galaxy-user November 2011

galaxy-user@lists.galaxyproject.org

85 participants
94 discussions

Error running tool
by Toqa Manasrah 25 Nov '11

25 Nov '11

Hello everybody, I am trying to run my tool Vispa but every time i try to i got this error messages: An error occurred running this job: /home/galaxy/galaxy-dist/tools/vispa/main.bash: line 13: ./parser_v.2.sh: No such file or directory /home/galaxy/galaxy-dist/tools/vispa/main.bash: line 16: ./vispa.bash: No such file or directory although all these files are reside under the same directory and have the permission 755. how can I solve the problem? Thanks and regards, Tuqa.

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Galaxy Upload tool
by Toqa Manasrah 24 Nov '11

24 Nov '11

Hi everybody, I am integrating my own tool with galaxy. the command to run is: ./main.bash <readFile> <referenceFile> threads n t > <log> & the input files read and reference are of type fasta. threads, t and n are integers. log is to prevent console outputs. should I load these files from the page which run the command. or i have to use the Galaxy upload tool. and how? on the other hand. the output is implied and should be on the same directory where the source files. Thank you so much. Tuqa.

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Upload executable in galaxy
by Giota Kottara 23 Nov '11

23 Nov '11

Dear galaxy developers, I am trying to integrate an executable tool in a private instance of galaxy. I stored the configuration .xml file and the executable in tools folder of Galaxy and the tool appears in the homepage. Nevertheless when i am running the tool it doesn't seem to find the executable. Am I forgetting something? Thank you in advanceGiota Kottara

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Galaxy test won't run a bwa job
by Carlos Borroto 22 Nov '11

22 Nov '11

Hi, I'm trying to test a workflow using tools only available on the test server, for this I have uploaded a limited subset of my data that should run fairly quickly. The first step is a BWA mapping, but the job has being in the queue since yesterday. Is it fine to run this kind of test there? Thanks, Carlos

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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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galaxy-user November 2011