- galaxy-user - lists.galaxyproject.org

Amazon AMI
by Daniel Muehlschlegel 31 Oct '11

31 Oct '11

Hi, I installed the Amazon Galaxy CloudMan today but am not able to load any of the Galaxy AMIs. The AMI on the user galaxy webpage does not exist, but 3 AMIs do. I tried the 2 most current ones and they don't load: It looks like everything is fine on the Amazon side: Thanks for your help, Danny

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Upcoming Galaxy Events
by Dave Clements 31 Oct '11

31 Oct '11

Hello all There are several Galaxy related events going on at Cold Spring Harbor Laboratory in November, but if you aren't already registered for those it is now too late to get in. However, there are several deadlines in November and events in the coming months. See the Events<http://wiki.g2.bx.psu.edu/Events>page ( http://wiki.g2.bx.psu.edu/Events) for a full listing of upcoming events. If you have a Galaxy related event please send it to outreach(a)galaxyproject.organd we will help you get the word out. Date Topic/Event Venue/Location Contact November 2-5 Best practices for variant discovery through Galaxy: Oscillating evolution within dual coding genes <http://meetings.cshl.edu/meetings/info11.shtml> Genome Informatics 2011 <http://meetings.cshl.edu/meetings/info11.shtml>, Cold Spring Harbor, New York, United States Dan Blankenberg <http://wiki.g2.bx.psu.edu/dan> November 8-21 Advanced Sequencing Technologies & Applications Course<http://meetings.cshl.edu/courses/c-seqtech11.shtml> Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> November 9-15 Compuational & Comparative Genomics Course<http://meetings.cshl.edu/courses/c-ecg11.shtml> Features Galaxy and much more. Cold Spring Harbor Laboratory, New York, United States James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 8-21 2012 2012 Workshop on Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kruml…> Features Galaxy and much more. *Application deadline is November 1.* Český Krumlov, Czech Republic James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 14-18 2012 Galaxy Session @ GMOD Workshop PAG 2012 <http://www.intlpag.org/>, San Diego, California, United States Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> January 17 2012 Reproducible workflows for next generation sequencing analysis<http://www.nowgen.org.uk/facilities/events/event.php?id=30> Nowgen <http://www.nowgen.org.uk/>, University of Manchester<http://www.manchester.ac.uk/>, United Kingdom Tom Hancocks <training(a)nowgen.org.uk> Thanks, Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Queuepool limit problem
by Cinto Queky 30 Oct '11

30 Oct '11

Hi All, We encountered queuepool limit problem after running the workflows for a few times. We have tried to increase these 2 parameters: database_engine_option_pool_size and database_engine_option_max_overflow to 20 and 40 respectively. Are there other parameters that we can change? Thanks,Cinto

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Problem launching cloud instance
by Clare Sloggett 30 Oct '11

30 Oct '11

Hi all, I wasn't sure whether to send this to galaxy-dev or galaxy-user. I'm having a problem launching a Galaxy instance on Amazon. I have done this in the past with no problems. I suspect I'm doing something trivial wrong but can't work out what! The problem is that after starting the instance, when I go to http://public-dns-url/cloud and the "Initial Cluster Configuration" window pops up, the initial storage size text box is disabled. That is, the text box after the first radio box ("Galaxy Cluster") is greyed out. So, I can't enter a size for the storage and if I just proceed without doing so, it (I think) causes CloudMan to fail. I thought I was probably just having browser issues but I get the same problem repeatedly in Chrome and Firefox. When I inspect the element, I see <input disabled="true" ... name="g_pss"...> so I think it really is disabled. This seems like a weird problem so I suspect it's me, but I can't work it out. Any help would be appreciated! Thanks, Clare -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759

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Re: [galaxy-user] Fwd: Cufflinks transcript-extract
by vasu punj 30 Oct '11

30 Oct '11

You should be able to do in Biomart I think fetch seq shoudl also allow you to do the same. Vasu ________________________________ Subject: Fwd: [galaxy-user] Cufflinks transcript-extract ---------- Forwarded message ----------From: dongdong zhaoweiming <zhaoweiming1983(a)yahoo.com.cn>Date: Sat, Oct 29, 2011 at 10:38 PMSubject: [galaxy-user] Cufflinks transcript-extractTo: galaxy-user(a)bx.psu.edu Hi, I use cufflinks to assemble my RNA-Seq reads which produced a GTF file, such as follows:(1)chr1 Cufflinks transcript 6234876 6235400 1000 + chr1 Cufflinks exon 6234876 6235060 1000 + chr1 Cufflinks exon 6235239 6235400 1000 + (2) chr1 Cufflinks transcript 6230065 6230437 1000 chr1 Cufflinks exon 6230065 6230437 1000 I want to extract transcrip sequence from the (1) and (2). But fetch sequence could only extract genomic sequence, it only fit for transcrit which had one exon,so are there any other tools to extract transcripts which had >=2 exons sequence and combine it? Thanks a lot! weimin zhao ___________________________________________________________The Galaxy User list should be used for the discussion ofGalaxy analysis and other features on the public serverat usegalaxy.org. Please keep all replies on the list byusing "reply all" in your mail client. For discussion oflocal Galaxy instances and the Galaxy source code, pleaseuse the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-devTo manage your subscriptions to this and other Galaxy lists,please use the interface at: http://lists.bx.psu.edu/

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Cufflinks transcript-extract
by dongdong zhaoweiming 30 Oct '11

30 Oct '11

Hi, I use cufflinks to assemble my RNA-Seq reads which produced a GTF file, such as follows:(1)chr1 Cufflinks transcript 6234876 6235400 1000 +chr1 Cufflinks exon 6234876 6235060 1000 +chr1 Cufflinks exon 6235239 6235400 1000 + (2)chr1 Cufflinks transcript 6230065 6230437 1000chr1 Cufflinks exon 6230065 6230437 1000 I want to extract transcrip sequence from the (1) and (2). But fetch sequence could only extractgenomic sequence, it only fit for transcrit which had one exon,so are there any other tools to extract transcripts which had >=2 exons sequence and combine it? Thanks a lot!weimin zhao

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how to transfer gene id into protein id
by Li, Jilong (MU-Student) 29 Oct '11

29 Oct '11

Hi, I have some refseq gene id, like NM_*****. How can I transfer these gene id into protein id, like NP_****? Thank you very much! Victor

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how to manage mailing list subscriptions
by Jennifer Jackson 28 Oct '11

28 Oct '11

Hello, I have removed you from galaxy-user. Instructions to manage list membership is at the bottom of this and all mailing list messages. In short, through this link: http://lists.bx.psu.edu/ Or request help from this email: galaxy-user-owner(a)lists.bx.psu.edu. Is best not to post to the mailing list for this sort of request, especially not as a reply to another thread. Thanks, Jen Galaxy team On 10/28/11 12:49 PM, Mahjoubeh Jalali wrote: > > Dear All > > How can I de-subscribe from the mailing list? > Any help would be appreciated > > Kind Regards > M. J > ___________________________________________________________ > 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 >

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Importing existing data into Galaxy
by Oren Livne 28 Oct '11

28 Oct '11

Dear All, We have a large collection of large data files on our shared file system. We would like to make a subset of them available to a galaxy user session (based on user privileges; different subsets for different users). We want to leave files in their original locations and point galaxy to their paths without copying them. What is the best option for implementing this bridge? Remote data source/data library uploaded on the fly/other? Thanks, Oren

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RNAseq Clostridium butyricum
by Benoit HENNUY 28 Oct '11

28 Oct '11

Hi, I would like to use Galaxy with RNAseq data generated from "Clostridium butyricum" species. Please, could you include this genome in your list ? Thank you in advance Best regards Benoit HENNUY

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