[galaxy-dev] dataset_*_file directory being compied to file_path when running fastqc
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 icho...@illumina.commailto:icho...@illumina.com 858-202-4582 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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 icho...@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 icho...@illumina.com 858-202-4582 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- 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; ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] dataset_*_file directory being compied to file_path when running fastqc
Thanks, that makes sense. Ilya -Original Message- From: Ross [mailto:ross.laza...@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 icho...@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 icho...@illumina.com 858-202-4582 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- 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; ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/