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mkiyer / oncoseq

Automatically exported from code.google.com/p/oncoseq
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Library XML files not written correctly #10

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
During the create_jobs.py script the FASTQ file locations are resolved and 
checked. Currently the absolute paths to the FASTQ files are written in the 
library XML file. This makes the library XML file store absolute paths instead 
of relative paths and these XML files are no longer portable between servers.

We should simply store the verbatim library XML information without resolving 
FASTQ locations and instead resolve FASTQ locations on the fly. To do this we 
should require that the 'server_name' be specified at runtime, or have 
create_jobs.py write a file 'server' into each job directory specifying the 
server name.

Original issue reported on code.google.com by matthew....@gmail.com on 11 Feb 2013 at 4:48