January 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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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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extracting a subset of sequences from a very large fasta file(1.5 million)
by Perumal Vijayan 15 Feb '13

15 Feb '13

I have successfully uploaded a large fasta file (2.5 million genomic sequence contigs) onto Galaxy server. I wish to extract a subset of sequences from this file. I have a list of the fasta headers. Is there a way I can accomplish this on Galaxy? -- Perumal Vijayan Saskatoon Canada

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can't download big files
by Allan Sun 01 Feb '13

01 Feb '13

Hello everyone, We have galaxy-dist-17d57db9a7c0 installed on our Mandriva 2009 64bit. There are 2 big fasta files, file A is 4.4G and file B is 3.3G which I tried to download without success. I've used browser download,including mozilla,IE and Chrome,also from suggestion by Jennifer: linux command: wget and curl -O.None of them work. For file A,the downloaded file size is always 450M(9% of total size),no matter which way ( mentionedabove )I use, For file B,the downloaded file size is 0 byte. Following is the error report by :curl -O curl: (18) transfer closed with 4294967296 bytes remaining to read Any help will be very appreciated. Allan

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does Galaxy have a tool for converting .sra files to fastq files?
by Elwood Linney 31 Jan '13

31 Jan '13

Hello, I would like to download some GEO files that complement my own research with zebrafish embryos but apparently GEO is now only providing .sra flles. For a not very experienced unix person, does Galaxy have a tool for this or is there a clear description somewhere else of how to do it for someone who is not a bioinformaticist? Thanks, el linney Duke University Medical Center

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running time of Cufflinks on main Galaxy
by Davide Degli Esposti 31 Jan '13

31 Jan '13

Dear Galaxy team, in the last two days I am trying to run Cufflinks on some sam files, but the work is kept in queue. Actually I performed cufflinks on the same files some times ago, but with different parameters and it worked after some hours. Is this a problem due to my new parameters or are the servers currently overused? Thank you for your help Davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

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Converting files to gd_snp format
by Sheehan, Michael - (michaelsheehan) 30 Jan '13

30 Jan '13

I would like to convert VCF files to gd_snp format to be used in some population genomic analyses. A tutorial online makes it seem like this is the correct path to follow to conduct such analyses: http://www.bx.psu.edu/~giardine/tutorials/example2/part1/snpTable.html I have been using Galaxy on the free public server and this tools does not appear to be present anywhere. Does anyone know where the tool has gone or is there a way to add the needed tools back? Thanks Mike

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Mapping miRNA data
by Mark Lindsay 30 Jan '13

30 Jan '13

Dear All I am interested in using Galaxy to compare miRNA sequencing data. I have previously groomed, clipped and then mapped miRNA data onto hg19 using bowtie. I have then identified differentially expressed miRNAs using cuffdiff and the UCSC downloaded miRNA/snoRNA database. However, I have recently tried to repeat this process but find the cuffdiff is unable to run. I just wondered why cuffdiff is no longer working or if there is alternative approach to comparing miRNA expression? Best wishes Mark

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How to determine differentially expressed genes using Galaxy?
by Ben Ben 30 Jan '13

30 Jan '13

Hi All, Could anyone tell *Which Version Galaxy* has the function to run DESeq (determine differentially expressed transcripts from read alignments)? Any alternative? As far as I know, *Penn State Version* doesn't integrate the DESeq function. * And Cuffdiff seems stop working in Penn State * Thanks very much for the response!! Best wishes,

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