November 2012 - galaxy-dev - lists.galaxyproject.org

Galaxy November 14, 2012 Distribution & News Brief
by Jennifer Jackson 14 Nov '12

14 Nov '12

*Galaxy November 14, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_11_14_DistributionNewsBrief>* * Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14> * *Highlights:* * *NGS: Picard (beta)* have moved from the *Galaxy distribution <https://bitbucket.org/galaxy/galaxy-dist>* to the*Galaxy Main Tool Shed* <http://toolshed.g2.bx.psu.edu/>. * The *Galaxy Project* is now using /Sphinx <http://sphinx-doc.org/> Python/ to document the *galaxy-central <http://galaxy-central.readthedocs.org>* and *galaxy-dist* <http://galaxy-dist.readthedocs.org> code base. * The *Intergalactic Utilities Commission* <http://wiki.g2.bx.psu.edu/ReviewingToolShedRepositories> will soon begin reviewing repositories in the *Galaxy Main Tool Shed <http://toolshed.g2.bx.psu.edu/>* (better repos, better tools) * *Tool Shed <http://toolshed.g2.bx.psu.edu/>* *"best practice"* advice: a single tool or a suite of tools per repository? <http://wiki.galaxyproject.org/AToolOrASuitePerRepository> * *Tophat <http://tophat.cbcb.umd.edu/>*, *Tophat2 <http://tophat.cbcb.umd.edu/manual.html>*, and *Cuffdiff <http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff>* *updated* to accept gene annotations in *GFF3 <http://wiki.galaxyproject.org/Learn/Datatypes#GFF3>* format. * Multiple *enhancements* to the *API* <http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14#API>targeting user and history actions. * Plus *updates to* *CloudLaunch <http://usegalaxy.org/cloud>*, new *Security Fixes* <http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14#Security_Fixes>, and several usability enhancements for *Datasets*, *Datatypes*, *Tools*, and *Tool Shed* functions. / http://getgalaxy.org/////// /http://bitbucket.org/galaxy/galaxy-dist/ /http://galaxy-dist.readthedocs.org/ new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 5dcbbdfe1087 *Thanks for using Galaxy!* Jennifer Jackson <http://wiki.galaxyproject.org/JenniferJackson> & the Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team> /http://galaxyproject.org/

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Galaxy-related job opening at the FMI in Basel, Switzerland
by Hotz, Hans-Rudolf 14 Nov '12

14 Nov '12

Hi I apologize for abusing the list for a job add: We are looking for a R/Bioconductor person which is familiar with Galaxy to help us expanding our sets of NGS tools in Galaxy, see http://www.fmi.ch/Careers/JobDetails.html?jobID=158 Please feel free to contact me for more details Regards, Hans-Rudolf Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Re: [galaxy-dev] [galaxy-user] Warning message
by Daniel Blankenberg 14 Nov '12

14 Nov '12

Hi Rolando, Please keep all replies on list. Without a little more information its hard to guess what is happening. Can you provide the log output for when you try to start the server? Is this a cloud instance? If I had to make a guess, it would be that there is a permissions problem due to the copy. Can you make sure that when you copied the .sample file over the .xml file that you did it as the galaxy user? Thanks for using Galaxy, Dan On Nov 13, 2012, at 10:08 PM, rolandomantilla1(a)gmail.com wrote: > I just copy the file datatypes_conf.xml.sample over datatypes_conf.xml like you told me and now I can't start galaxy it tells me Galaxy deamon not running,please help > Sent from my Verizon Wireless BlackBerry > From: Daniel Blankenberg <dan(a)bx.psu.edu> > Date: Tue, 13 Nov 2012 10:10:43 -0500 > To: Rolando Mantilla<rolandomantilla1(a)gmail.com> > Cc: <galaxy-user(a)lists.bx.psu.edu> > Subject: Re: [galaxy-user] Warning message > > Hi Rolando, > > You'll need to remove the old blast datatypes from your datatypes_conf.xml file. If you haven't added any new datatypes manually yourself, you can copy the datatypes_conf.xml.sample file over of your datatypes_conf.xml file. > > Also, in the future questions about local Galaxy instances should be sent to the galaxy-dev mailing list. > > > Thanks for using Galaxy, > > Dan > > > On Nov 12, 2012, at 10:31 PM, Rolando Mantilla wrote: > >> I'm having issues with the FASTQ_Groomer. What I have done it first I downloaded an SRA file created by an Ion torrent sequencer from the NCBI site. Then used the fastq-dump app from the NCBI site to covert the .sra file to .fastq file. When I uploaded the data into galaxy it recognized it as a fastq(as it should) but when I try to run the FASTQ groomer I get the message and warnings below. I also have already downloaded the the blast_datatypes tool from the tool_shed. I truly don't know what the issue is, any help >> An error occurred running this job: Groomed 12376 sanger reads into sanger reads. WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with extension 'blastxml', using datatype from /mnt/galaxyData/tmp/tmpdP_cZ7. >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >

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Trackster error after upgrade
by Joachim Jacob 14 Nov '12

14 Nov '12

Hi all, After upgrading to the latest galaxy-dist, Trackster does not behave. Nearly all saved viz's just show a blank main window, while just displaying the Galaxy header and the trackster header bar. In contrast, one visualisation gives this error: ConverterDependencyException: 'A dependency (bgzip) was in an error state.' Any help appreciated, thanks. Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Local data
by Perez, Ricardo 13 Nov '12

13 Nov '12

Hi, I am sorry for the trivial question. Does anyone know how I can make a local instance of Galaxy use our local database files? We have downloaded the database from USCS and would like to use the downloaded files instead of retrieving it from the UCSC Table Browser when processing data. Thank you very much for your help, --Ricardo Perez

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GalaxyAdmins meeting -- Nov 14 at 10 AM Central
by IIHG Galaxy Administrator 13 Nov '12

13 Nov '12

Hello, The next meeting of the GalaxyAdmins group will be held on November 14 at 10 AM Central time. Curtis Hendrickson of the University of Alabama Birmingham's Center for Clinical and Translational Science (UAB CCTS) will speak on "Deploying Galaxy on a shared-node cluster at UAB". The meeting will also include time for open discussion. Your active participation is encouraged. Thank you! Notes: * Link to the webinar: https://globalcampus.uiowa.edu:443/join_meeting.html?meetingId=1262339408056<https://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262339408056> * Meeting invite is attached * This information is also posted at http://wiki.galaxyproject.org/News/2012_11GalaxyAdmins -- Srinivas Maddhi Senior Systems Administrator Iowa Institute for Human Genetics The University of Iowa

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Galaxy tool error report from yaximik@gmail.com
by yaximik＠gmail.com 13 Nov '12

13 Nov '12

GALAXY TOOL ERROR REPORT ------------------------ This error report was sent from the Galaxy instance hosted on the server "127.0.0.1:7070" ----------------------------------------------------------------------------- This is in reference to dataset id 13 from history id 6 ----------------------------------------------------------------------------- You should be able to view the history containing the related history item 13: FastQC_SC2T252P15_S1_L001_R1_001.fastq.html by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. 127.0.0.1:7070/history/view?id=e03374982e5c9d8a ----------------------------------------------------------------------------- The user 'yaximik(a)gmail.com' provided the following information: This was returned upon attempt to run FasQC on one Illumina gromed dataset. Local galaxy install on RHEL58 ----------------------------------------------------------------------------- job id: 7 tool id: fastqc ----------------------------------------------------------------------------- job command line: python /home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py -i "/home/GalaxyUpload/SC2T252P15_S1_L001_R1_001.fastq" -d "/home/galaxy/galaxy-dist/database/job_working_directory/000/7/dataset_13_files" -o "/home/galaxy/galaxy-dist/database/files/000/dataset_13.dat" -n "FastQC" -f "fastq" -j "SC2T252P15_S1_L001_R1_001.fastq" -e "/home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc" ----------------------------------------------------------------------------- job stderr: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 158, in <module> assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - cannot find executable /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc ----------------------------------------------------------------------------- job stdout: ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).

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RuntimeError: maximum recursion depth exceeded while calling a Python object ( when trying to run blast)
by Liisa Koski 13 Nov '12

13 Nov '12

Hello, I'm using the latest Galaxy distribution and am getting an error when trying to run any of the ncbi blast tools. Error executing tool: maximum recursion depth exceeded while calling a Python object This is what I find in paster.log I'm attaching it because the traceback is 1500 lines long. Thanks in advance for your help, Liisa

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Can't edit galaxy workflow
by Richard Park 13 Nov '12

13 Nov '12

Hi Guys, I updated to the latest galaxy distribution today and I cant seem to edit existing workflows. I've seen others with this error from a Sept 07 distribution ( http://dev.list.galaxyproject.org/Can-t-edit-Galaxy-Workflow-ElementInterfa…) but Jeremy Goecks mentioned that this might of been fixed in the Sept 20 distribution. Any ideas on how to fix this? Thanks, Richard Server error URL: http://127.0.0.1:8080/workflow/load_workflow?id=f597429621d6eb2b&_=13524955… Module weberror.evalexception.middleware:*364* in respond >> <http://127.0.0.1:8080/workflow/editor?id=f597429621d6eb2b#>app_iter *= * self*.*application*(*environ*,* detect_start_response*)* Module paste.debug.prints:*98* in __call__ >> <http://127.0.0.1:8080/workflow/editor?id=f597429621d6eb2b#>environ*,* self*.*app*)* Module paste.wsgilib:*539* in intercept_output >> <http://127.0.0.1:8080/workflow/editor?id=f597429621d6eb2b#>app_iter *= * application*(*environ*,* replacement_start_response*)* Module paste.recursive:*80* in __call__ >> <http://127.0.0.1:8080/workflow/editor?id=f597429621d6eb2b#>*return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*632* in __call__ >> <http://127.0.0.1:8080/workflow/editor?id=f597429621d6eb2b#>*return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*160* in __call__ >> <http://127.0.0.1:8080/workflow/editor?id=f597429621d6eb2b#>body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*73* in decorator >> <http://127.0.0.1:8080/workflow/editor?id=f597429621d6eb2b#>*return* simplejson*.*dumps*(* func*(* self*,* trans*,* ***args*,* ****kwargs *)* *)* Module galaxy.webapps.galaxy.controllers.workflow:*733* in load_workflow >> <http://127.0.0.1:8080/workflow/editor?id=f597429621d6eb2b#>'tooltip'*: * module*.*get_tooltip*(* static_path*=*url_for*(* '/static' *)* *)**,* Module galaxy.workflow.modules:*258* in get_tooltip >> <http://127.0.0.1:8080/workflow/editor?id=f597429621d6eb2b#>*return* self*.*tool*.*help*.*render*(* static_path*=*static_path *)* *AttributeError: 'NoneType' object has no attribute 'render'* []

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Uploading to history via JavaScript
by Ted Goldstein 13 Nov '12

13 Nov '12

Essentially, this the similar to a dataset upload where the origin is from a web page when a user clicks on a HTML button. The button is not part of the tool framework but any number of possible I am writing a variety of data editors in JavaScript and it would be convenient to upload the dataset into the user's current history list. of JavaScript actions. I think I should be able to use the regular upload1 (upload.py) machinery. But So far, I have not had success in tricking it with my JavaScript function. I know that I could add web api. But there is a lot hairy code in the history dataset association that looks like it will change. So I'd rather keep it simple. Does anyone have any suggestions? Thanks, Ted function UploadToHistory(name, value) { var payload = { tool_id: "upload1", 'file_type': 'tabular', 'file_name', name, 'dbkey': '?', 'files_0|url_paste': value}; $.ajax( { async: false, type: "POST", url: "/tool_runner/index", data: payload, dataType: "json", success: function(array_obj, status) { console.log("success", array_obj, status); }, failure: function() {console.log("fail");} } ); }

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