "uploading" state, or has it changed to queued/running? Thanks, --nate > > Many thanks in advance > > > Martin > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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problems with MACS peak calling tool
by Yuelin Zhu 22 Nov '10

22 Nov '10

Hi all, We got the Galaxy installed locally in our cluster and most tools are working well. But for some reason the MACS peak calling tool is not working. Basically it runs very quickly (a few seconds) with empty bed file. When I try to download the html file (very small, just 377.0 bytes) I always get this error: "Unable to remove temporary library download archive and directory" Our Galaxy is installed on a Linux system (Linux 2.6.31.12 #16 SMP Sat Jun 19 11:23:12 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux). Our another Galaxy instance on a Mac OS does not have such any problems with the MACS. Apparently I did not install the MACS correctly. Could anyone give me any clues about this? Your help will be greatly appreciated. Jack

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Skipping BLAST+ tests
by Peter 22 Nov '10

22 Nov '10

Hi Nate, Regarding this: http://bitbucket.org/galaxy/galaxy-central/changeset/cb6787fcc256 Do you plan to install BLAST+ on the Galaxy Test machine? [I think you could even install it on the main Galaxy instance if you avoid all the large databases. The NCBI vector database is tiny and useful, also FASTA vs FASTA is handy.] Also, I made sure all the tests to date use FASTA vs FASTA so that you don't need to worry about the blastdb.loc file for the tests. However, some things like XML output are not supported like this (you have to BLAST against a DB). Regards, Peter

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Local Galaxy installation
by Singh, Indresh 22 Nov '10

22 Nov '10

Greetings, First of all you guys are doing exceptional job building and supporting Galaxy! I would like to download and install galaxy for our JCVI users and hopefully also contribute building and enhancing Galaxy. Is there any documentation which described installation and configuration, I'm mainly looking for document which will help me estimate server requirement. Regards, Indresh Singh J. Craig Venter Institute(JCVI) 9704 Medical Center Drive Rockville, MD 20850, USA Phone: (301)-795-7129 Fax: (240)-243-0600 www.jcvi.org <http://www.jcvi.org>

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Sample tracking dataset upload file browser
by Sarah Diehl 22 Nov '10

22 Nov '10

Hi, I just updated our Galaxy to the newest version in http://bitbucket.org/galaxy/galaxy-dist/. Now I am wondering why I don't have the nice dynamic file browser in the sample tracking dataset upload anymore. There is no extra window with a scroll bar and when I select a file and press "select datasets" nothing happens. I attached a screenshot so you can see what I'm talking about. Thank you very much for your help! Best regards, Sarah

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Error in requests_admin.py
by Sarah Diehl 22 Nov '10

22 Nov '10

Hi again, I think I found another error. After I solved the last issue, I got an error in line 568 of GALAXY_ROOT/lib/galaxy/web/controllers/requests_admin.py. I think the line should be if option == options.EXPERIMENT_NAME: Can somebody confirm this? Best regards, Sarah

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Display of tabular data in Galaxy
by Peter 22 Nov '10

22 Nov '10

Hi all, I've noticed in the right hand column for tabular data Galaxy shows the first few lines with a nice column based layout. Looking at the source, you actually define an HTML table for this. However, on the main central column, when viewing a tabular dataset (by clicking on the eye icon from an entry in the right hand column), the data is shown as raw text. As long as the data in each column is about the same length, this works OK. However, if you have variable length fields then the columns do not line up. It would be nice if the main display showed the data respecting the columns. Has this been considered? My guess is that doing this was rejected due to the computational load to reformat it, and the network load to send the marked up data. (I did try and search the mailing list archives but didn't find any discussion of this) Regards, Peter

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galaxy-dev November 2010