galaxy-user January 2011

galaxy-user@lists.galaxyproject.org

47 participants
59 discussions

Re: [galaxy-user] moving files between galaxy servers
by Jeremy Goecks 11 Jan '11

11 Jan '11

Hi David, I'm having trouble exporting the history, and it's likely because it's continuing to change. If you're exporting a history but change it, the export will restart because it's old. You'll need to stop working with a history in order to fully export it. J. On Jan 10, 2011, at 5:23 PM, David Matthews wrote: > Hi, > > When I ask it to export, it directs me to a new page where it says its exporting it all to http://main.g2.bx.psu.edu/history/export_archive?id=7c3a5dc0aaa612c6. I may have been a bit greedy in asking it to export the whole thing - is this the reason? I probably only need to export a subset of the files, but even if I right click on a file and as it to provide a link I can paste in to the "upload file" portion of the Ratsch server nothing happens. > I've also added you to the shared list. > Thanks for your help with this. > > Cheers > David > > > > On 10 Jan 2011, at 22:05, Jeremy Goecks wrote: > >>> >>> I am trying to move my histories from the galaxy server at psu to the one at the Ratsch lab (http://galaxy.tuebingen.mpg.de) but all my attempts seem to be taking forever. I have tried moving the whole set or individual parts of it but with no success. From the Ratsch lab server I get the following message: The resource could not be found. >>> File Not Found (/home/galaxy/galaxy-2.1.2009/database/files/064/dataset_64040.dat). >>> >>> Any ideas? >> >> The first question it to determine whether the problem is in exporting the history or importing the history. When you click on the link provided by Galaxy for exporting the history, do you get a valid gzipped tar file that you can unpack and view? Within the unpacked directory, is there a datasets directory with a large number of non-zero size files? >> >> If not, the problem is likely with the public/PSU server. If so, the problem is probably with the Ratsch Galaxy server. Can you determine which server is problematic? >> >> Also, if this doesn't make much sense to you, you can share your history with me (Options --> Share/Publish) and I can take a look myself. >> >> Thanks, >> J. >> >> >> > J.

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How to get coordinate information
by vaibhav jain 11 Jan '11

11 Jan '11

Hello everyone, I have list of such Id's obtained from ENSRNOG00000000000 and I want to get the information of the transcription coordinates. So how can I get in Galaxy or can I get it directly from UCSC ??? Vaibhav Jain Research Scholar @IGIB Delhi, INDIA

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Help w SAM to BAM
by DAR78＠pitt.edu 11 Jan '11

11 Jan '11

Hi, We're loving Galaxy. This is an excellent interface and set of tools. The issue we're having is running SAM to BAM. We've been following the "Illumina Mapping: Single Reads" screencast, with the only significant difference (I think) being that we're using our own uploaded reference genomes instead of a pre-built index for the Bowtie alignment. When we get to the SAM to BAM step, we have two options for "Choose the source for the reference list": 1. Locally Cached, 2. History. 1. If we try to use "Locally Cached", we get the following error before the job is even added to the queue: "Unspecified genome build, click the pencil icon in the history item to set the genome build". We've tried to follow those directions, but don't see the reference genome we want in the list. 2. If we try to use "History" and specify the SAM file and then the FASTA file we used to do the bowtie alignment, we get the following error: An error occurred running this job: Samtools Version: 0.1.12 (r862) Error creating indexes from reference (/galaxy/home/g2main/galaxy_main/database/files/001/894/dataset_1894598.dat), [fai_build_core] different line length in sequence 'gi|118467340|ref|NC_008596.1|'. Segmentation fault Any guidance would be wonderful. My user name is: dar78(a)pitt.edu Thanks for your help, Dan Russell University of Pittsburgh

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moving files between galaxy servers
by David Matthews 10 Jan '11

10 Jan '11

Hi, I am trying to move my histories from the galaxy server at psu to the one at the Ratsch lab (http://galaxy.tuebingen.mpg.de) but all my attempts seem to be taking forever. I have tried moving the whole set or individual parts of it but with no success. From the Ratsch lab server I get the following message: The resource could not be found. File Not Found (/home/galaxy/galaxy-2.1.2009/database/files/064/dataset_64040.dat). Any ideas? Best Wishes, David

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How do i view the version of Galaxy
by Sonali Amonkar 10 Jan '11

10 Jan '11

Hi, I am new to Galaxy and would like to know where does Galaxy maintain versions? How can I view the version of Galaxy that I have downloaded? Regards, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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MACS follow up
by Keith E. Giles 10 Jan '11

10 Jan '11

To be more specific, I continually get error's that say, NO records for chromosome X (or any other), minus strand! I just don't understand what the problem is here, because there are millions of tags on each strand. Could it be that the "-" characters is not recognized by the MACS program so its ignoring all those tags?

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Galaxy (and GMOD) at PAG 2011, Jan 15-19
by Dave Clements 09 Jan '11

09 Jan '11

Hello all, Below is an announcement that went out to the larger GMOD community about GMOD related content at Plant and Animal Genome in a week. Some particular highlights for the Galaxy Community are * Dan Blankenberg's hour long seminar on Galaxy on Wednesday, * Anne-Francoise Adam-Blondon's talk on the GnpIS portal * and the INRA posters on using Galaxy for SNP detection (#188) and using Galaxy in the GnpIS portal (#805). See http://gmod.org/wiki/PAG_2011 for details and links. Also, if you are presenting work that uses Galaxy at PAG (or any other conference), please feel free to post that to the list as well. Thanks, Dave C ---------- Forwarded message ---------- From: Dave Clements <clements(a)nescent.org> Date: Sat, Jan 8, 2011 at 9:32 PM Subject: [Gmod-announce] GMOD at PAG 2011, Jan 15-19 To: GMOD Announcements List <gmod-announce(a)lists.sourceforge.net>, GMOD Comparative Genomics and Phylogeny List <gmod-cogephy(a)lists.sourceforge.net> Hello all, GMOD will have a stronger presence then ever at the Plant and Animal Genome Conference (PAG 2011) <http://gmod.org/wiki/PAG_2011>, being held January 15-19 in San Diego. This includes, for the first time, *an all day GMOD Workshop <http://www.intl-pag.org/19/19-gmod.html>* on Wednesday, January 19th, featuring extended talks on - MAKER <http://gmod.org/wiki/MAKER>: An easy to use genome annotation pipeline <http://www.intl-pag.org/19/19-gmod.html#MAKER> - Galaxy <http://gmod.org/wiki/Galaxy>: Analyze, Visualize, Communicate<http://www.intl-pag.org/19/19-gmod.html#Galaxy> - JBrowse <http://gmod.org/wiki/JBrowse>: A Next Generation Genome Browser <http://www.intl-pag.org/19/19-gmod.html#JBrowse> - Tripal <http://gmod.org/wiki/Tripal>: A Construction Toolkit for Online Genomic Databases <http://www.intl-pag.org/19/19-gmod.html#Tripal> - GMODviews <http://gmod.org/wiki/GMODviews>: A web-based knowledge-base and user-configurable interface for GMOD databases and tools, including Tripal, GBrowse, and Chado DBs<http://www.intl-pag.org/19/19-gmod.html#GMODviews> - GBrowse_syn <http://gmod.org/wiki/GBrowse_syn>: The Generic Synteny Browser <http://www.intl-pag.org/19/19-gmod.html#GBrowse_syn> PAG 2011 <http://gmod.org/wiki/PAG_2011> will also feature workshops and tutorials covering - BioMart <http://gmod.org/wiki/BioMart>: Ensembl and Ensembl Genomes<http://www.intl-pag.org/19/abstracts/W29_PAGXIX_188.html> - GBrowse <http://gmod.org/wiki/GBrowse>: The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse<http://www.intl-pag.org/19/19-gbrowse.html> - CMap <http://gmod.org/wiki/CMap>: Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses<http://www.intl-pag.org/19/19-gramene.html> Plus *at least 25 more talks<http://gmod.org/wiki/PAG_2011#Projects_Using_GMOD_Components>and posters <http://gmod.org/wiki/PAG_2011#Posters>* about or using Pathway Tools <http://www.intl-pag.org/19/abstracts/C02_PAGXIX_903.html>, GBrowse<http://www.intl-pag.org/19/abstracts/P08b_PAGXIX_828.html>, Galaxy <http://gmod.org/wiki/Galaxy>, CMap <http://gmod.org/wiki/Cmap>, Apollo <http://gmod.org/wiki/Apollo>, Chado <http://gmod.org/wiki/Chado>, GBrowse_syn <http://gmod.org/wiki/GBrowse_syn>, JBrowse<http://gmod.org/wiki/JBrowse>, BioMart <http://gmod.org/wiki/BioMart>, MAKER <http://gmod.org/wiki/MAKER>, Tripal <http://gmod.org/wiki/Tripal>, and the GMOD Evo Hackathon<http://www.intl-pag.org/19/abstracts/P08a_PAGXIX_814.html>. See http://gmod.org/wiki/PAG_2011 for a more complete list. Many GMOD users<http://gmod.org/wiki/PAG_2011#Projects_Using_GMOD_Components>and GMOD developers, including Stephen Ficklin <http://gmod.org/wiki/User:Sficklin> (Tripal<http://gmod.org/wiki/Tripal>), Carson Holt <http://gmod.org/wiki/User:Carsonholt> (MAKER<http://gmod.org/wiki/MAKER>), Barry Moore <http://gmod.org/wiki/User:Bmoore> (SOBA<http://gmod.org/wiki/SOBA>, MAKER <http://gmod.org/wiki/MAKER>), Dan Blankenberg<http://gmod.org/wiki/User:DanB>( Galaxy <http://gmod.org/wiki/Galaxy>), Mitch Skinner<http://gmod.org/wiki/User:MitchSkinner>( JBrowse <http://gmod.org/wiki/JBrowse>), Ken Youens-Clark (CMap<http://gmod.org/wiki/CMap>), Mike Caudy <http://gmod.org/wiki/User:Mcaudy> (GMODviews<http://gmod.org/wiki/GMODviews>), Rob Buels <http://gmod.org/wiki/User:RobertBuels> (Bio::Chado::Schema<http://gmod.org/wiki/Bio::Chado::Schema>, GBrowse_syn <http://gmod.org/wiki/GBrowse_syn>), and Scott Cain<http://gmod.org/wiki/User:Scott>( Chado <http://gmod.org/wiki/Chado>, GBrowse <http://gmod.org/wiki/GBrowse>, ...) will be attending PAG this year. Please seek each other out. Dave Clements <http://gmod.org/wiki/User:Clements> Galaxy Project <http://gmod.org/wiki/Galaxy> PS: In addition, three of the GMOD developers (Dan, Mitch, Scott) are also available to visit organizations in the San Diego area<http://gmod.org/wiki/GMOD_News#GMOD_Roadshow_in_San_Diego>during the meeting. -- http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://usegalaxy.org/ ------------------------------------------------------------------------------ Gaining the trust of online customers is vital for the success of any company that requires sensitive data to be transmitted over the Web. Learn how to best implement a security strategy that keeps consumers' information secure and instills the confidence they need to proceed with transactions. http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Gmod-announce mailing list Gmod-announce(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gmod-announce -- http://usegalaxy.org/

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Seeing time taken for jobs
by Peter 07 Jan '11

07 Jan '11

Hi all, I'm curious if there is any way to see how long a task took to complete (or related to this, how long a workflow took to run)? I realise that the timings will be highly dependent on the machine load, but nevertheless it could be useful if trying to estimate how long a job is going to take (having tried it on a sub sample of the data). It would also be quite nice when giving Galaxy demos - although asking the audience to time it is quite good for getting people to pay attention ;) I've clicked on all the task icons, the peep information, etc, but it looks like this information isn't shown to the user (if it is collected at all). Have I overlooked something? Thanks, Peter

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Re: [galaxy-user] Question about megablast_wraper.xml - blastdb file
by Jeremy Goecks 07 Jan '11

07 Jan '11

Eric, You'll want to direct Galaxy usage questions such as this one to galaxy-user(a)lists.bx.psu.edu (cc'd) so that you can reach a wide audience--including other Galaxy developers--and receive a good response. I have no experience with megablast, so I won't even venture a guess about what the problem might be. Thanks, J. > I would like to use the megablast program, but I don't have the blastdb file. > So, I would like to know how I can create this file and where (what folder). > I have tried to create the file blastdb with two columns separated by TAB, directly on the tool folder, but this failed. > > I would greatly appreciate your help. > > Best regards

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parallel processing of multiple files on a multi-processor box?
by Yury Bukhman 06 Jan '11

06 Jan '11

Hi, I have an RNA-seq study with 6 runs. The output is 6 Illumina fastq files. I would like to be able to run FASTQ Groomer and Bowtie on all 6 in parallel, utilizing a multi-processor box. Is this possible? It appears (to our IT group) that Galaxy won't be able to utilize multiple processors on an SMP box for the same user session, and we would need to set up a cluster to do things like this. Is this so? Is there a work-around? Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman(a)glbrc.wisc.edu

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galaxy-user January 2011