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cgsb / hitscore

NYU CGSB Genomics Core Facility
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add option to choose BaseCalls directory #27

Closed agarwal closed 11 years ago

agarwal commented 11 years ago

So far, we've hardcoded the use of Data/Intensities/BaseCalls as the directory to use with CASAVA. However, recently we've had to run OLB, which creates a separate BaseCalls directory, e.g. Data/Intensities/Bustard1.9.4_11-04-2013_sm4431. Need to support selection of this alternative directory.

smondet commented 11 years ago

Done: https://github.com/agarwal/hitscore/commit/e281c652267b843606a0f8414f8fda13df2401bf

smondet commented 11 years ago

But the choice is not part of the bcl_to_fastq function in the DB.

smondet commented 11 years ago

The migrator only sets the default basecalls path, so after release of 1.5, the function 15592 will have tobe changed manually.

smondet commented 11 years ago

So, still todo when 1.5 is released: