May 2013 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] finding parts of tool_conf.xml
by Dannon Baker 28 May '13

28 May '13

So tool_conf.xml only contains references to the other tool wrapper files. Those tools are either be in the distribution (which you can find in your galaxy-central/tools directory) or in the toolshed, at toolshed.g2.bx.psu.edu. -Dannon On Tue, May 28, 2013 at 1:32 PM, vijayalakshmi <vijiraghs(a)gmail.com> wrote: > I am trying to integrate the following tools in galaxy but I am not able > to find their corresponding code in the "tool_conf.xml" file. If you can > point me to those, it'd we swell. > > 1) NGS: Variant detection > 2) NGS: Picard(beta) > 3) BEDTools > 4) SnpEff > > Thanks, > VJ. > > On Tue, May 28, 2013 at 12:42 PM, Dannon Baker <dannon.baker(a)gmail.com>wrote: > >> I'm assuming you're referring to main.g2.bx.psu.edu's tool configuration >> as a reference. Some of these components are installed via the tool shed, >> and others may have been manually added to main and are not included in the >> base tool_conf.xml.sample. I may be able to point you in the right >> direction, though -- what is it that you're trying to do? >> >> -Dannon >> >> >> On Tue, May 21, 2013 at 3:31 PM, vijayalakshmi <vijiraghs(a)gmail.com>wrote: >> >>> Hi all, >>> >>> I am trying to get the *"tool_conf.xml"* <section> code >>> corresponding to the following topics listed below. I am unable to find it >>> in both the default build and the stable build in bitbucket. If you can >>> point me to where I can find it, it'd be swell. >>> >>> 1) NGS: Variant detection >>> 2) NGS: Picard(beta) >>> 3) BEDTools >>> 4) SnpEff >>> >>> Thanks, >>> VJ. >>> >>> ___________________________________________________________ >>> 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/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> >

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finding parts of tool_conf.xml
by vijayalakshmi 28 May '13

28 May '13

Hi all, I am trying to get the *"tool_conf.xml"* <section> code corresponding to the following topics listed below. I am unable to find it in both the default build and the stable build in bitbucket. If you can point me to where I can find it, it'd be swell. 1) NGS: Variant detection 2) NGS: Picard(beta) 3) BEDTools 4) SnpEff Thanks, VJ.

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very long load times for some shared libraries...
by Langhorst, Brad 28 May '13

28 May '13

All of a sudden, some larger libraries are taking a very long time to open. [cid:BB83AE73-EAE2-44B9-B294-918CDE8C18F4@neb.com] This one timed out… Anybody else seen this? Could this be a database issue? Didn't see any really long queries in the postgres log (and i log anything longer than 1000ms) brad -- Brad Langhorst Applications and Product Development Scientist langhorst(a)neb.com<mailto:langhorst@neb.com>

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maximum recursion depth error
by Ann Holtz-Morris, M.S. 28 May '13

28 May '13

Hi, I used the SAM to FASTQ tool to divide78 lines of Illimina paired end sequences in SAM format to FASTQ format. The read 2 data set works fine, and I used the FASTQ masker and then FASTQ to FASTA tools. I went to repeat those steps with the the read 1 data set. It errors with: Error executing tool: maximum recursion depth exceeded while calling a Python object. Thinking maybe the format was corrupted, I ran FASTQ groomer. Same result: Error executing tool: maximum recursion depth exceeded while calling a Python object. Thinking the SAM to FASTQ had a problem, I repeated it. Same result: Error executing tool: maximum recursion depth exceeded while calling a Python object. You get thepicture. Anything I try with this data gives the same error. When I googled the error, the top results were all about large data sets, but this isn't a large set. Any help greatly appreciated, Ann Thanks for your help. CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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missing new job lock function
by Leon Mei 28 May '13

28 May '13

Dear list, I recently updated our local Galaxy to galaxy-dist (version 9320:47ddf167c9f1, May 1st 2013). I noticed that the lock preventing new jobs dispatching in "Manage jobs" of the admin panel is missing. Is this a new feature? Or am I having problem with my configuration? If this is indeed a Galaxy update, is there any other way to lock the job queue in Galaxy? Thanks, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl<https://wiki.nbic.nl/index.php/Next_Generation_Sequencing> Skype: leon_mei Mobile: +31 6 41709231

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Problem changing username
by Thomas Haverkamp 28 May '13

28 May '13

Hi, I have been trying to change my username in Galaxy, since the e-mail address I was using is going to be discontinued. But somehow, if I try to change it I get an error, and the change can not be done. The error code that was generate is the following: GURU MEDITATION: #53cc2dae7660426b8a53c1f6db2d3fc6 cheers Thomas

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User expiration date
by Nikos Sidiropoulos 28 May '13

28 May '13

Hi Is it possible to set an expiration date for specific user accounts? Bests, Nikos

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pre-commit hook for easier deployment of complex repository definitions
by Björn Grüning 27 May '13

27 May '13

Hello all, in the same spirit of Ira's galaxy_repo_bundler [1] I have uploaded my mercurial pre-commit hook: https://github.com/bgruening/galaxy-toolshed-hooks It integrates in mercurial and (in an ideal world ;)) should not interfere with your normal workflow. The two hooks will: - creates a backup of your tool_dependencies.xml and/or repository_dependencies.xml - updates the changeset_revision and toolshed attributes - commit the changed files - restores the backup In combination with a small script iterating over a set of dependent repositories (in the right order) I was able to update the entire ChemicalToolBoX (>20 repositories) in one step. Maybe it can be of any help for someone. Cheers, Björn [1] https://bitbucket.org/iracooke/galaxy_repo_bundler/

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Re: [galaxy-dev] Displaying BED files in IGV
by menorca chaturvedi 27 May '13

27 May '13

Hello, I am trying to use IGV on local Galaxy to view BED and other kinds of files. I added the xml file and made changes in the datatypes_conf.xml file too but the error says: Unable to parse header with error: File not found:..for input source.. The same file works for IGB though. Please suggest the correct settings for this case. Best regards, Menorca Ann Black-Ziegelbein annblack at eng.uiowa.edu Thu Mar 15 23:42:32 EDT 2012 Hello - I am wanting to be able to display bed files from Galaxy in IGV. I have created a bed.xml display application description, and edited the datatypes_conf.xml to enable the igv display of datasets of bed format. However, when I select the link in Galaxy to "Display with IGV local" I get the following error message in Galaxy: You must import this dataset into your current history before you can view it at the desired display application. I am attaching my bed.xml file I created based off of existing IGV display types. I was hoping someone either has a working display descriptors for bed files for IGV, or might know what my error is. Thanks much, Ann

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login to ftp server failed
by Barbara Susanne Sixt 27 May '13

27 May '13

Hello, I am completely new to Galaxy and I am not quite sure to which mailing list this question should have been addressed. I apologize if I got it wrong. I created an account one week ago and tried to upload data via ftp (using WinSCP). However logging in to the ftp server at main.g2.bx.psu.edu always fails, although I am using a valid password. A colleague of mine successfully logged in at my computer with his account. I thus guess there may be a problem with my account. Is there anything I have to do after registering in order to enable access to the ftp server? Thanks already in advance for your support! Best wishes, Barbara Sixt

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