February 2013 - galaxy-user - lists.galaxyproject.org

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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Why don't we get FPKMs from this gene?
by Dikla Aharonovich 07 Mar '13

07 Mar '13

Hello, We are using BAM to map Illumina reads to a bacterial genome, followed by Cufflinks o get the FPKMs. We have come across many genes for which we get FPKM=0 (using both gene and transcript expression) even though there are reads mapping to these gene IDs (e.g. the region between the dashed lines in the attached screenshot). Can anyone suggest a reason/fix for this? Thanks Dikla

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Filter Pileup in SAM tools
by Andrew South 04 Mar '13

04 Mar '13

NGS: SAM Tools I have generated a simple 6 column pileup from my BAM file but when I try to use the Filter Pileup tool it doesn't recognise my pileup file, I receive the message "History does not include a dataset of the required format / build". Build is hg19. Curiously in the same history I have ran the tool through a workflow without a hitch. Any advice to successfully filter my pileup would be gratefully received. Many thanks, Andy The University of Dundee is a registered Scottish Charity, No: SC015096

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Error / Nebula and RepeatMasker
by Sarah Maman 04 Mar '13

04 Mar '13

Hello, I've installed NEBULA tools and "RepeatMasker" tool on our local Galaxy instance. For some tools (others work), I get the following errors: * - *Here is the error I get when running the tool *FilterControl * *** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 *** *** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 *** *** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 *** *** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 *** /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh: line 80: 61310 Abandon java -classpath $LOCAL_PATH/ -Xmx6g FilterPeaks -f $inputfile -c $controlfile -t $minHeight -v $minRatio -o $output > /dev/null *** glibc detected *** java: double free or corruption (!prev): 0x00007f1f5800ecd0 *** /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh: line 81: 61351 Abandon - Here is the error I get when running the tool *IntersectBed *//work/galaxy/database/pbs/galaxy_4129.sh: line 13: Erreur de syntaxe près du symbole inattendu « ;; » /work/galaxy/database/pbs/galaxy_4129.sh: line 13: `bedtools intersect -f 0.05/ - Here is the error I get when running the tool *ChIPmunk (thanks Alban for you help (*ChIPMunk v2 is used and all librairies are found) *but here is a new error, maybe a problem of "dirname" ?) */mv: impossible d'évaluer « /work/galaxy/database/job_working_directory/004/4132/galaxy_dataset_5992.dat_0.xml.png »: Aucun fichier ou dossier de ce type mv: impossible d'évaluer « /work/gala /- Here is the error I get when running the tool *PeaksToBed * readline() on closed filehandle FILE at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 124 (#1) (W closed) The filehandle you're reading from got itself closed sometime before now. Check your control flow. Use of uninitialized value $fields[1] in concatenation (.) or string at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 154, <FILE> line 1 (#2) (W uninitialized) An undefined value was used as if it were already defined. It was interpreted as a "" or a 0, but maybe it was a mistake. To suppress this warning assign a defined value to your variables. To help you figure out what was undefined, perl will try to tell you the name of the variable (if any) that was undefined. In some cases it cannot do this, so it also tells you what operation you used the undefined value in. Note, however, that perl optimizes your program and the operation displayed in the warning may not necessarily appear literally in your program. For example, "that $foo" is usually optimized into "that " . $foo, and the warning will refer to the concatenation (.) operator, even though there is no . in your program. Use of uninitialized value in concatenation (.) or string at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 154, <FILE> line 1 (#2) Use of uninitialized value in numeric ge (>=) at /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 156, <FILE> line 1 (#2) ...... /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 156, <FILE> line 63 (#2) Use of uninitialized value $fields[1] in conc ** I dowloaded tool "RepeatMasker" from Galaxy Tool Shed,and RepeatMasker is installed on our cluster. Here is the error I get when running the tool RepeatMasker: An error occurred running this job: /Epilog : job finished at jeu. janv. 31 14:39:16 CET 2013 /work/galaxy/database/pbs/galaxy_4134.sh: line 13: Erreur de syntaxe près du symbole inattendu « ;; » /work/galaxy/database/pbs/galaxy_4134.sh: line 13: `RepeatMasker -parallel 8 -speci/ Do you have any ideas ? Thank you in advance for your help, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

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Support Question
by Thomas Muench 28 Feb '13

28 Feb '13

Hi, i have installed RepeatExplorer on our local galaxy instance, but with every try, i see only this error message and i don't know why? All installation steps of RepeatExplorer was correctly. Thank you for your help Thomas Münch leibniz-institute for plant genetics and crop plant research Gatersleben, Germany Traceback (most recent call last): File "/opt/galaxy/lib/galaxy/jobs/runners/local.py", line 56, in run_job job_wrapper.prepare() File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 368, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1524, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/opt/galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/opt/galaxy/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1362033265_04_79640.py", line 92, in respond NotFound: cannot find '__root_dir__' failure preparing job

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Viral metagenomics
by Mohammad Mohiuddin 27 Feb '13

27 Feb '13

Hi, Can you please tell me how to work with viral metagenomics in Galaxy? When uploading the data files, there is an option to select the reference genome but in case of viral metagenomics, I can't select any individual genome. What will I do in this step? After uploading and processing the data, I will have to BLAST all my sequences using NCBI BLAST but there is no BLAST option in galaxy. How can I do that? And, is there any way to change the default E-value of Galaxy? Thanks, Mohiuddin

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"join,subtract and group" tools can't be used
by Lu, Mengmeng 26 Feb '13

26 Feb '13

Hi galaxy group, I found the tools of "join,subtract and group" can't be used in the Galaxy main. I am curious when it will come back. Thanks! Mira

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How to create a tool from a script that loads additional source code files?
by Samuel Lampa 25 Feb '13

25 Feb '13

Hi, I have aGalaxy toolwith some R code which is split up into a few files, which are loaded by a "master R script", which orcestrates and executes the whole thing. I realize that when the master script ("run.R" in my case) is run, it will not find the other files, since it is itself moved away to a temporary working directory (something like ".../galaxy/database/job_working_directory/000/165"). Is there any "standard way" of dealing with this, any special toolconfig syntax etc? ... or do I have to just hard code the absolute paths to the extra files in my script? :| Best Regards // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se

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2013 Galaxy Community Conference (GCC2013) Registration and Abstract Submission are Now Open
by Dave Clements 25 Feb '13

25 Feb '13

Dear Galaxy Community, We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo <http://uio.no/>. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then please consider attending. GCC2013 is aimed at: - Bioinformatics tool developers and data providers - Workflow developers and power bioinformatics users - Sequencing and Bioinformatics core staff - Data archival and analysis reproducibility specialists *Early registration <http://wiki.galaxyproject.org/Events/GCC2013/Register>* *saves up to 75% off regular registration costs,* and is very affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. Early registration closes 24 May. *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> * for oral presentations closes 12 April, and for posters on 3 May. Please consider presenting your work. If you are working with big biological data, then the people at this meeting want to hear about your work. Thanks, and hope to see you in Oslo! The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> ! -- http://galaxyproject.org/GCC2013 <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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