Re: [galaxy-dev] database/files/_metadata_files

2011-08-23 Thread Daniel Blankenberg 
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: icho...@illumina.com
 Website: www.illumina.com
  
  
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Re: [galaxy-dev] database/files/_metadata_files

2011-08-23 Thread Chorny, Ilya 
Great, thanks!!

From: Daniel Blankenberg [mailto:d...@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:d...@bx.psu.edu]mailto:[mailto:d...@bx.psu.edu]
Sent: Tuesday, August 23, 2011 1:18 PM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edumailto: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: icho...@illumina.commailto:icho...@illumina.com
Website: www.illumina.comhttp://www.illumina.com


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