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CloudMan - The connection has timed out
by mailing list 22 Dec '11

22 Dec '11

Hi Everyone, I'm trying to set up Cloud man. I believe I followed the instructions listed here to a T: http://wiki.g2.bx.psu.edu/Admin/Cloud After launching the instance I even waited 20 minutes before trying to access the public DNS ec2-xxx-xx-xx-xx.compute-1.amazonaws.com/cloud, but my browser just says: The connection has timed out The server at ec2-xxx-xx-xx-xx.compute-1.amazonaws.com is taking too long to respond. Any ideas what I should check? I'm stuck. What information would be useful? Info: Zone is us-east-1a Type is m1.large root devide is ebs AMI Name: galaxy-cloudman-2011-03-22 Region is US East (Virginia) I used this format for user data: cluster_name: <DESIRED CLUSTER NAME> password: <DESIRED Galaxy CloudMan WEB UI PASSWORD> access_key: <YOUR AWS ACCESS KEY> secret_key: <YOUR AWS SECRET KEY> However this screenshot shows a pipe delimited deal? Maybe I should try that? http://userwww.service.emory.edu/~eafgan/content/galaxy_cloud/AWSconsole-4.… Thanks, Greg

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How to determine version of Galaxy from main page
by Greg Edwards 22 Dec '11

22 Dec '11

Hi folks, I've researched this in the new global Google Search tool http://galaxy.psu.edu/search/web/ but didn't see the answer I needed. Is there actually a single "version" of Galaxy ? or is it a collection of components with their own versions ? Can that can be seen on or near the Main front page ? I can't see a Version/About type of item, either in menus or lurking in some rev stamp at the bottom of pages etc. Thanks. -- Greg Edwards gedwards2(a)gmail.com

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suggestions for de novo assembly plant transcriptome without reference
by Jane Song 21 Dec '11

21 Dec '11

Dear Galaxy Expert, I would like to use Galaxy to de-novo assembly single-end read illumina data (140bp) for plant transcriptomes (without reference). I remember early emails mention trinity in Galaxy. But I could not see at Galaxy web http://main.g2.bx.psu.edu/root . Maybe it is installed in Amarzon EC2? Other suggestions in de-novo assembly plant transcriptomes without reference. Many thanks and look forward to hearing back from you, Jane <galaxy-user(a)bx.psu.edu>

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De novo assembly plant transcriptome
by Bao-Hua Song 21 Dec '11

21 Dec '11

Dear Galaxy Expert, I would like to use Galaxy to de-novo assembly single-end read illumina data (140bp) for plant transcriptomes (without reference). I remember early emails mention trinity in Galaxy. But I could not see it at Galaxy web http://main.g2.bx.psu.edu/root. Maybe it is installed in Amarzon EC2? Other suggestions in de-novo assembly plant transcriptomes without reference. Many thanks and look forward to hearing back from you, Baohua <galaxy-user(a)bx.psu.edu>

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Re: [galaxy-user] RE : % On-Off target
by Ross 21 Dec '11

21 Dec '11

Hi Antoine. Thanks - sorry, I haven't analysed that particular platform - anyone? http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics seems comprehensive... Why not try the Galaxy picard Hybrid Selection metrics tool on your data? On Wed, Dec 21, 2011 at 6:25 PM, Antoine ROUSSELIN <a.rousselin(a)baclesse.fr> wrote: > > Hello, > > My English is very bad, it's a shame! > > My I have a file for my baits (create a bed file of your Agilent SureSelect targets with exons and introns captured). Sequencing output, I get the files. Bam, my result sets of alignments on the human genome complete (with CASAVA). I try to get the coverage I only exonic regions (+ or - 50 bp). > > Thanks > > ROUSSELIN Antoine > Clinical Biology and Oncology Laboratory > Centre François BACLESSE > France/Caen > a.rousselin(a)baclesse.fr > Tel : (33) 02.31.45.40.44 > Fax : (33) 02.31.45.50.53 > > > > -------- Message d'origine-------- > De: Ross [mailto:ross.lazarus@gmail.com] > Date: mer. 12/21/2011 03:16 > À: Antoine ROUSSELIN > Cc: galaxy-user(a)lists.bx.psu.edu > Objet : Re: [galaxy-user] % On-Off target > > Hello Antoine, > I'm not sure I really understand your question but if the metrics described > at http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics are > of use, you could try the picard hybrid selection metrics Galaxy tool or > use it on the command line. Otherwise perhaps you can get a more helpful > response if you provide a clear explanation of the data formats you have > and the measures you want. > > > On Wed, Dec 21, 2011 at 2:59 AM, Antoine ROUSSELIN > <a.rousselin(a)baclesse.fr>wrote: > > > ** > > > > hello, > > I'm looking for a tool (or command line) to determine the % On-Off target > > + or - 50 bp of exon from my capture file but not annotated (!!!). Capture > > SureSelect agilent home. > > > > Current pipeline: > > GAIIx Illumina > > CASAVA1.8 > > IGV > > CNV-seq > > SAMtools > > BEDtools > > GALAXY > > NextGENe > > > > Please HELP > > > > ROUSSELIN Antoine > > Clinical Biology and Oncology Laboratory > > Centre François BACLESSE > > France/Caen > > a.rousselin(a)baclesse.fr > > Tel : (33) 02.31.45.40.44 > > Fax : (33) 02.31.45.50.53 > > > > > > ___________________________________________________________ > > 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/ > > > > > > -- > Ross Lazarus MBBS MPH; > Associate Professor, Harvard Medical School; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; > -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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% On-Off target
by Antoine ROUSSELIN 21 Dec '11

21 Dec '11

hello, I'm looking for a tool (or command line) to determine the % On-Off target + or - 50 bp of exon from my capture file but not annotated (!!!). Capture SureSelect agilent home. Current pipeline: GAIIx Illumina CASAVA1.8 IGV CNV-seq SAMtools BEDtools GALAXY NextGENe Please HELP ROUSSELIN Antoine Clinical Biology and Oncology Laboratory Centre François BACLESSE France/Caen a.rousselin(a)baclesse.fr Tel : (33) 02.31.45.40.44 Fax : (33) 02.31.45.50.53

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Search the Galaxy!
by Dave Clements 20 Dec '11

20 Dec '11

Hello all, I am happy to announce that Galaxy now has several Google Custom Searches that make it much easier (really - way, way easier) to find answers to your questions about Galaxy. They are available at http://galaxyproject.org/search/. *Name & URL * * Description * ** *Galaxy Web Search <http://galaxyproject.org/search/web>* http://galaxyproject.org/search/web Searches *everything:* Galaxy Main <http://wiki.g2.bx.psu.edu/Main>, the mailing list archives <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>, the Galaxy wiki <http://wiki.g2.bx.psu.edu/FrontPage>, Galaxy's source code at Bitbucket <https://bitbucket.org/galaxy/galaxy-central/src/tip/>, and the Tool Shed <http://wiki.g2.bx.psu.edu/Tool%20Shed>. The results are returned in a unified list, and are also grouped into several categories. *Galaxy Mailing List Search <http://galaxyproject.org/search/mailinglists>* http://galaxyproject.org/search/mailinglists Searches all the Galaxy mailing list archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>. The results are returned in a unified list, and are also grouped by mailing list.** *UseGalaxy Search <http://galaxyproject.org/search/usegalaxy>* http://galaxyproject.org/search/usegalaxy Search for information about *using* Galaxy. Searches Galaxy Main<http://wiki.g2.bx.psu.edu/Main>( UseGalaxy.org <http://usegalaxy.org/>), the wiki<http://wiki.g2.bx.psu.edu/Learn>(excluding the Admin <http://wiki.g2.bx.psu.edu/Admin> pages), and the Galaxy-User and Galaxy-Announce mailing list archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>. *GetGalaxy Search <http://galaxyproject.org/search/getgalaxy>* http://galaxyproject.org/search/getgalaxy Search for information about installing, customizing, and developing Galaxy. Searches the Galaxy Bitbucket (source) site<https://bitbucket.org/galaxy/galaxy-central/src/tip/>, the Tool Shed <http://toolshed.g2.bx.psu.edu/>, the wiki<http://wiki.g2.bx.psu.edu/Admin>(excluding the Learn <http://wiki.g2.bx.psu.edu/Learn> pages), and the Galaxy-Dev and Galaxy-Announce mailing list archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>. We strongly encourage you to give these try. Please send feedback and suggestions to Galaxy Outreach <outreach(a)galaxyproject.org>. Happy searching (and a Happy New Year!), Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Velvetoptimiser error
by Makis Ladoukakis 20 Dec '11

20 Dec '11

Dear Galaxy users, Has anyone worked with velvetoptimiser tool from the Tool shed? I have been trying both the stable and the test version of the velvetoptimiser tool and i keep getting the same error: Traceback (most recent call last): File "/home/ladoukef/galaxy_dist/tools/myTools/velvetoptimiser/velvet_optimiser.py", line 102, in if __name__ == "__main__": __main__() File "/home/ladoukef/galaxy_dist/tools/myTools/velvetoptimiser/velvet_optimiser.py", line 67, in __main__ for line in open(contigs_path ): IOError: [Errno 2] No such file or directory: 'contigs.fa' Can someone identify where the error is? The file missing (contigs.fa) is supposed to be built by the tool itself. Thank you, Efthymios Ladoukakis

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Workflows & Multiple datasets
by Adhemar 19 Dec '11

19 Dec '11

Hi, I was searching for how to run a workflow for multiple input files and I was very happy to find it's already implemented as mentioned here: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20 The problem is that it's not working for me. When I select two files, for example, it runs the workflow only in the first file. Even if I check 'Send results to a new history', it only creates a new history called 'test 1' and not the others. Is my instance somehow misconfigured or it's happening to others as well? I'm also looking for a way to add datasets to a library from different histories. Do I really need to open each history one by one and use 'Import datasets from your current library'? Thank you, Adhemar

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Tophat jobs not starting
by Magdalena Strzelecka 19 Dec '11

19 Dec '11

Hi, I have submitted some jobs to Tophat, but they have not started since yesterday (Dec 13th); i.e they were in a queue for >12 hrs. I have re- submitted everything again (2 jobs), but the same situation is happening. Is there some issue with Tophat at the moment? Thanks. M. ------------------------------ Magdalena Strzelecka, PhD Heald Lab University of California, Berkeley Department of Molecular & Cell Biology 315 Life Sciences Addition # 3200 Berkeley, CA 94720-3200 phone: (510) 643-5002 fax: (510) 643-6791 e-mail: strzelecka(a)berkeley.edu

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