On Thu, Jun 9, 2011 at 10:12 AM, John David Osborne <ozborn@uab.edu> wrote:

Thanks Ross, I don't see it under my local install - are there any pre-written scripts to integrate it with a local galaxy instance?

I assume you are talking about this tool here: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

Hi, John. it's on main and test - ie the FastQC wrapper is distributed with the current stable and central branches so your local tool_conf.xml may be out of date since it's not automagically refreshed from the distro .sample ? If you do a diff of your local tool_conf.xml with the current distributed sample, you should see the lines you need to add which points to rgenetics/fastqc.xml Thu,Jun 09 at 10:22am grep -i fastqc tool_conf.xml <label text="FastQC: fastq/sam/bam" id="fastqcsambam" /> <tool file="rgenetics/rgFastQC.xml" /> Like everything else, you'll want to install the jar locally so it can be found by the cluster - the default location is tool-data/shared/jars/FastQC so the tool can find the fastqc perl script (yes, I know...but it's worth it!) <command interpreter="python"> rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc I hope this helps?

 -John

________________________________________ From: Ross [ross.lazarus@gmail.com] Sent: Wednesday, June 01, 2011 11:41 AM To: John David Osborne Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics

You can avoid the space/time overhead of grooming and get comprehensive QC reports using the new wrapper for FastQC (under NGS: QC) - it takes fastq of any flavour (and bam) groomed or not, producing a superset of the compute quality stats output without the need for an intermediate step. Highly recommended.

On Wed, Jun 1, 2011 at 12:02 PM, John David Osborne <ozborn@uab.edu> wrote:

...

I noticed that for our new Ilumina data (which generate Sanger format) the FastQ groomer output is identical to the Ilumina FastQ input file.

I was hoping to go ahead and just use the raw FastQ files as input (saving disk space) for computing quality statistics to look at box plots, but it appears that the tool "Compute Quality Statistics" appears to require that the data have been run through FastQ Groomer first.

Is there a way to get around this and is this a bug? I assuming this is some sort of safety measure built into this tool?

 -John

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-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;