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] 
Sent: Tuesday, August 23, 2011 1:18 PM
To: Chorny, Ilya
Cc: 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

Website: www.illumina.com

 

 

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