January 2012 - galaxy-user - lists.galaxyproject.org

Adding "read group" tag
by Eric Guo 10 Jan '12

10 Jan '12

Hi all, Does anyone know any program on the Galaxy server, which can be used to add "read group" tag to .sam file? Thanks in advance for your help. -Eric

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Re: [galaxy-user] How to find out SNPs and point mutations in RNA-Seq data using Galaxy?
by Jeremy Goecks 10 Jan '12

10 Jan '12

Wei, The best way to move individual datasets b/t Galaxy instances is by link: right click on the dataset's save icon (a disk), copy the link, and paste that into the upload form. A couple word of caution about our test server: it is experimental and may be nonfunctional or unavailable periodically, there is little/no support is offered for new tools, and quotas are quite low. For analyses that require multiple steps, test most likely will not meet your needs. Finally, please always cc the mailing list when replying. Good luck, J. On Jan 9, 2012, at 7:48 PM, Wei Liao wrote: > Hi, Jeremy, > Thank you for your help，I will try to use pileup tool. > I noticed that there are many great tools I am interested on the test server such as GATK, however, all my data are on main server and the bam files are huge (5-7GB), do you know a fast way to transfer data from main server account to test server? > > Wei It > > > On Mon, Jan 9, 2012 at 10:40 AM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: > Wei, > > The pileup tool will help you find SNPs in your data; you'll want to read the documentation to understand how best to use it for your needs. You can also try the Unified Genotyper on our test server ( http://test.g2.bx.psu.edu/ ), but it's in alpha/beta status and we aren't providing any support for it yet. > > Good luck, > J. > > > On Jan 9, 2012, at 1:28 AM, <ericliaowei(a)gmail.com> <ericliaowei(a)gmail.com> wrote: > >> HI, >> I am new to the RNA-seq, and the only available sources for me to do analysis is the Galaxy server. I want find out SNP and point mutations in RNA-Seq data using Galaxy (I do not know if anyone using RNA-seq data to find point mutations, because there is whole Genome sequencing for reporting mutations and SNPs). I have been searching in the forum for a step-by-step protocols for doing it, but could not find it. >> I have one normal sample and two cancer samples, a TopHat produced "accepted Hits.bam" file for each one. >> I want to find out SNP and point mutations in the cancer samples, so How do I go from here? Can anyone show me how to do it in Galaxy main server? >> Thanks! >> >> Wei >> ___________________________________________________________ >> 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/ > > > > > -- > Wei Liao > Research Scientist, > Brentwood Biomedical Research Institute > 16111 Plummer St. > Bldg 7, Rm D-122 > Sepulveda, CA 91343 > 818-891-7711 ext 7645 >

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How to find out SNPs and point mutations in RNA-Seq data using Galaxy?
by ericliaowei＠gmail.com 09 Jan '12

09 Jan '12

HI, I am new to the RNA-seq, and the only available sources for me to do analysis is the Galaxy server. I want find out SNP and point mutations in RNA-Seq data using Galaxy (I do not know if anyone using RNA-seq data to find point mutations, because there is whole Genome sequencing for reporting mutations and SNPs). I have been searching in the forum for a step-by-step protocols for doing it, but could not find it. I have one normal sample and two cancer samples, a TopHat produced "accepted Hits.bam" file for each one. I want to find out SNP and point mutations in the cancer samples, so How do I go from here? Can anyone show me how to do it in Galaxy main server? Thanks! Wei

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CloudMan - Galaxy - How does sharing work?
by mailing list 09 Jan '12

09 Jan '12

I was wondering how the sharestring feature works? Enis mention it a little bit here: http://biostar.stackexchange.com/questions/15467/galaxy-cloudman-best-way-t… So as I understand it, I do my customizations and persist them, and then I get a sharestring so others can load my customizations. How does this work behind the scenes? Also where are my customizations stored? Am I charged by Amazon for storing them? How do others have permissions to pull them from my Amazon account? (I'm new to all of this, sorry if my questions are obvious) -Greg

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How to add a tool to Cloud Galaxy
by Greg Edwards 07 Jan '12

07 Jan '12

Hi Folks, I could use some help on adding a tool to the cloud version of Galaxy. The Cloud startup process creates, among other things, /mnt/galaxyTools/galaxy-central which has tools_conf.xml, and subdir tools etc. This seems not accessible before starting the cloud. I assume I need to add my tool into the structure as per a local Galaxy instance, and then get Galaxy to restart, or re-read it's config ? Would appreciate some advice there. Just as background .. I have got a custom proteomics Perl script running ok under a local version of Galaxy on Mac. Added in to tools_conf.xml, tools etc. Made several mods to the Perl to stop any writing to stderr except for fatal show-stopper errors, everyone seems to hit that one, and other small things to make it play better with Galaxy. Also quite familiar with AWS EC2, have been using that for a while. I have Galaxy Cloudman running well, start/stop extra servers etc. Using the free t1.micro AMI for now, slowish but ok for testing. Or a Spot Instance of m1.large when I'm impatient. I couldn't find the answer in a search of Galaxy archives, apologies if it's there, or obvious in some other way. Thanks! -- Greg Edwards, Port Jackson Bioinformatics Consulting. gedwards2(a)gmail.com

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Galaxy @ PAG 2012
by Dave Clements 06 Jan '12

06 Jan '12

Hello all, Plant and Animal Genome XX (PAG2012) starts in San Diego on January 14. If you are attending PAG then you will have (at least) a half-dozen opportunities to learn more about Galaxy and how it is being used to support research. There will be workshops introducing Galaxy, and on deploying Galaxy in the cloud, and talks and posters on using Galaxy and several local Galaxy deployments. See the Galaxy @ PAG2012 page (http://wiki.g2.bx.psu.edu/Events/PAG2012) and the conference website (http://www.intlpag.org/) for more information. Dannon Baker and Dave Clements from the Galaxy Team ( http://wiki.g2.bx.psu.edu/Galaxy%20Team) will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself. Hope to see you in San Diego, Dave Clements and Dannon Baker -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Requesting uploading of genomes
by Kenneth McDowall 06 Jan '12

06 Jan '12

Hi, Would be grateful I the following genomes were uploaded into Galaxy Streptomyces coelicolor A3(2) ; ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Streptomyces_coelicolor_A3_2__uid57… Propionibacterium acnes KPA171202 (pre-salt downshift); ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Propionibacterium_acnes_KPA171202_u… Thanks in advance, Kenneth Dr Kenneth McDowall * Astbury Centre for Structural Molecular Biology Tel +44 (0) 113 343 3109 or Mob. 0783 793 5384 | Ext 33109 | k.j.mcdowall(a)leeds.ac.uk<mailto:k.j.mcdowall@leeds.ac.uk> | www.fbs.leeds.ac.uk IMCB Director of Taught Programmes * Institute of Molecular and Cellular Biology Faculty of Biological Sciences | University of Leeds | Manton Building Room 10.05 | Leeds LS2 9JT | UK 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. Access, copying, dissemination and re-use of information in it by anyone else are unauthorised. If you have received this message in error, please contact the sender as soon as possible.

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Error Handling in Galaxy Workflows ?
by John Major 06 Jan '12

06 Jan '12

Hi All- Is there any plumbing in place for handling errors that occur in component tools of workflows? I'm thinking about a case where you might want to follow path 'A' if a tool succeeds, but path 'B' if there is some specific kind of exception, and fail completely if any other error is thrown. If this is in place, a pointer to the relevant docs would be awesome. I've looked around and did not come up with anything. Thanks! John

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Default Display replicate libraries with different colors
by Eric Guo 06 Jan '12

06 Jan '12

Hi all, I have two small RNA libraries that are biological replicates. I mapped the reads onto the genome using Bowtie and displayed the BAM files as two individual tracks on the UCSC genome browser. However, this is not very nice. Ideally, I would like to color the reads from each library with a different color, so that I could display them in the SAME track. Because the two replicates are color labeled, I would be able to tell which experiment a particular read comes from. I have two BAM files from each library. All I need to do is to label them with different colors, then merge them before displaying on genome browser. Does anyone know how to do this? Thanks in advance for your help! -Eric

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Make Galaxy continue running when i close the browser
by Makis Ladoukakis 05 Jan '12

05 Jan '12

Dear Galaxy users, I have installed a local Galaxy instance on a server and I use it to run certain genomic assembly workflows. Nevertheless with larger datasets completion may take up to one day. How can i make Galaxy to continue the operation even when i close the browser? Is that possible on a local instance or on the main server? Thank you, Efthymios Ladoukakis

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