galaxy-user September 2013

galaxy-user@lists.galaxyproject.org

60 participants
68 discussions

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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SNP finding
by Xiefan Fang 03 Dec '13

03 Dec '13

Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads per biological sample. Can I do it with galaxy? If not, is there other programs available in windows? Considering that I am not very familiar with programming. Thanks, Xiefan University of Florida

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posting supplementary information on galaxy server
by Jainy Tharun 24 Oct '13

24 Oct '13

Hello, I would like to know whether I can post my supplementary data for an article in the galaxy server. I have .docx files and .xlsx files. I am planning to upload these data in a folder and share the link at first and later publish it. When I tried uploading xlsx file, it is getting automatically converted to .xml files. Please let me know if it is possible provide the supplementary information through galaxy that includes doc and excel sheets.. Thank you so much for your help Jainy

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Need your helps about Galaxy
by Lei Yan 16 Oct '13

16 Oct '13

Dear Dannon, I built a new cloud Galaxy instance today. Would you please tell me how to transfer given accounts from an old Galaxy to this new one? This is old Galaxy: http://galaxylocal.genenetwork.org:8080/ This is new Galaxy: http://galaxyclass.genenetwork.org/ Thanks a lot. Lei Yan Center for Integrative and Translational Genomics UTHSC

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Free Training (Boston): Analyzing NGS Data with Galaxy
by Anushka Brownley 15 Oct '13

15 Oct '13

Galaxy Community, Based on popular demand, we are pleased to announce another Galaxy training event for this year. BioTeam and the Galaxy Team are offering a training session that will focus on analyzing NGS Data using Galaxy. In addition to learning about the NGS related Galaxy features, you will also learn about what it takes to host your own Galaxy instance. This event is kindly hosted by Dana-Farber Cancer Institute. For more information about this training please visit the event website at http://bioteam.net/slipstream/galaxy-edition/galaxy-training/. Date: Tuesday October 22nd, 2013 Time: 9:00am – 12:00pm Location: Dana Farber Cancer Institute, Boston, MA, USA Cost: Free Space is limited so please register for this free event soon. REGISTER NOW: http://bioteam.net/slipstream/galaxy-edition/galaxy-training/galaxy-trainin… Anushka Brownley Senior Scientific Consultant www.bioteam.net SlipStream Appliance Galaxy Edition http://bioteam.net/slipstream/galaxy-edition/ SlipStream Appliance White Paper http://bioteam.net/wp-content/uploads/2013/03/SlipStream_Galaxy-White_Paper…

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add nglims to galaxy-dist
by Peter Huang 04 Oct '13

04 Oct '13

Hi Brad, I am curious if you could tell me the way that I could add your nglims to my galaxy-dist production system. I have read your step by step procedure here: http://wiki.galaxyproject.org/Admin/Sample%20Tracking/Next%20Gen but it didn't mention how to add it to the galaxy-dist. Do you have a patch name for it? Should I use hg pull or hg patch? Thanks Best, Peter

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queue rules for multi-step workflows
by zuzmus 03 Oct '13

03 Oct '13

Dear Galaxy managers, I would like to ask about the queuing rules for the workflows before processed on the server? I use my customized Galaxy workflow which contains 22 following steps (basically, filtering, trimming and format change of NGS data). I guess the server is generally very busy during last weeks/months (?), so my job was waiting about 24 hours in a queue (which would not be a problem), and then the first step of the workflow was processed, but the following 21 is again/still waiting (already for another couple of hours...). It makes me wondering about the queuing rules because I expected that the whole workflow is queued as one job.. Then my question is if the whole workflow, once submitted, is listed in the queue, or does the following step queue only after the previous step is finished (which would mean to wait the whole queue for each step of the workflow...)? I routinely used those wrokflows before (months ago) without any problems... I tried to search similar question in the archive before I posted this one... Thanks a lot for your answer, My best Zuzana Musilova -- Zuzana Musilova, PhD. (zuzmus(a)gmail.com) Zoological Institute University of Basel Vesalgasse 1, CH-4051 Basel Switzerland - Europe

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URL problem
by Kucukural, Alper 03 Oct '13

03 Oct '13

Hi, I have a problem in galaxy to get host/domain name in two different pages. First one is in the tool installation from toolshed, I got the error below, ##### Not Found The requested URL /admin_toolshed/prepare_for_install was not found on this server. ##### The second one is in the saved histories. When I click the buttons of the saved histories. I got the similar error like below. ##### Not Found The requested URL /history/list was not found on this server. ##### I haven't seen these any other pages yet. My installation is working on LDAP authentication with Proxy. So, I could not find a place to set the domain or host name in these two places that they can actually find the requested URLs. In the paster.log file. I don't get any error when I install a tool or go to another history. It doesn't report any error. Thanks for your help, Alper Kucukural

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bwa indexing not automatic?
by Joshua Orvis 01 Oct '13

01 Oct '13

I installed a new copy of galaxy today and then added the bwa_wrappers tool. After I upload my reference genome and left/right reads I get output like this each time I try to run bwa for illumina: The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwt_restore_bwt] fail to open file '/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat.bwt'. Abort! /bin/sh: line 1: 11607 Aborted bwa aln -t 4 -I /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_2.dat > /tmp/tmpMuj4l2/tmpUIdxXT If I manually do the 'bwa index' command on dataset_4.dat it works but in the past this seemed to happen automatically. Any clue what's going on here?

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main galaxy server is down?
by garzetti 30 Sep '13

30 Sep '13

I have the same problem with the BWA mapping tool (jobs waiting for run since Friday), but other tools (e.g. SAMtools) are working. My analysis also depends a lot on these mapping data! Debora > Message: 1 > Date: Sat, 28 Sep 2013 16:47:01 +0000 > From: "Yardley, Nathan" <ny2217(a)cumc.columbia.edu> > To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > Subject: Re: [galaxy-user] main galaxy server is down? > Message-ID: > <9633FF819ABAF94A82A38D94B64B664501291F43(a)SGWAEXM003.mc.cumc.columbia.edu> > > Content-Type: text/plain; charset="us-ascii" > > I'm wondering the same. I have a mapping job that hasn't moved into the queue since I put it there on Thursday. It's the last sample set I need to move forward with some analysis and I've been trying to get it for more than a week now. :/ > > Nathan > ________________________________________ > From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] on behalf of Boaz Shaanan [bshaanan(a)bgu.ac.il] > Sent: Friday, September 27, 2013 5:37 PM > To: galaxy-user(a)lists.bx.psu.edu > Subject: [galaxy-user] main galaxy server is down? > > Hi, > > Is the main galaxy server down? Or very sloooow? I have a Lastz job (not too demanding and one that has been run several times before) waiting for a long time already. > > Thanks, > > Boaz > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > -- Debora Garzetti, PhD Student AG Rakin Max von Pettenkofer-Institute, LMU Pettenkoferstraße 9A 80336 Munich E-mail: garzetti(a)mvp.uni-muenchen.de Phone: +49 (0)89 2180 72915

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galaxy-user September 2013