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TrackHub/generate bigBed files #14
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stolarczyk
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Feb 19, 2021
stolarczyk
reviewed
Feb 19, 2021
nsheff
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Feb 19, 2021
pep_schema.yaml
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| @@ -49,6 +50,7 @@ properties: | |||
| required: | |||
| - input_file_path | |||
| - output_file_path | |||
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should we rename output_file_path?
it's weird to see:
output_file_pathoutput_bigbed_path.
expect both or neither to include format.
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I agree.
Also, I'm not sure why (derived attribute) has been included in the property description in both cases. Technically, it does not have to be derived
| max_file_size cores mem time | ||
| 0.001 1 8000 00-18:00:00 | ||
| NaN 1 16000 01-00:00:00 |
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does this really require 16G of memory? this seems like a lot...
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does this really require 16G of memory? this seems like a lot...
Some of the encode files needed more than 16G.
I changed the code from using pandas to awk. I still need to test how much memory it needs after the change.
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generate bigBed files for visualization and create BED set trackHub on Genome Browser.