October 2011 - galaxy-user - lists.galaxyproject.org

SamTools processing issue
by Golbus, Jessica 04 Oct '11

04 Oct '11

Hi- I am currently working with one of Illumina's older Bam files and trying to run SamTools Pileup. Unfortunately, the server has repeatedly timed out on me and I am unable to run the program on my file. I was wondering if other people are having trouble running Samtools on human genome .bam files or whether this is secondary to the way the file is configured (i.e. it was first run through Illumina's proprietary software and provided as a .bam without an accompanying fastq file)? Thanks for your help! Jessie ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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SNPEff 2.0.2 Wrapper Problem / Partial Fix
by John David Osborne 03 Oct '11

03 Oct '11

Hi Pablo, We recently installed 2.0.2 SnpEff at the UAB Galaxy instance (thanks for adding those mycoplasma genomes to SNPEff!) but we ran into some problems with the galaxy wrapper. It looks like it is for an older version of SnpEff and it chocks on the input options it is fed. I replaced the input format section in snpEff.xml with: <param name="inputFormat" type="select" label="Input format"> <option value=" -i txt ">Text</option> <option value=" -i pileup ">Pileup</option> <option value=" -i vcf ">VCF 4</option> <option value=" -i bed ">BED</option> </param> It runs now, although I am sure there are other additional fixes that could be made to update the wrapper. Right now there is no option in the galaxy wrapper to output to VCF. If you could fix this that would be great, otherwise I can look into the format of the galaxy wrapper xml – something I need to do at eventually anyway. -John

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upload zip file to custom tool
by Brent Pedersen 03 Oct '11

03 Oct '11

Hi, I have followed the wiki and built a custom tool on a local galaxy installation. One of the inputs is a zip file. It seems galaxy automatically unpacks it and keeps only the first file. Is there any way I can tell galaxy not to unzip the file? I tried to register .zip as a datatype, but that didn't seem to change the behavior. thanks for any help. $tool.xml is below in case it helps. -Brent <command interpreter="python">charmqc.py $xyszip $output $organism</command> <inputs> <param format="xys.zip" name="xyszip" type="data" label="Zip of .xys files"/> <param type="select" name="organism" label="organism"> <option value="Human">Human (hg18)</option> <option value="Mouse">Mouse (mm8)</option> </param> </inputs> <outputs> <data format="data" name="output" /> </outputs>

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