- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Add Genome
by Jennifer Jackson 21 Jul '11

21 Jul '11

Hello Somayyeh, These data are from the same authors/release build. At Ensembl, the same 5 core chromosomes plus an additional 78 unplaced scaffolds are available. The data authors decided not to include these scaffolds in their publication at NCBI. For a primary genome, I suggest that we use the core 5 chromosomes as this is what was published externally to NCBI by the authors. Would this also be your preference? Both options are possible. Many genomes have unmapped scaffolds included in the Galaxy genome builds, however they are usually published at NCBI if/when the genome is submitted there. Thank you! Jennifer On 7/21/11 5:41 AM, Somayyeh Fahiminiya wrote: > Hi Jen, > > > Thanks for your email and sorry to be late . > > Please look at : > wget > ftp://ftp.ensemblgenomes.org/pub/plants/current/fasta/brachypodium_distachy… > > I dont know if it is more recent or the same version as yours > > > > Thanks again > > somayyeh > > > > > On Mon, Jul 11, 2011 at 9:05 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hello, > > To confirm: the correct source would be this project, only has > chromosomes 1-5, at NCBI? Or is there a preferred (more > complete/recent) source? > > http://www.ncbi.nlm.nih.gov/__bioproject/32607 > <http://www.ncbi.nlm.nih.gov/bioproject/32607> > > Once we have the source confirmed, we can add this genome to our > to-add list, > > Best, > > Jen > Galaxy team > > > On 7/7/11 6:25 AM, Somayyeh Fahiminiya wrote: > > Hello everyone, > > Could you plz add the genome of "*Brachypodium distachyon*" to > the Galaxy. > > Thanks in advance > > > > _____________________________________________________________ > 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/ > > > -- > Jennifer Jackson > http://usegalaxy.org/ > http://galaxyproject.org/ > > -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

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workflows are broken in current galaxy-central version
by Edward Kirton 21 Jul '11

21 Jul '11

URL: https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8 Module paste.exceptions.errormiddleware:*143* in __call__ Module paste.debug.prints:*98* in __call__ Module paste.wsgilib:*539* in intercept_output Module paste.recursive:*80* in __call__ Module paste.httpexceptions:*632* in __call__ Module galaxy.web.framework.base:*145* in __call__ >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#>body * =* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*84* in decorator >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#>* return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.web.controllers.workflow:*686* in editor >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#>* return* trans*.*fill_template*(* "workflow/editor.mako"*,* stored*=*stored*, * annotation*=*self*.*get_item_annotation_str*(* trans*.*sa_session*,* trans *.*user*,* stored *)* *)* Module galaxy.web.framework:*661* in fill_template >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#>* return* self*.*fill_template_mako*(* filename*,* ****kwargs *)* Module galaxy.web.framework:*672* in fill_template_mako >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#>* return* template*.*render*(* ****data *)* Module mako.template:*296* in render >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#>* return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#>**** _kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#> _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)* Module mako.runtime:*718* in _exec_template >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#> callable_*(*context*,* ***args*,* ****kwargs*)* Module _base_panels_mako:*87* in render_body >> <https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#> __M_writer*(*unicode*(*self*.*overlay*(*visible*=*self*.*overlay_visible*)** )**)* *TypeError: render_overlay() got an unexpected keyword argument 'visible'*

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Detailed SGE timing information about galaxy jobs
by Assaf Gordon 21 Jul '11

21 Jul '11

Hi all, I got around to writing the report I always needed: how much time each job actually runs and how much time it spends waiting in the SGE queue. The attached shell script produces the report, combining information from SGE's QACCT with the galaxy job/dataset information. The output contains: job, user, tool name, dbkey, total input size in bytes, waiting time in SGE queue, actual SGE executiong running time, and some other tidbits. This allows finding how much running time each user had on the cluster, how much time each tool/user spend idly waiting, and some possible correlations between tools, dbkeys, input size and running time. The script is tightly coupled with SGE and PostgreSQL, but can probably be adapted to PBS/MySQL. Hope this helps someone, -gordon

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Re: [galaxy-dev] EpiGRAPH
by Greg Von Kuster 21 Jul '11

21 Jul '11

Hello Christoph, This is the result of a bug that I've corrected in change set 5819:0f15591f2acd, which should be available in our main Galaxy instance, as well as the distribution, within the next few weeks. Thanks for pointing this out, and very sorry for the inconvenience. Greg Von Kuster On Jul 21, 2011, at 12:58 AM, Christoph Bock wrote: > Hi Greg, Anton, > > I received a user bug report asking why the “Send Data -> EpiGRAPH” function in Galaxy doesn’t work anymore. > Is this a temporary technical issue or did you do a general cleanup and removed this link? > > Best regards, > Christoph > > From: Christoph.Schmid(a)unibas.ch [mailto:Christoph.Schmid@unibas.ch] > Sent: 13 July 2011 3:56 AM > To: cbock(a)mpi-inf.mpg.de > Subject: EpiGRAPH > > Dear Christoph, > > I am trying to get an overview on existing computational solutions in the public domain to compare epigenetic maps. > > One interesting solution is your EpiGRAPH Software (Genome Biol 10, R14.[2009]). I have the following questions: > > 1) Could I get access to the most recent source code release, & installation instructions (I saw the pre-print of the tutorial paper)? Any comments on current and future development activities on EpiGRAPH? > > 2) What is the state of the integration of EpiGRAPH into the Galaxy framework? As far as I remember EpiGRAPH was available for a short moment onhttp://main.g2.bx.psu.edu/, but now I can no longer see it? Is it still available on another mirror? > > thanks in advance for your help > ->Christoph > > ******************************************************** > Christoph D. Schmid, PhD > > Swiss Tropical and Public Health Institute > Socinstrasse 57 > CH-4002 Basel > Switzerland > > skype: chimborazo93 > Tel +41 61 284 8323 > Fax +41 61 284 8101 > > www.swisstph.ch > > > -------------------------------------------------------------------------- > This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error, please notify us immediately by reply e-mail and delete this message from your system. > -------------------------------------------------------------------------- Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Best location for galaxy environmental variables
by michael burrell (TSL) 21 Jul '11

21 Jul '11

Good afternoon, More of a general discussion point, where is the best place to put the environmental variable declarations within galaxy. To date I have been placing them as exports in the run.sh, though I can not help but wonder if there is a better place, which is appropriate whatever method you use to kick off galaxy. Thanks Michael.

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Newer Version of Cufflinks Wrapper
by Chorny, Ilya 20 Jul '11

20 Jul '11

Has anyone produced a newer version of the cufflinks wrapper? The current wrapper is for version 0.9.1. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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Error in exporting workflow
by chan fook mun 20 Jul '11

20 Jul '11

Hi All, I have encountered the following error (image attachment) when i try to export a workflow: No JSON object could be decoded: line 1 column 0 (char 0) I try to google but to no avail. I wonder if anyone has encountered similar problems before. Regards, Chan Fook Mun

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use remote data without duplication
by Caroline Prenoveau 19 Jul '11

19 Jul '11

Hi, We are a small lab and we would like to use galaxy to do our analysis. However we have a very large amount of data that is stored on several machines and that we cannot afford to duplicate. Our galaxy server is set up on a different machine. We are looking for a way to use our remote data inside galaxy without copying it locally. Any ideas/hints? Thanks, Caroline

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Pull request for Galaxy
by Nick Semenkovich 19 Jul '11

19 Jul '11

Hi -- I just submitted a tiny first pull request for some minor Galaxy changes (to correct wiki links): https://bitbucket.org/galaxy/galaxy-central/pull-request/2/update-galaxy-wi… (Not sure if I should e-mail the dev list about these or what. How do these get approved?) Thanks! Nick -- Nick Semenkovich 314.374.4434 Medical Scientist Training Program School of Medicine Washington University in St. Louis http://web.mit.edu/semenko/

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Re: [galaxy-dev] fyi: can't upload to toolshed
by Greg Von Kuster 19 Jul '11

19 Jul '11

Hello Ed, This one was tough to track down, but I believe I have it resolved. On Linux, the mercurial api's call to commit seems to bump into issues intermittently, throws an exception, and rolls back the transaction. Although I can reproduce it on Linux, I cannot produce this behavior on a Mac. I've added exception handling in the latest version of the tool shed that uses a different approach to committing the changes whenever the intermittent exception is thrown. Thanks for finding this issue, and please let me know if you bump into any problems in the future. Greg Von Kuster On Jul 15, 2011, at 1:20 PM, Edward Kirton wrote: > it was for an upload of MUSCLE. the error only occurred when i uploaded the XML file uncompressed. it worked fine later when i put it in a tarball. > > On Fri, Jul 15, 2011 at 6:48 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello Ed, > > Looking at the logs, I see that you uploaded to your Roche454 tool suite repo. Is that correct? I don't see any exceptions in the logs, so not sure what happened. Are you still having this issue? > > Thanks, > > Greg Von Kuster > > On Jul 14, 2011, at 9:32 PM, Edward Kirton wrote: > >> Server Error >> >> An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) ___________________________________________________________ >> 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/ > > Greg Von Kuster > Galaxy Development Team > greg(a)bx.psu.edu > > > > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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