- galaxy-dev - lists.galaxyproject.org

tool_id for tool_shed tools
by Andreas Kuntzagk 15 Nov '12

15 Nov '12

Hi, I upgraded to the latest version and again some tools moved to tool_shed. I now need to set job runners for these tools. Is there an easy way to get the tool_ids other then hovering the mouse over the tool name and write down the id? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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Database upgrade 108 and SQLite
by Peter Cock 15 Nov '12

15 Nov '12

Hi all, Is this likely to cause problems using Galaxy on SQLite (the default and very handy for a development machine)?: $ sh manage_db.sh upgrade 107 -> 108... Add the ExtendedMetadata and ExtendedMetadataIndex tables SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html No handlers could be found for logger "0108_add_extended_metadata" done Thanks, Peter

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Display of HTML type broken in new Galaxy ?
by Lukasse, Pieter 15 Nov '12

15 Nov '12

Hi, I noticed that in the new Galaxy version the preview of HTML files seems to be broken. When I try to preview a HTML file generated by a tool, it displays a HTML that has all style "stripped off". So the HTML display is in fact changing the generated HTML before displaying it. Has anyone noticed this as well? What are the fixes/workarounds? [cid:image001.jpg@01CDAC4F.72D92640] Regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Join (Operate on Genomic Intervals)
by George Maliha 14 Nov '12

14 Nov '12

Hello, I am using the Galaxy public server to conduct a join operating on genomic intervals. However, my job has not completed in over 2 days. Is there a bug, and what can I do to speed up the process? Thank you, George

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ftp file upload error question
by Tony Szempruch 14 Nov '12

14 Nov '12

Dear Galaxy Devs, I have tried to upload 2 files though the ftp upload using FileZila. I have been getting the following error: Response: 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) [::ffff:128.118.250.4] Command: USER ************** Response: 331 Password required for ************** Command: PASS ***** Response: 530 Sorry, the maximum number of clients (3) for this user are already connected. Error: Critical error Error: Could not connect to server I have seen that some one else had this issue and posted online. What should I do to try to get around this issue? Thank you Tony Szempruch

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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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