September 2011 - galaxy-dev - lists.galaxyproject.org

Error in displaying data in galaxy browser with less than 1MB size.
by Jerico Nico De Leon Revote 27 Sep '11

27 Sep '11

Hi, I've a setup a local instance of galaxy in our server using PostgreSQL/nginx. I've followed the instructions from the production server configuration as stated from here: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server. Galaxy is running and tried the "Galaxy 101" tutorial but I get http 404 error when trying to view any dataset with less than 1MB in size in the galaxy browser: Not Found The resource could not be found. No route for /_x_accel_redirect/home/galaxy/galaxy-dist/database/files/000/dataset_4.dat The dataset files are definitely present on the server and resides on galaxy's database files directory (e.g. /database/files/000). I can load and view in the browser any dataset that has >1MB in size, at least those ones produced from the "Galaxy 101" tutorial. Any suggestion is appreciated. Regards, Jerico

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EST download from any source?
by Timothy Wu 27 Sep '11

27 Sep '11

Hi, I'm trying to wrap up my own tool in Galaxy. The input to my tool include the set of EST (such as the entire human collection). I tried using UCSC genome browser but it doesn't seem to let me download the whole human collection due to the size of the data. I tried to implement my own FTP client and try to wrap that up in galaxy. I intend to have the FTP client download data from NCBI's FTP server directly, and have the downloaded files as output files to feed back into galaxy. I intend to make the FTP client somewhat generic, so as not to enforce the type of files. Though in my case, I would be download gzipped genbank files. But galaxy support for multiple output files kind of tripped me over. I do not know exactly what to do, since it looks as if galaxy requires a strict naming convention for the outputs, according to http://gmod.827538.n3.nabble.com/Multiple-output-not-known-until-tool-run-t… case I have is obviously that the number of files would not be known until run time). I guess it doesn't really, really matter, if I send those files, whatever the naming convention are, and fed it to a gzip decompressor (which I am planning to do a simple wrap up, just to be able to handle my stuff). Then it should all work out fine. Alternatively, I can just ask user to download from NCBI ftp themselves, decompress them, and upload it to galaxy. What's the best approach here? And I noticed that file types does not include genbank types nor gzip types. Is there some generic type I could use? Just Data class? Timothy

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Passing the number of mpi processors to SGE from xml file
by Chorny, Ilya 27 Sep '11

27 Sep '11

Any thoughts on how to pass the number of processor I want to use from my xml wrapper to the job template. I am trying to wrap pBWA and use mpi. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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Re: [galaxy-dev] picard error.
by Ross 26 Sep '11

26 Sep '11

A fix for these warnings is in revision 6048 of galaxy-central - again, thanks for pointing them out Michael. For the record, the warnings were from the HSmetrics and GCbias tools and arose because there is a user configurable maxheap parameter that is not available by default - it is commented out in the tool form - but it had not been commented out from the test - since it is not enabled by default that generated a warning. The test parameter is now also commented out by default and must be uncommented for sites running into ram limits with very large datasets. On Tue, Sep 27, 2011 at 8:04 AM, Ross <ross.lazarus(a)gmail.com> wrote: > Michael, > > Thanks for pointing these warning errors out. I think they're harmless > and can be ignored but I'll definitely take a look later today and > check in a fix. > As I recall, we had some discussion some months ago about whether to > allow the user to set the size of the java heap and decided that it > was not necessary - these messages suggest the parameter is still > somewhere in the tool tests - oddly enough I can't see it but I'm > seeing the same messages! > I'll let you know what I find once I've had a chance to take a look. > > > On Mon, Sep 26, 2011 at 11:06 PM, michael burrell (TOC) > <michael.burrell(a)nbi.ac.uk> wrote: >> Good afternoon, >> >> >> >> When starting galaxy I find the following errors logged in the paster.log >> >> >> >> galaxy.tools DEBUG 2011-09-26 13:58:21,577 Loaded tool: PicardASMetrics 0.03 >> >> galaxy.tools.test DEBUG 2011-09-26 13:58:21,625 Error in add_param for >> maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure >> that the parameter exists and that any container groups are defined first. >> >> >> >> galaxy.tools DEBUG 2011-09-26 13:58:21,703 Loaded tool: PicardInsertSize >> 0.3.0 >> >> galaxy.tools.test DEBUG 2011-09-26 13:58:21,737 Error in add_param for >> maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure >> that the parameter exists and that any container groups are defined first. >> >> >> >> Our galaxy version is. >> >> >> >> galaxy@jic55666:~/software/galaxy-central$ hg tip >> >> changeset: 6042:2469c53051ea >> >> tag: tip >> >> user: Daniel Blankenberg <dan(a)bx.psu.edu> >> >> date: Sun Sep 25 13:27:14 2011 -0400 >> >> summary: Some random lines tool tweaks. >> >> >> >> Thank you for your assistance. >> >> >> >> Michael. >> >> >> >> ________________________________ >> Please note, that my email address is no longer >> givenname.surname(a)bbsrc.ac.uk. Please update your records to reflect my new >> email address of givenname.surname(a)nbi.ac.uk as shown on this email. >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ >> > > > > -- > Ross Lazarus MBBS MPH; > Associate Professor, Harvard Medical School; > Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; > -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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Proxy login issues
by Alex R Bigelow 26 Sep '11

26 Sep '11

Hi, I've set up an apache proxy server to allow external access to my galaxy instance, following the directions at http://wiki.g2.bx.psu.edu/Admin/Config/Apache Proxy<http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy>. When I access galaxy directly (locally), everything works fine. When I try to access it through the proxy server, I get a login screen that works like it should - it gives me errors if I enter non-existent usernames or wrong passwords - but when I enter the correct information, it shows this screen for half a second, and then immediately redirects back to the login page: [cid:d04125f7-b29c-4492-b075-4073921c3fc3@umail.utah.edu] I prefer Galaxy handling usernames and passwords on its own, so I didn't add the "External user authentication" bits - are these required for a proxy server? I've attached the relevant parts of my httpd.conf, as well as my universe_wsgi.ini file if they help at all. Thanks again for the excellent support, Alex Bigelow

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cloud instance missing /opt/sge/default/common directory
by Joseph Hargitai 26 Sep '11

26 Sep '11

Hi, Upon restarting a saved cloud instance I am missing: -bash: /opt/sge/default/common/settings.sh: No such file or directory -bash: /opt/sge/default/common/settings.sh: No such file or directory all the other mounts are there and well preserved. Is this pulled from a special place i may have not saved? The instance now does not boot beyond this point. Have login and admin console access. joe

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Export Galaxy workflows to gUSE workflows
by Sandra Gesing 26 Sep '11

26 Sep '11

Dear all, we work in different projects with two portals - Galaxy for our local clusters and WS-PGRADE for grid projects (e.g., MoSGrid, SCI-BUS) with the respective grid security infrastructure based on X.509 certificates. I developed for Galaxy an export of workflows to gUSE workflows. WS-PGRADE is a workflow-enabled grid portal and an user interface of gUSE. Please find below and attached more information on gUSE and WS-PGRADE. I would like to suggest this extension for Galaxy so that users could easily collaborate on Galaxy workflows and gUSE workflows. I had a look at your Galaxy Tool Shed but I'm not sure whether this is the right place to submit the extension. As far as I have seen, there are tool extensions and not extensions of basic features. For the export, I changed two files: * workflow.py (I added the function download_to_wspgrade_file) * export.mako (I added <%def name="render_download_to_wspgrade_file(item)">) Furthermore, two files are added: * wspgrade_download.mako * wspgrade_download_content.mako (All four files are attached.) Thank you for your time and consideration in this matter, Sandra Gesing University of Tübingen Applied Bioinformatics Group Sand 14 72076 Tübingen Germany Phone: +49-7071-2970456 ------------------------------------------------------------------------------- WS-PGRADE (Web Services Parallel Grid Runtime and Developer Environment) as graphical user interface of gUSE (grid User Support Environment) is the second generation of the workflow-enabled grid portal P-GRADE. The collaborative, community-oriented application development environment of WS-PGRADE offers a graphical workflow editor and enables the users to create, change, invoke, and monitor workflows. The latter may contain jobs on local resources and distributed resources in grid and cloud infrastructures. Existing workflows, workflow graphs, workflow templates, and sophisticated workflow applications can be shared via a local repository. gUSE is a virtualization environment providing a large set of high-level Distributed Computing Infrastructures (DCI) services by which interoperation among classical service and desktop grids, clouds and clusters, unique web services, and user communities can be achieved in a scalable way. Internally, gUSE is implemented as set of Web services, which dynamically provide user services in DCI and/or Web services environments. WS-PGRADE uses the client APIs of gUSE services to turn user requests into sequences of gUSE specific Web service calls. WS-PGRADE hides the communication protocols and sequences behind JSR168/JSR286 compliant portlets and its GUI can be accessed via Web browsers. See details of WS-PGRADE and gUSE at: http://www.guse.hu/ P-GRADE or WS-PGRADE, respectively, are used by * National Grid portals (UK, Ireland, Croatia, Turkey, Spain, Belgium, Malaysia , Kazakhstan, Switzerland, Australia, ClGrid, etc.) * HP-SEE/SEE-GRID-SCI, BalticGrid * US Open Science Grid, TeraGrid * IDGF (International Desktop Grid Federation) * SHIWA Simulation Platform * Economy-Grid, Swiss BioGrid, Bio és * Biomed Virtual Organisations, MathGrid, etc. * the German MosGrid project * EU FP7 EDGI * UK ProSim project * CancerGrid project A new 3-year, large FP7 Gateway project (called as SCIence gateway Based User Support - SCI-BUS) will be started in October as the flagship EU Gateway project with the goal of establishing 27 science gateways and portals (based on WS-PGRADE/gUSE) for various user communities and NGIs in Europe. gUSE/WS-PGRADE is open source and downloadable from sourceforge: http://sourceforge.net/projects/guse/ For further information you can read: P. Kacsuk: P-GRADE portal family for Grid infrastructures, Concurrency and Computation: Practice and Experience journal, Volume: 23, Issue: 3, 2011, pp. 235-245

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picard error.
by michael burrell (TOC) 26 Sep '11

26 Sep '11

Good afternoon, When starting galaxy I find the following errors logged in the paster.log galaxy.tools DEBUG 2011-09-26 13:58:21,577 Loaded tool: PicardASMetrics 0.03 galaxy.tools.test DEBUG 2011-09-26 13:58:21,625 Error in add_param for maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools DEBUG 2011-09-26 13:58:21,703 Loaded tool: PicardInsertSize 0.3.0 galaxy.tools.test DEBUG 2011-09-26 13:58:21,737 Error in add_param for maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure that the parameter exists and that any container groups are defined first. Our galaxy version is. galaxy@jic55666:~/software/galaxy-central$ hg tip changeset: 6042:2469c53051ea tag: tip user: Daniel Blankenberg <dan(a)bx.psu.edu> date: Sun Sep 25 13:27:14 2011 -0400 summary: Some random lines tool tweaks. Thank you for your assistance. Michael. ----------------------------------------------------------------------------------------------------- Please note, that my email address is no longer givenname.surname(a)bbsrc.ac.uk. Please update your records to reflect my new email address of givenname.surname(a)nbi.ac.uk as shown on this email.

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Error in FastQC
by Matthew J. Thomas 25 Sep '11

25 Sep '11

Hello, I am working on a local install of Galaxy and when running a test data set I get this error when invoking the Fastqc commans: /home/mnkyboy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 20 class FastQC(): ^ SyntaxError: invalid syntax This is Illumina data from a single tile of qseq.txt data converted to FASTQ and run through the FASTQ groomer. Fastqc is working properly outside of Galaxy so any advice would be appreciated. Thanks, Matt T.

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Re: [galaxy-dev] Specifying a range of inputs?
by Peter Cock 24 Sep '11

24 Sep '11

I realise we went off list accidentally. On Saturday, September 24, 2011, Timothy Wu <2huggie(a)gmail.com> wrote: > On Sat, Sep 24, 2011 at 6:52 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: >> >> Elegant maybe, but the UI side does not seem >> practical with the current Galaxy. > > Is there any future plan for a better multiple file support? It has been discussed a little in other contexts, Like running a workflow many times in parallel. >> >> I would write a tool to get the data from the NCBI into >> Galaxy as a single FASTA file in this situation. I'm >> assuming there is some rule to pick the particular >> set (e.g. An Entrez search, perhaps by taxonomy). > > Yeah, I think that's what I'll have to do. Thanks. :) > > Timothy Peter

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