June 2012 - galaxy-user - lists.galaxyproject.org

2012 Systems Bioinformatics Workshop
by Christopher Bare 25 Jun '12

25 Jun '12

Hello, The 2012 Systems Bioinformatics Workshop will be held at the Institute for Systems Biology in Seattle on September 10th & 11th. We invite your participation. The workshop will be a two day meeting featuring talks, tutorials and a hackathon, bringing together engineers and scientists building software for biological data analysis. Themes for this year's workshop include networks, visualization, and software architecture for collaborative research computing. Speakers ============ Paramvir Dehal, Computational Research Scientist/Engineer, MicrobesOnline, KBase Max Franz, Software Engineer and User Interface Designer, Cytoscape Web Michael Kellen, Director of Technology at Sage Bionetworks Mike Smoot, Chief Architect of the Cytoscape project James Taylor, The Galaxy project Matt Wood, Amazon Web Services Tutorials ============ Regulatory network inference with cMonkey Cloud Computing with EC2 Graph data storage with Neo4j Visualization and D3 More information can be found on the workshop website: http://gaggle.systemsbiology.net/workshop2012/

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Include a data folder into Galaxy
by Norbert Grundmann 25 Jun '12

25 Jun '12

Hello, hopefully this is a simple question: How can I include a folder into the Galaxy server? The backgroud is, that I installed Galaxy on one of out server, which has access to the data folders used everywhere at our institute. So, instead of uploading and copying serveral big files (and waisting space on servers) I want to make a link to the appropiate folder, so it can be used like as the data has been uploaded. I hope I explained enough details... The question is: is it possible? Thanks for help, Norbert -- Institute of Bioinformatics Faculty of Medicine University of Muenster, Germany Use *BSD because Linux is a patch for Linux

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Bowtie and BWA queue..other jobs dont
by Antony Jose 25 Jun '12

25 Jun '12

Hi, Bowtie and BWA jobs seem to be forever on queue, but other jobs run normally. Is there a problem or is this expected? Thank you. Antony -- Antony M Jose, Dept. of Cell Biology & Molecular Genetics, University of Maryland, Rm 2116, Bioscience Research Building, College Park, MD - 20742.

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jobs stuck on Galaxy
by Fatih Ozsolak 21 Jun '12

21 Jun '12

Hi, I submitted Bowtie and BWA alignment jobs on two relatively small fastq files, and the jobs still appear as gray after multiple hours. can you please check and see if the system if functioning properly? thanks, fatih

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CUFFLINK does not work!
by Jennifer Jackson 20 Jun '12

20 Jun '12

Hello Di Nguyen, Without seeing your history, my initial guess is that the SAM output from the mapping runs need to be sorted before running Cufflinks. (Tophat, which is designed to map spliced RNA-seq data, sorts the SAM output as part of the data processing, but BWA and Bowtie do not). The workflow provided on this FAQ can be followed to sort SAM files for Cufflinks: https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2 If you continue to have problems, please submit a bug report (click on "green bug" icon from the error Cufflinks dataset as run on the main public Galaxy instance (http://usegalaxy.org) leave all inputs and the error dataset undeleted, note this email address in the comments if it differs from your Galaxy account email address (so that I can link the two issues together), and we can provide more feedback. http://wiki.g2.bx.psu.edu/Support#Error_from_tools Hopefully this helps, Jen Galaxy team On 6/20/12 1:28 PM, Di Nguyen wrote: > Hi Jen, > > I mapped with BWA and Bowtie for my RNAseq but Cufflink DID not run. > This is the error message: > > "An error occurred running this job: /cufflinks v1.3.0 > cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 > -b /galaxy/data/hg19/sam_index/hg19.fa > Error running cufflinks. > return code = 1 > cufflinks: /lib64/libz.so.1: no version information available > (required by cufflinks)" > > /What should I do?/ > > Di Nguyen > / -- Jennifer Jackson http://galaxyproject.org

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Tophat and Bowtie2
by Luciano Cosme 20 Jun '12

20 Jun '12

Hi, I installed bowtie2 and when running tophat I get the following error: Error in tophat: [2012-06-19 14:02:39] Beginning TopHat run (v2.0.3) ----------------------------------------------- [2012-06-19 14:02:39] Checking for Bowtie Bowtie version: 2.0.0.6 [2012-06-19 14:02:39] Checking for Samtools Samtools version: 0.1.18.0 [2012-06-19 14:02:39] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2) I was wondering if I can create the index files using bowtie2 via command line and then change the universe_wsgi.ini to: # Temporary files are stored in this directory. new_file_path = database/tmp and put the index files there. Anyway, why is it not creating the indexes? I created links to all bowtie2 executable files. If I remove bowtie 0.12.8, then I get a error from tophat (bowtie not installed). Is it creating the index with bowtie 0.12.8? Thank you. Luciano

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generate pileup not working?
by Lilach Friedman 19 Jun '12

19 Jun '12

Hi, I am trying to do variants call with "generate pileup". My steps where: 1. BWA 2. select only lines with the pattern Matching pattern: XT:A:U 3. SAM-to-BAM 4. then I tried to use "Generate pileup<https://main.g2.bx.psu.edu/tool_runner?tool_id=sam_pileup>from BAM dataset" However, it does not work, and I get the error message: 114: Generate pileup on data 97: converted pileup 0 bytes An error occurred running this job: *Samtools Version: 0.1.16 (r963:234) Error running Samtools pileup tool Floating point exception* Did I do anything wrong, or is it a bug? The parameters are copied below. Thanks, Lilach The parameters are: Tool: Generate pileup Name:Generate pileup on data 97: converted pileup Created:Jun 14, 2012 Filesize:0 bytes Dbkey:hg_g1k_v37 Format:tabular Tool Version: Tool Standard Output:stdout<https://main.g2.bx.psu.edu/datasets/d038161e3fe9072e/stdout> Tool Standard Error:stderr<https://main.g2.bx.psu.edu/datasets/d038161e3fe9072e/stderr> Input Parameter Value Conditional (refOrHistory) 0 Select the BAM file to generate the pileup file for 97: SAM-to-BAM on data 94: converted BAM Whether or not to print the mapping quality as the last column Do not print the mapping quality as the last column Whether or not to print only output pileup lines containing indels Print all lines Where to cap mapping quality 60 Conditional (c) 1 Theta parameter (error dependency coefficient) in the MAQ consensus calling model 0.85 Number of haplotypes in the sample 2 Expected fraction of differences between a pair of haplotypes 0.001 Phred probability of an indel in sequencing/prep 40

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FTP Error 530 Sorry, the maximum number of clients (3) for this user are already connected.
by Christopher M. Weber 18 Jun '12

18 Jun '12

Hello, I have been unable to get a solid FTP connection to main.g2.bx.psu.edu for ~24hrs. Two things have occurred: 1) I get the error "530 Sorry, the maximum number of clients (3) for this user are already connected" or 2) when finally connected, some files fail during transfer with 'incorrect password' while others continue uploading and eventually the entire connection is lost where attempts to reconnect give the 530 error in situation 1. To troubleshoot, I have tried all suggestions through FileZilla and Cyberduck, essentially limiting number of connections and disabling all before connecting, to no avail. It seems likely that this might be a server issue. Any insight is appreciated.

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Inconsistency between cufflinks and cuffdiff. This is killing me.
by Jia Meng 18 Jun '12

18 Jun '12

<<Problem>> The cufflinks and cuffdiff results are not consistent with each other. This is killing me. Does it make sense? << Obseration >> We have 3 control samples and 3 treated sample. For many genes, their FPKM in cufflinks and cuffdiff are far from consistent. In cufflinks result, for a gene’s FPKM are control group (sample: 1,2,3)：0， 0， 4.8 treated group(sample: 1,2,3)：0， 0， 6.0 In cuffdiff, the estimated FPKM are control group： 12.6 treated group：2.0 <<Method>> Use ucsc gene annotation gtf file, mm9, downloaded from UCSC table database Use cufflinks on each individual sample. Cufflinks: galaxy mirror at cistrome, minimal count:10, no quantile normalization, use gtf as reference, no background correction Use cufflinks on treated groups (3 biological replicates) and control groups (3 biological replicates) Cuffdiff: galaxy mirror at cistrome, minimal count:10, no normalization, use gtf as reference, no background correction <<Additional Comments>> Cufflinks returns 55350 transcripts, while cuffdiff return 55418 transcripts, even though they use the same gene annotation gtf file. For the 6 cufflinks results (corresponding to 6 samples), the transcript ids are all the same, but the order are not, <<Question>> Does it make sense? Or did I do anything wrong?

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jobs not running on main server
by Jacob Musser 18 Jun '12

18 Jun '12

Hello, I uploaded a couple small files via ftp to do some basic text manipulation on them in the main galaxy server. I have queued up several jobs (including just importing the files I uploaded into a history) but after two hours of waiting they are still gray and "waiting to run." I have been using galaxy regularly lately and have never had to wait very long for a job to start running (usually a matter of seconds). I am not above my quota so this is not the problem. Is there something else I need to do or is there a problem with the servers that would explain why jobs aren't being run? All the best, Jake

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