Great, thanks!! From: Daniel Blankenberg [mailto:dan@bx.psu.edu] Sent: Tuesday, August 23, 2011 1:26 PM To: Chorny, Ilya Subject: Re: [galaxy-dev] database/files/_metadata_files Run a tool (or auto-detect metadata) that creates any BAM or MAF output file. The file will originally be created in a temporary location and then moved into the final location in Galaxy's job finish methods. On Aug 23, 2011, at 4:20 PM, Chorny, Ilya wrote: I am setting metadata externally so how do I get a file to be generated in that directory? From: Daniel Blankenberg [mailto:dan@bx.psu.edu]<mailto:[mailto:dan@bx.psu.edu]> Sent: Tuesday, August 23, 2011 1:18 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] database/files/_metadata_files Hi Ilya, Tools should not ordinarily write to this directory, but will often read from it. These files are generated by Galaxy's Metadata functionality. If you are setting metadata externally (settings in universe_wsgi.ini) and using a cluster, then this will occur as part of the tool/job script, as a separate entry (calling set_metadata.sh) in the e.g. .sh file submitted to pbs. Certain filetypes, e.g. BAM and MAF, use these for storing index data. Thanks for using Galaxy, Dan On Aug 23, 2011, at 4:04 PM, Chorny, Ilya wrote: Can someone point me to a tool which writes to this directory? I made some changes to the code to run as actual user but cannot find a tools that writes to this directory. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com> ___________________________________________________________ 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/