galaxy-user August 2013

galaxy-user@lists.galaxyproject.org

58 participants
85 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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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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Slice bam
by lilach noy 18 Sep '13

18 Sep '13

hello all, Does anyone know if in order to use Slice bam I need to sort the bam file first or does galaxy automatically sort any bam file uploaded? Many thanks, Lilach Noy

2 1

What's the PV of Galaxy
by liubiao 17 Sep '13

17 Sep '13

Hello Nabble, I am interested the Galaxy and want to set up a local galaxy. Could you address me the PV of galaxy one day? Best Regard, Biao Liu System Engineer Email: liubiao(a)genomics.cn | M. +86 186 7677 1486 China National GeneBank http://nationalgenebank.org/en/index.html Building No.11 | Beishan Industrial Zone | Yantian | Shenzhen China

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NoClassDefFoundError in Picard Paired Read Mate Fixer
by Nicolas Quizon 05 Sep '13

05 Sep '13

Dear Galaxy Gurus, I am a student and still new to Galaxy. I am encountering an error when trying to run the Picard Paired Read Mate Fixer with default settings on Galaxy. The code only runs for a few seconds before failing and displaying the error message. ## exit code=1; stdout= [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation INPUT=[/usr/lib/galaxy-server/database/files/000/dataset_85.dat] OUTPUT=/usr/lib/galaxy-server/database/tmp/tmpxhbz3T SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Aug 19 16:46:15 EDT 2013] Executing as root@biolinux-pbcn6 on Linux 3.2.0-43-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_27-b27; Picard version: 1.91() [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=378470400 To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp Exception in thread "main" java.lang.NoClassDefFoundError: org/itadaki/bzip2/BZip2InputStream at net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:84) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) at net.sf.picard.sam.FixMateInformation.main(FixMateInformation.java:76) Caused by: java.lang.ClassNotFoundException: org.itadaki.bzip2.BZip2InputStream at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) ... 4 more For input I am using data that I have successfully mapped with BWA for Illumina. I currently have Python version 2.7.3 and Java version 1.6.0_27, and an working on a machine running Ubuntu 12.04.2 LTS. Any help is greatly appreciated! Thanks!

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About tool classify in the tool box panel
by XiaoTao Jiang 31 Aug '13

31 Aug '13

Dear all I want to know how to part the tool panel into several group just like the public Galaxy. It classify the tools into NGS Tools Box and RECENTS. I can not find tag that up <section> tag in the wiki document. Anyone can tell me how to configure to classify tools? Thank you for all your help Regards, Xiaotao JIANG The University of HongKong

2 1

Tophat Error: segment-based junction search failed with err
by Delong, Zhou 30 Aug '13

30 Aug '13

Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this error for all of them.. segment-based junction search failed with err = 1 or -9 Here is an example of full error report: Error in tophat: [2013-08-23 11:56:58] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2013-08-23 11:56:58] Checking for Bowtie Bowtie version: 2.0.2.0 [2013-08-23 11:56:58] Checking for Samtools Samtools version: 0.1.18.0 [2013-08-23 11:56:58] Checking for Bowtie index files [2013-08-23 11:56:58] Checking for reference FASTA file [2013-08-23 11:56:58] Generating SAM header for /usr/local/data/bowtie2/hg19/hg19 format: fastq quality scale: phred33 (default) [2013-08-23 11:58:04] Preparing reads left reads: min. length=50, max. length=50, 145339247 kept reads (34946 discarded) right reads: min. length=50, max. length=50, 145340153 kept reads (34040 discarded) [2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2 [2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2 [2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-25 01:40:37] Searching for junctions via segment mapping Coverage-search algorithm is turned on, making this step very slow Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory. [FAILED] Error: segment-based junction search failed with err =-9 Collecting potential splice sites in islands cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed': No such file or directory cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed': No such file or directory I did some research on the internet and it seems to be a memory problem to me, is there any solution other than rerun these jobs on a more powerful machine? And why has Bowtie/Tophat discard different numbers of reads? What will be the impact? Does it means that if I don't have exact matches between the paired end input, it is still be possible to run the job? Thanks, Delong

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galaxy-user August 2013