On Thu, Jun 9, 2011 at 10:12 AM, John David Osborne <ozb...@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out of date since it's not automagically refreshed from the distro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.laza...@gmail.com]
> Sent: Wednesday, June 01, 2011 11:41 AM
> To: John David Osborne
> Cc: galaxy-u...@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 <ozb...@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
>>
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
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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;

___________________________________________________________
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