- galaxy-user - lists.galaxyproject.org

tools for exome sequence
by shamsher jagat 22 Nov '11

22 Nov '11

Is there any tool (work flow) in galaxy for exome sequence analysis (human/ mouse) Thanks.

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Using Galaxy Cloudman for a workshop
by Clare Sloggett 21 Nov '11

21 Nov '11

Hi all (especially Enis :) ), We are planning to use Amazon (Galaxy CloudMan) to run a workshop for about 50 people. We won't need to transfer any data during the workshop, but need the virtual cluster to be reasonably responsive and cope with: a) the load on the front end b) the workshop participants each trying to run a bwa alignment - at the moment each alignment would be of about 2.8M reads, but we could cut it down c) any other scalability issues I may not have thought of? I wanted to ask if anyone has used CloudMan for a similar purpose, or has an understanding, based on running a Galaxy cluster, of any problems we might encounter? I can add enough nodes to the cluster on the day to cope with the computational load (I assume) but I'm not sure if I should be expecting any other problems. Is the size of the node (e.g. Amazon's 4-core vs 8-core nodes) very important? I can scale out by adding more nodes, but should I be concerned about the capacity of the master node which handles the traffic? Also, is there any sensible way for me to test it in advance (in terms of the user load)? Many thanks for any advice! Clare -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759

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Save These Dates! July 25-27: Galaxy Community Conference
by Dave Clements 21 Nov '11

21 Nov '11

Hello all, I am pleased to announce that the 2012 Galaxy Community Conference (GCC2012) has been scheduled for July 25-27, 2012 at the University of Illinois Chicago. See http://galaxyproject.org/wiki/Events/GCC2012 for more information on the meeting, and for sponsorship opportunities. Abstract submission and registration deadlines will be announced in the coming months. Please reserve July 25-27 on your calendar now, and hope to see you in Chicago next summer! Dave Clements PS: If your curious to know what goes on at a Galaxy meeting, see the GCC2011 page for an idea: http://galaxyproject.org/wiki/Events/GCC2011 -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Running shell script
by Toqa Manasrah 21 Nov '11

21 Nov '11

Hi everybody, I am integrating my software ViSpA inside galaxy and I have two questions: 1: the main program is a shell script (.sh) which call another shell script, which call Java executables. should I include any interpreter inside the .xml <command > tag? and what that should be? 2. how to guarantee that the output files destination are on the use local host rather than the server which is running galaxy? Thanks and regards, Tuqa.

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November 18, 2011 Galaxy Development News Brief
by Jennifer Jackson 19 Nov '11

19 Nov '11

November 18, 2011 Galaxy Development News Brief This release http://galaxyproject.org/wiki/News%20Briefs/2011_11_18 Release history http://galaxyproject.org/wiki/News%20Briefs Source http://getgalaxy.org Support http://galaxyproject.org/wiki/Support new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r b258de1e6cea Highlights GCC2012 is Scheduled! Galaxy tool sheds enabling sharing of workflows & tools New wrappers, new tool upgrades: Python, FASTQC, Picard, TopHat Direct Galaxy link to IGV Plus new Trackster features, UI and Source updates, Bug fixes All News & Events GCC 2012 is Scheduled! Upcoming Workshops and Presentations What's New Tool Shed: Enabling Workflow Sharing Using Tool Sheds Python Support Updated & Improved Tools Galaxy Track Browser (Trackster) Workflows User Interface (UI) External Display Applications Source Bug Fixes Thanks for using Galaxy!

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Fwd: BioMart - DATABASE Special Issue
by Arek Kasprzyk 19 Nov '11

19 Nov '11

For those of you who use BioMart as a Galaxy data source Dear All, I am very pleased to announce the publication of the DATABASE special issue dedicated to the BioMart project http://www.oxfordjournals.org/our_journals/databa/biomart_virtual_issue.html BioMart is a unique open source data federation technology that provides unified access to distributed databases storing a wide range of data. This DATABASE issue recognizes BioMart's outstanding contributions to bioinformatics and documents the achievements of the BioMart community, which has grown impressively over the last ten years to become what it is today, a collaboration between numerous database projects on five continents: Asia, Australia, Europe, North America and South America. I would like to thank and congratulate the BioMart community on this impressive achievement. This issue would have not been possible without their dedication, expertise, passion and enthusiasm. Arek Kasprzyk *Have a look at our new website at www.biomart.org!* (You may need to shift+reload a few times to get new pages)

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Gene Ontology Help
by Nicole Lynn Jacobs 18 Nov '11

18 Nov '11

To Whom it May Concern: My name is Nicole McDaniels. I am a Ph.D. candidate at Syracuse University. I am attempting to use RNAseq to look at changes in the transcriptome of zebrafish embryos upon morpholino injection. I have been using Galaxy Main to manage my data thus far. Recently, I completed the cufflinks/cuffcompare/cuffdiff analysis. I now have cuffdiff files in the tabular format. I would like to assess the gene ontologies of the differentially expressed transcripts, but I'm having trouble figuring out how to transfer over to GO Galaxy and then what exactly I should be doing in GO Galaxy. Is there a different program or server that would be better/easier for the gene ontology analysis than GO Galaxy? I've also looked at the GOseq R package, but again I'm not sure about the tabular file format or how to change it to a more appropriate format. Any help you can give me with this would be greatly appreciated. I thank you in advance for your time. All the best, Nicole McDaniels Ph.D Candidate Syracuse University Department of Biology

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combine data
by dongdong zhaoweiming 18 Nov '11

18 Nov '11

Hi, Can galaxy combine lots of data into a single file using "cat"? I have a 2GB sam type data, but I can't upload it by URL under my condition, so I want to spilt it into three files and upload it to galaxy and then combine it? Thanks a lot!weimin zhao

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GATK
by Metge, Franziska 17 Nov '11

17 Nov '11

Dear happy users of Galaxy, We are running Galaxy locally. It's a very fine tool! By now everything works fine, except when I try to run any GATK program. I usually get this error message: ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 1.3-14-g348f2db): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: The fasta file you specified (/tmp/tmpp0oxJu/hg19) does not exist. ##### ERROR ------------------------------------------------------------------------------------------ my picard_index.loc line for the hg19 reference looks like this: hg19 hg19 hg19 hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa gatk also the bam file I am submitting to GATK has the reference genome specified in it's attributes. Could please anyone help me. Thank you Franzi

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Tools appearing without inputs in workflow editor
by Paul-Michael Agapow 17 Nov '11

17 Nov '11

A peculiar bug, presented for your input: A colleague has built a few tools and is trying to incorporate them into a workflow. However: 1. When he creates an new empty workflow, edits it and adds the tools, they appear without inputs (i.e. the icons/boxes on the diagram have no input "sockets") 2. When he tries to save a history using these tools as a workflow, a error results in which Galaxy complains about an unrecognised name, being one of the tool inputs. Depending on which tool he includes in the workflow, the missing name occurs in whichever tool is earlier in the workflow. (Traceback available on request) Puzzling. And even more puzzling when I tried to debug this: 1. Other tools (not written by him) behave in the workflows as expected. 2. Pulling a copy of his config file across to my own instance of Galaxy and creating a dummy tool to house it, it worked perfectly 3. We're running the same version of Galaxy, albeit different versions of Python (2.5 vs 2.6.4) 4. The tools work fine in normal analysis mode. 5. Line-ending unix, XML seems to parse fine. I'm stymied here and unsure what to look at next. Ideas? ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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