galaxy-user November 2012

galaxy-user@lists.galaxyproject.org

53 participants
59 discussions

Help: determining the exon number of exonic variants
by Luis Santomé 07 Nov '12

07 Nov '12

Hi everyone, I have a list of genomic coodinates corresponding to exonic variants, and I'd like to determine the exon number they are in. Some of them are known variants but many other are not, so I can't retrieve this information by combining my set of variants with a dataset of genomic variants (i.e. dbSNP). Any suggestion? Thank you in advance! ;) -- *J. Luis Santomé Collazo*

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Create an index with samtools within a pipeline?
by Joshua Orvis 06 Nov '12

06 Nov '12

I want to make a pipeline that grabs a reference genome, indexes it, then aligns reads to it via bwa. The bwa tool has a menu option for using an index "from the history" (see attached image) but I don't see any option within the bwa wrappers to actually create an index on the fly. This is also true for samtools and other aligners. The following link describes the conf/loc files required to add indexes to the system: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup But how can they be created dynamically in the course of a pipeline run instead of preconfigured in this way? Regards - Joshua

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Cluster Install - Trouble finding drmaa egg
by greg 06 Nov '12

06 Nov '12

I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the $DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg

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Perpetual "Job is waiting to run"
by Burger, Francois, Mnr <nfvburger＠sun.ac.za> 04 Nov '12

04 Nov '12

Hi there I've recently submitted jobs to the Lastz mapping tool on the main galaxy server and would like to know what the recommended length of time is that I should wait for a job to start running. I've submitted several jobs but as of 48 hours later all are yet to run. I read on the Q&A that when the server is overloaded your request waits in the queue to be initialized, or that when too many jobs are submitted, only the first 8 are primed for execution. Would this be my problem (either too many jobs or a server issue) and how will I know this in the future? Thank you for your time! Best regards Francois Burger ------------------------------------------------------- Technical Officer for Cereal Genomics Group Lab 239 JC Smuts Building University of Stellenbosch Stellenbosch Western Cape South Africa ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige lêers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

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Re: [galaxy-user] cufflinks visualization
by Jeremy Goecks 04 Nov '12

04 Nov '12

(cc'ing back to galaxy-user because this information may be useful to others) The problem is that the reference gene annotation that you're using, RefGene from UCSC, has an error. Specifically, a transcript_id attribute is duplicated for two different transcripts, one on chr1 and one on chr19: -- chr1 Cufflinks transcript 34611 36081 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr1 Cufflinks exon 34611 35174 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr1 Cufflinks exon 35277 35481 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr1 Cufflinks exon 35721 36081 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr19 Cufflinks transcript 76220 77690 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr19 Cufflinks exon 76220 76783 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr19 Cufflinks exon 76886 77090 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr19 Cufflinks exon 77330 77690 1 - . gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; -- When trying to visualize either the reference annotation or Cufflinks datasets created using this annotation, an error occurs because Galaxy tries to reconcile these two transcripts. More graceful error handling is planned. To avoid this error, use the iGenomes reference available in the iGenomes data library (hg19 and mm9 only right now). There are other benefits to this annotation as well; it has additional attributes useful for Cuffdiff. I was able to visualize your Cufflinks data, as well as the iGenomes gene annotation, using Trackster. Best, J. On Nov 2, 2012, at 7:16 PM, i b wrote: > > On Fri, Nov 2, 2012 at 12:33 PM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: >> Please share the history with me and I'll take a look. >> >> Thanks, >> J. >> >> On Nov 2, 2012, at 4:54 AM, i b wrote: >> >>> Hi Jeremy, >>> I was trying to visualize "assembled transcripts". none of these works >>> from any of my jobs. >>> >>> The line where I should see the assembled transcript is empty and you >>> can click on "visualize error". I have attached what the error says, >>> If I click "try again", after a while it comes out the same view (the >>> lien describing view error and try again) >>> >>> thanks for your help, >>> ib >>> >>> On Fri, Nov 2, 2012 at 12:58 AM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: >>>> I'm able to visualize Cufflinks assembled transcripts in Trackster. Can you please be more specific about (a) which datasets you're having trouble using and (b) what errors you're seeing? >>>> >>>> Thanks, >>>> J. >>>> >>>> On Oct 31, 2012, at 1:10 PM, i b wrote: >>>> >>>>> Hi all, >>>>> can anyone explain me wh how can I visualize cufflinks outputs in trackster? >>>>> galaxy keep sending me errors >>>>> >>>>> thanks, >>>>> ib >>>>> ___________________________________________________________ >>>>> 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/ >>>> >>> <Presentation1.pptx> >>

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Export to file
by Dave Corney 02 Nov '12

02 Nov '12

Hi list, Is there a currently a known problem with the "export to file" function? I'm trying to migrate some data from the public galaxy to a private one; the export function worked well with a small (~100mb) dataset, but it has not been working with larger datasets (>2GB) and I get the error: Server Error. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). Is there a limit on the file size of the export? If so, what is it? Thanks in advance, Dave

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cufflinks visualization
by i b 02 Nov '12

02 Nov '12

Hi all, can anyone explain me wh how can I visualize cufflinks outputs in trackster? galaxy keep sending me errors thanks, ib

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Latest supported Cufflinks?
by Bidwell, Christopher A. 01 Nov '12

01 Nov '12

I am interested in using Cufflinks 2.0 on our local instance of Galaxy but I am not sure if it is supported yet. We did Galaxy update in early October and we tried to install cufflinks V2.0 and it seems to run. I get the output files and they have the genes listed but 0.000 for all results (using files that worked on previous version). The output file summaries contain the following: Info: ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/opt/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/opt/galaxy/galaxy-d Is there a fix for this error or do we need to go back to the latest supported version of Cufflinks and if so which version? Thanks Chris Bidwell

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Getting error in Bismark
by Sachit Adhikari 01 Nov '12

01 Nov '12

I am getting this error at the top while opening Bismark Mapper: Data table named 'bismark_bs_indeces' is required by tool but not configured. I got Bismark from official toolshed.

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galaxy-user November 2012