February 2013 - galaxy-user - lists.galaxyproject.org

cufflinks output for cummeRbund
by Mike Shamblott 13 Feb '13

13 Feb '13

I have been using cufflinks on Galaxy Main. I have downloaded the files generated but they do not correspond to the file names expected by cummeRbund. For example: cummeRbund expects 4 tracking files (e.g isoforms.fpkm_tracking) , 4 .diff files (e.g isoform_exp.diff). Here is a trimmed version of the output I download, grouped by what Im guessing is the tracking, diff and usage files: TRACKING ...Galaxy109_transcript_FPKM_tracking.tabular ...Galaxy107_gene_FPKM_tracking.tabular ...Galaxy105_TSS_groups_FPKM_tracking.tabular ...Galaxy103_CDS_FPKM_tracking.tabular .DIFF ...Galaxy108_transcript_differential_expression_testing.tabular ...Galaxy106_gene_differential_expression_testing.tabular ...Galaxy102_CDS_FPKM_differential_expression_testing.tabular USAGE ...Galaxy99_splicing_differential_expression_testing.tabular ...Galaxy100_promoters_differential_expression_testing.tabular ...Galaxy101_CDS_overloading_differential_expression_testing.tabular Given that cummeRbund is a common next step in the workflow, is there an option to save the output in the expected format, perhaps with a galaxy history number prepend? I'm not sure which files are to be renamed and to what name and it seems that one file is missing. If there were a cummeRbund implementation on Main it probably wouldn't matter as much but until that happens, I (and i'm guessing other newcomers) would appreciate the help! Thanks, mike

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Galaxy Join takes too long?
by Milad Bastami 12 Feb '13

12 Feb '13

I'm trying to joint two large intervals (one with 800,000 intervals and the other with about 350,000 intervals) using operates on intervals > join tool . I have no idea how long it should takes normaly. Two days have past and it is still runnig. Is there any limitation in file size for this tool? Any help would be appreciated. Regards, Milad Bastami PhD student of Medical Genetics Department of Medical Genetics Shahid Beheshti's university of Medical Science

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Discrepancy between Intersect and Join
by Aaron Quinlan 09 Feb '13

09 Feb '13

Dear list, I have a student that found an unexplained discrepancy between the results produced by the "Operate on Genomic Intervals" (OGI) intersect operation versus the OGI join operation. In particular, we know for certain that there are exactly 1105 intersection of at least 1bp between the two files we are testing, as we have confirmed this with our own bedtools and the ucsc table browser. An example intersection (intersecting positions: 10012008 - 10012013): file 1: chr1 10012008 10012021 5.6186 file 2: chr1 10011813 10012013 5_Strong_Enhancer 0 + 10011813 10012013 250,202,0 However, OGI intersect find 0 intersections between the files (settings: return overlapping intervals, >= 1bp). In an effort to make sure we didn't goof up on file formats (BED) or genome builds (hg19), we tested the exact same two files with the OGI join operation and found 1105 intersections as expected. I also tested the files with the bx-python bed_intersect.py and bed_intersect_basewise.py scripts and get the expected results. Does anyone have a suggestion for how to resolve this? Thanks for your help and for providing such a fantastic resource to the genomics community. Best, - Aaron quinlanlab.org

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Galaxy February 8, 2013 Distribution & News Brief
by Jennifer Jackson 09 Feb '13

09 Feb '13

Galaxy Feb 8, 2013 Distribution & News Brief <http://wiki.galaxyproject.org/News/2013_02_08_GalaxyNewsBrief> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08> * *Highlights:* * /Improvements/ to our release process <http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08#Improvements_to_Rele…>. *Release tag must be used in the hg update command to upgrade*. More at *usegalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy>*. * Tool Shed /Complex repository dependencies/ <http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_reposi…> are introduced, streamlining core dependency use across individual tools. * Also updated in the Tool Shed: multiple repository installation, dependency installation (when defined), and many usability enhancements and fixes. * New /Bedgraph-to-bigwig/ <http://wiki.galaxyproject.org/Learn/Datatypes#BedGraph> tool plus /Filter/ tool updated. * /Workflows/ now include option to export an image and the core /Framework/ now allows more unified reference genome usage and access. * /Ten Community Pull-Requests/ incorporated, plus another contribution to the tool Shed, addressing general usability, API, tools, error handling, workflows, and more. Thanks!! * Review highlights from the latest monthly */Galaxy Update/* <http://wiki.galaxyproject.org/GalaxyUpdates> newsletter and Galaxy Project Stats <http://wiki.galaxyproject.org/Galaxy%20Project/Statistics>! * Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools. *http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org * new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull $ hg update release_2013.02.08 To ensure that you continue to receive updates about *Galaxy Distributions and News Briefs* <http://wiki.galaxyproject.org/DevNewsBriefs>, be sure to subscribe to the Galaxy-Announce mailing list <http://wiki.galaxyproject.org/MailingLists#The_lists>, a low-volume list dedicated to News Items <http://wiki.galaxyproject.org/News> and priority messages from the Galaxy community <http://wiki.galaxyproject.org/Community> and project core team <http://wiki.galaxyproject.org/Galaxy%20Project>. /Thanks for using Galaxy,/ The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>

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Why SGE needed for galaxy ?
by Zeeshan Ali Shah 08 Feb '13

08 Feb '13

Hi, It seems that cloud man need SGE for scaling . Does SGE need also when run cloud on private cloud ? Zeeshan

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gather results from multiple histories
by mark.rose＠syngenta.com 07 Feb '13

07 Feb '13

Hi All Let's say that I have results produced from a step in multiple different histories and that I now want to gather these results into a new history so that they can be joined. Is there a way to do this without exporting results to my desktop and then uploading? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Re: [galaxy-user] Galaxy Help
by Jennifer Jackson 04 Feb '13

04 Feb '13

Hi John, If you have other sequence types, there are other alignment tool choices on the public Main server. The est2genome tool has a fairly specific use, so I thought that this was your input/goal. For ChIP-seq, RNA-seq, or other NGS datatypes, please see the tools under 'NGS: Mapping' and 'NGS: RNA Analysis'. We have tutorials for these tools - from the top menu bar follow 'Shared Data -> Published Pages". Good places to start are 'Galaxy Exercises', 'Galaxy RNA-seq Analysis Exercise', and 'Using Galaxy' (but review the others as wanted, I am not sure what type of data you are working with). More tutorials are in our wiki here: http://wiki.galaxyproject.org/Learn#Other_Tutorials Other public Galaxy sites offer specialized tools for working with certain data types - the best way to find out what they have to is visit them and review. We keep a list of links in our wiki here: http://wiki.galaxyproject.org/Big%20Picture/Choices -> http://wiki.galaxyproject.org/PublicGalaxyServers Good luck with your project! Next time, or if you have followup, please be sure to leave the mailing list in the cc to help us with tracking. Thanks! Jen Galaxy team On 2/4/13 8:08 AM, John Phillips wrote: > Are you sure that there is no way for me to align multiple sequences? I > apologize if I did not use the correct technical language, but from what > I understand, everyone seems to be citing you guys for sequence alignments. > > Thank you, > -John > > > On Sun, Feb 3, 2013 at 1:34 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi John, > > The current link is: > > http://wiki.galaxyproject.org/__FTPUpload > <http://wiki.galaxyproject.org/FTPUpload> > > We changed our wiki base and many of the older links do not > redirect. I'll let our wiki admin Dave know about this and see what > can be done. If this comes up again soon, the base always redirects > to "http://galaxyproject.org -> http://wiki.galaxyproject.org"__, > and clicking into "Learn" will likely take to you want to go - the > primary hub page for user documentation - including the links in > tutorials (plus the wiki side navigation bar with a few different > search options). > > And is true that we do not offer large scale EST to genomic > alignment on the public server. Galaxy choices such as > BLAST+/Megablast are for use with a local or cloud Galaxy instance. > > When using a local instance, the tool wrapper can be obtained from > the Tool Shed (http://toolshed.g2.bx.psu.edu__) A cloud ami would > have these tools as part of the package. You can also check the Tool > Shed for other options - more are added all the time. > > Local: http://getgalaxy.org > Cloud: http://usegalaxy.org/cloud > > Hopefully this helps, > > Jen > Galaxy team > > > On 2/2/13 3:17 PM, John Phillips wrote: > > 1. > > > To Whom it May Concern: > > > I am using the Galaxy interface, and according to the tutorial > screencast, I should be able to upload my own reference genome. The > address given in the tutorial > (http://galaxyproject.org/__FTPUpload > <http://galaxyproject.org/FTPUpload>) leads > to a 404 file not found page. I was wondering if there is an > alternative > site that can allow me to do this. > > Also, I tried to use the est2genome tool in order to try and > align my > uploaded sequences. It would only allow me to compare two > sequences at a > time. Is it possible to align a larger number of sequences at > once? I > understand there are other programs that allow for this kind of > procedure (e.g. Sequencher), but I would like to do this in Galaxy. > > Thank you for your time, > > -- > -John G. Phillips > Graduate Research Assistant > University of Tulsa > 231-233-6914 <tel:231-233-6914> > > > _____________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org <http://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 > <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/ > > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org > > > > > -- > -John G. Phillips > Graduate Research Assistant > University of Tulsa > 231-233-6914 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Galaxy Help
by John Phillips 03 Feb '13

03 Feb '13

1. To Whom it May Concern: I am using the Galaxy interface, and according to the tutorial screencast, I should be able to upload my own reference genome. The address given in the tutorial (http://galaxyproject.org/FTPUpload) leads to a 404 file not found page. I was wondering if there is an alternative site that can allow me to do this. Also, I tried to use the est2genome tool in order to try and align my uploaded sequences. It would only allow me to compare two sequences at a time. Is it possible to align a larger number of sequences at once? I understand there are other programs that allow for this kind of procedure (e.g. Sequencher), but I would like to do this in Galaxy. Thank you for your time, -- -John G. Phillips Graduate Research Assistant University of Tulsa 231-233-6914

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Re: [galaxy-user] Fwd: Converting files to gd_snp format
by Cathy Riemer 02 Feb '13

02 Feb '13

Hello Mike, The tutorial you were looking at was made using one of our local Galaxy instances, in advance of updating the main public server. The main server already includes most of the tools used in the examples, but two of the format conversion tools ("MasterVar to gd_snp" and "pgSnp to gd_snp") are not posted there yet. I apologize for the delay. We are in the process of moving some of the tools from the Phenotype Association section of the toolbox to the Convert Formats section, while simultaneously migrating those and the rest of the Phenotype Association tools from their current, manually configured installation method to the new Galaxy Tool Shed paradigm. We have encountered some technical difficulties with that, but we hope to have the update accomplished within the next few weeks. If you need it sooner, let me know and I'll send you the underlying Perl script for the "pgSnp to gd_snp" tool, so you can run that locally to convert your file and then upload the output to your Galaxy history. Thanks for your patience! -Cathy Riemer > ---------- Forwarded message ---------- > From: Sheehan, Michael - (michaelsheehan) <michaelsheehan(a)email.arizona.edu> > Date: Wed, Jan 30, 2013 at 1:30 AM > Subject: [galaxy-user] Converting files to gd_snp format > To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > > > I would like to convert VCF files to gd_snp format to be used in some > population genomic analyses. A tutorial online makes it seem like this > is the correct path to follow to conduct such analyses: > > http://www.bx.psu.edu/~giardine/tutorials/example2/part1/snpTable.html > > I have been using Galaxy on the free public server and this tools does > not appear to be present anywhere. Does anyone know where the tool has > gone or is there a way to add the needed tools back? > > Thanks > Mike >

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can't download big files
by Allan Sun 02 Feb '13

02 Feb '13

Hello everyone, We have galaxy-dist-17d57db9a7c0 installed on our Mandriva 2009 64bit. There are 2 big fasta files, file A is 4.4G and file B is 3.3G which I tried to download without success. I've used browser download,including mozilla,IE and Chrome,also from suggestion by Jennifer: linux command: wget and curl -O.None of them work. For file A,the downloaded file size is always 450M(9% of total size),no matter which way ( mentionedabove )I use, For file B,the downloaded file size is 0 byte. Following is the error report by :curl -O curl: (18) transfer closed with 4294967296 bytes remaining to read Any help will be very appreciated. Allan

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