Thanks, that makes sense. Ilya -----Original Message----- From: Ross [mailto:ross.lazarus@gmail.com] Sent: Thursday, July 28, 2011 10:14 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] dataset_*_file directory being compied to file_path when running fastqc It's a feature although arguably necessitated by what some might consider a design bug in FastQC FastQC insists on writing the html report with links to the generated images which it writes to a subdirectory. That won't work for Galaxy's html datatype, so the wrapper script unpacks that structure into a Galaxy html datatype and adjusts the links in the html so they work correctly when viewed in a history. On Fri, Jul 29, 2011 at 2:47 PM, Chorny, Ilya <ichorny@illumina.com> wrote:

I am testing the latest galaxy central distribution by running FASTQC. It creates a directory call dataset_*_file in the job_working_directory and then copies that directory to file_path when the job is complete. Is that on purpose or is that a bug?

Thanks,

Ilya

Ilya Chorny Ph.D.

Bioinformatics - Intern

ichorny@illumina.com

858-202-4582

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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;