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Post operational attribute file analysis and attribute management
by Dennis Gascoigne 14 May '10

14 May '10

We are working with some very large sequence libraries (paired end 70M reads+ each end - 15Gbx2). We already know what the file types are and that they are appropriate for the pipeline. There seems to be a large amount of the processing effort expended after the completion after each step in the workflow analysing the files and determining their attributes - this is related to the size of the files (which are large at every step) and is of no practical use to us, except maybe on the final step. Is there any way to suppress post processing steps and simply accept the file as specified in the tool output tags? If not would there be any unexpected implications if we revise the scripts and remove any of these steps? Which scripts should we focus on? Cheers Dennis

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user reference vs. built-in index
by Viren Patel 13 May '10

13 May '10

Hi. I created a workflow to map IGA reads using bowtie and generate a pileup at the end. The workflow is FASTQ Groomer -> Map with Bowtie for Illumina -> SAM-to-BAM -> Generate pileup. I ran the workflow successfully using the built-in mm9 index as reference for both bowtie and the pileup generation. Then I changed the workflow to use a reference file I uploaded (fasta format) and now I get an error on the pileup generation step: An error occurred running this job: /The output file is empty. Your input file may have had no matches, or there may be an error with your input file or settings./ The prior SAM-to-BAM step shows a sizeable BAM file being generated. So I am wondering if the Generate pileup tool requires the reference in a special format. V. Patel Dept. of Human Genetics Emory University School of Medicine

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BAM, Galaxy and GBrowse
by Steve Taylor 12 May '10

12 May '10

Hi, I saw in the latest GBrowse 2.04 release you can now paste remote BAM URLs into "import a track" field. Has anybody tied this in with Galaxy, so when you have generated a BAM file you can click on a link (like you can with UCSC) to see the output as reads or an xyplot? Thanks for any advice, Steve

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Bowtie wrapper
by Kelly Vincent 11 May '10

11 May '10

Everyone, We have had several bug reports regarding Bowtie over the past weeks, so I wanted to let everyone know that it's been corrected. The bug proved easy to fix but somewhat difficult to track down. Please feel free to start using it again. Regards, Kelly

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File extensions
by Nils Homer 11 May '10

11 May '10

One issue I have stumbled upon is that the tmp files fed into the program do not preserve the file extension attributed to the type of file (.bam, .fastq, .fasta) but instead use ".dat". Is there a way to force this, as tools that I am trying to wrap require the file extension to be present. Also, is there a way to model a map reduce style workflow in Galaxy. Say I have a fastq splitter that splits the fastq file into 100 pieces, then I want to run a process on each piece, then finally merge the results (3 tools, one workflow). Since Galaxy can submit to SGE/PBS/etc this would be extremely useful for cluster users (or cloud users). Is this possible? Nils

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Server Error
by Rathi Thiagarajan 11 May '10

11 May '10

Hi there, Just to notify that there is currently a Server Error. Thursday 10pm (EDT) Cheers, Rathi

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Making Galaxy see RPy and NumPy
by Rodolfo Aramayo 10 May '10

10 May '10

People, I have installed Galaxy on my laptop following standard procedures I have installed R, NumPy and RPy via MacPorts yet Galaxy seems to complain it cannot connect to them == An error occurred running this job: Traceback (most recent call last): File "/Library/WebServer/Documents/galaxy_dist/tools/stats/gsummary.py", line 4, in <module> from rpy import * ImportError: No module named rpy == Any ideas/suggestions would be greatly appreciated Thanks Rodolfo Aramayo

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Workflow Questions
by Jesse Erdmann 07 May '10

07 May '10

I have two questions about constructing a workflow, or possible requests for changes. 1) Is it possible to rename a file output by a task in the workflow? For instance, it would be nice to specify the name of two files concatenated together rather than have it named something like "Concatenation of Dataset X and Y", half of which doesn't show in the left history pane. 2) If multiple tools use the same input, for example one tool uses a threshold and another tools performs analysis based on the threshold used in the previous tool without including the threshold value in a output file. Or more simply, I want to use a user selected value input into one tool as input into another tool later in the workflow without the user having to re-enter the value and without having to pull the value from a file. -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann

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Galaxy + SGE
by Erick Antezana 07 May '10

07 May '10

Hi, I just installed and configured Galaxy to run on our SGE cluster. I tried to upload a file (fasta, ggff3, ...) without any success... it seems I missed something at the level of the config. the log shows the following message: galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2010-05-06 17:17:06,940 Error: this request returned None from get_history(): http://machine/Galaxy/tool_runner/upload_async_create any tip where to look at? I am making use of the proxy config too (http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy) which actually works very fine in our other instances that are running on local (not clustered). thanks, Erick

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D Mel reference genome for mapping
by Farhat Habib 07 May '10

07 May '10

Dear Galaxy devs, Would it be possible to include drosophila Melanogaster (dm3) genome for mapping in NGS toolbox? D Mel is a widely used model organism and I am sure many biologists could use it. Thanks, -Farhat -- Farhat Habib, PhD IISER Fellow, Biology Indian Institute of Science Education & Research, Sai Trinity Building, Garware Circle, Sutarwadi, Pashan, Pune-411 021. http://www.iiserpune.ac.in/~farhat Office: +91 20 2590 8015 Cell: +91 973 0996 233

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