Re: [galaxy-dev] Integrating generated graphics from cli tool?
Alex, xvfb http://www.xfree86.org/4.0.1/Xvfb.1.html works for our headless node R graphics and possibly other packages. I seem to remember writing a wiki entry but a search didn't find it... I see someone on the dev list found the toolfactory code which does a lot of sensible things automatically to create a pretty useful html index for a folder full of pdfs/pngs/xls/ On Mon, Dec 17, 2012 at 11:14 PM, Bossers, Alex alex.boss...@wur.nl wrote: Samual, We do the same as Peter mentioned. We generate pdfs or you could generate a mixed datatype html file linking to seperate documents/images (like the fastQC tool). If you get the export to png working on a headless server without desktop/gui..please let me know. In our hands it only works on full desktop linux environments somehow. Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] Namens Samuel Lampa Verzonden: zondag 16 december 2012 23:14 Aan: Peter Cock CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Integrating generated graphics from cli tool? On 12/14/2012 07:40 PM, Peter Cock wrote: On Fri, Dec 14, 2012 at 6:18 PM, Samuel Lampa samuel.la...@gmail.com wrote: There are existing tools which produce a PDF file as a Galaxy output, shown as its own 'green box' in the history. This works quite nicely if the browser shows the PDF in-line, but one one of my machines (not sure which browser off hand) it insists on downloading the PDF and opening it instead - which isn't quite as smooth an interface. Thanks for the info! Seems like that could be one way of doing it. I would probably output png rather than pdf, and that might work better. Best // Samuel ___ 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/
Re: [galaxy-dev] Integrating generated graphics from cli tool?
Ross, Thanks! I will check it out. Alex Van: Ross [mailto:ross.laza...@gmail.com] Verzonden: donderdag 20 december 2012 9:52 Aan: Bossers, Alex CC: Samuel Lampa; galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Integrating generated graphics from cli tool? Alex, xvfb http://www.xfree86.org/4.0.1/Xvfb.1.html works for our headless node R graphics and possibly other packages. I seem to remember writing a wiki entry but a search didn't find it... I see someone on the dev list found the toolfactory code which does a lot of sensible things automatically to create a pretty useful html index for a folder full of pdfs/pngs/xls/ On Mon, Dec 17, 2012 at 11:14 PM, Bossers, Alex alex.boss...@wur.nlmailto:alex.boss...@wur.nl wrote: Samual, We do the same as Peter mentioned. We generate pdfs or you could generate a mixed datatype html file linking to seperate documents/images (like the fastQC tool). If you get the export to png working on a headless server without desktop/gui..please let me know. In our hands it only works on full desktop linux environments somehow. Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Samuel Lampa Verzonden: zondag 16 december 2012 23:14 Aan: Peter Cock CC: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Integrating generated graphics from cli tool? On 12/14/2012 07:40 PM, Peter Cock wrote: On Fri, Dec 14, 2012 at 6:18 PM, Samuel Lampa samuel.la...@gmail.commailto:samuel.la...@gmail.com wrote: There are existing tools which produce a PDF file as a Galaxy output, shown as its own 'green box' in the history. This works quite nicely if the browser shows the PDF in-line, but one one of my machines (not sure which browser off hand) it insists on downloading the PDF and opening it instead - which isn't quite as smooth an interface. Thanks for the info! Seems like that could be one way of doing it. I would probably output png rather than pdf, and that might work better. Best // Samuel ___ 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/
[galaxy-dev] liftOver Exception caught attempting conversion
Hi I downloaded and extracted the .chain files for liftOver and edited the .loc file. After restarting Galaxy I have the option to convert my files to the respective coordinates but when running the job I get the same error for each. Traceback (most recent call last): File /steno-internal/projects/galaxy/galaxy-dist/tools/extract/liftOver_wrapper.py, line 81, in raise Exception, 'Exception caught attempting conversion: ' + str( e ) Exception: Exception caught attempting conversion I also found this in the handler.log file: galaxy.tools DEBUG 2012-12-20 11:37:09,902 Error opening galaxy.json file: [Errno 2] No such file or directory: '/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/000/98/galaxy.json' Do you know how could this be sorted? Thanks in advance, Nikos ___ 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/
Re: [galaxy-dev] Reference Genomes for NGS Tools - A Couple Questions
Thanks Jen! That makes more sense to me. Can you explain more about the 'custom reference genome'? Do you just mean uploading the reference genome in the normal fashion, (FTP or web form) and then it's available to the NGS tools? -Greg On Wed, Dec 19, 2012 at 12:46 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Greg, At the very top of this wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup is a link to a related wiki: http://wiki.galaxyproject.org/Admin/Data%20Integration that has additional required set-up info. This page also includes information about how to rsync the indexes currently available on the public Main server. These are planned to be updated with many new genomes and indexes over the next few weeks, so check back in mid January if you do not find what you want now and do not want to build it yourself. Releasing Bowtie2 indexes (also used by Tophat2) into this area is planned to start in later Jan, pending any issues, but to build yourself, the basic guidelines for Bowtie can be followed with adjustments to use bowtie2-build and bowtie2_indices.loc. The Bowtie2 source tool documentation has the exact options and should be used along with our guidelines (this is true for all tools that require indexes). If you choose not to populate genomes as an admin, users can use most tools with a 'custom reference genome'. Please be aware that running tools this way will take more processing resources and storage disk for user's histories. The size of the genome is the primary factor to consider - some mix of built-in and custom genomes may be good solution. Also, FTP upload will almost certainly need to be enabled. Complete how-to details from a user's perspective are here: http://wiki.galaxyproject.org/Support#Custom_reference_genome Hopefully this gives you an option that will work, Jen Galaxy team On 12/18/12 9:40 AM, greg wrote: Hi all, I'm finishing up installing Galaxy on our local cluster. I'm at this step regarding setting up reference genomes: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup#Setting_Up_the_Reference_Genomes_for_NGS_Tools But it looks like a whole lot of manual work that needs to be done by a system administrator. I was kind of expecting this would be something end users would be able to do. I'm actually not sure we have the resources for a sys admin to install all of these reference genomes every time someone needs one. I guess here are my questions: Am I misunderstanding the process? Is there a different way that normal users can add reference genomes instead? Is there anything in the works that lets users easily add these? Is there a way to use NGS tools without installing reference genomes? Thanks, Greg ___ 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://galaxyproject.org ___ 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/
Re: [galaxy-dev] Urgent: Seems like tophat2 does not support --transcriptome-mismatches
This thread addresses your issue: http://dev.list.galaxyproject.org/tophat-option-transcriptome-mismatches-not-recognized-td4657568.html In the future, please use the mailing list search before posting your question. You'll save time for both yourself and others. http://galaxyproject.org/search/mailinglists/ Best, J. On Dec 20, 2012, at 2:03 AM, Sachit Adhikari wrote: It seems like tophat2 does not support --transcriptome-mismatches option but Galaxy is still configured to call tophat2 with this option when run with Full parameter setting option within Galaxy. Is there new wrapper with this fix? If not, how to remove this option from Galaxy so that tophat2 is not call with this option. I am assuming that this is specified somewhere in the wrapper. Thanks, Sachit ___ 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/ ___ 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/
[galaxy-dev] Galaxy December 20, 2012 Distribution News Brief
*Galaxy Dec 20, 2012 Distribution News Brief http://wiki.galaxyproject.org/News/2012_12_20_DistributionNewsBrief* *Complete News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20* *Highlights:* * *Required Metadata Reset* for instances running *Tool Shed http://wiki.galaxyproject.org/Tool%20Shed* repositories. Be sure to *learn how http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories*. * *Simplified tool config*: all tools (including tool shed repos) can now have handlers and runners assigned based on their short id. * *New* GFF http://wiki.galaxyproject.org/Learn/Datatypes#GFF/GFF3 http://wiki.galaxyproject.org/Learn/Datatypes#GFF3 annotation support for *Cuffcompare/merge/diff http://cufflinks.cbcb.umd.edu/manual.html*. * *More Updated* tools: *TopHat2 http://tophat.cbcb.umd.edu/manual.html*, *Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml*. * *Multiple pull-requests* contributed by community (thanks!): *#83 https://bitbucket.org/galaxy/galaxy-central/pull-request/83/allow-a-datatypes-merge-method-to*, *#85 https://bitbucket.org/galaxy/galaxy-central/pull-request/85/another-round-of-bug-fixes-and*, *#90 https://bitbucket.org/galaxy/galaxy-central/pull-request/90/patch-to-make-extended_metadata-loader*, *#91* https://bitbucket.org/galaxy/galaxy-central/pull-request/91/fixing-missing-jobwrapper-import. * *Issue tracking help* is now covered in detailed in our new wiki: *Using the Galaxy Issue Board http://wiki.galaxyproject.org/Issues* * *GCC2013 Training Day Topic Nominations http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay are now open* through /*January 11th*/ http://wiki.galaxyproject.org/Events/GCC2013/KeyDates * *Plus* more *Tool Shed http://wiki.galaxyproject.org/Tool%20Shed* updates, *Bug Fixes*, and improvements to *Trackster, UI, Libraries, and Histories*. * getgalaxy.org http://getgalaxy.org* *bitbucket.org/galaxy/galaxy-dist http://bitbucket.org/galaxy/galaxy-dist* *galaxy-dist.readthedocs.org http://galaxy-dist.readthedocs.org * new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 36ad8aa7b922 *Best wishes for a safe and happy holiday*, /*The Galaxy Team http://wiki.galaxyproject.org/Galaxy%20Team*/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
