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databio / bedhost

API and UI for BEDbase
http://api.bedbase.org
BSD 2-Clause "Simplified" License
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bedset auto PEP #25

Closed nsheff closed 4 years ago

nsheff commented 4 years ago

2 issues with the demo PEP you can download from bedhost:

  1. The auto PEP for bedsets says: output_dir: $HOME. we should at least give it a bedset-specific name.

  2. There are spaces in some of the values. (" Lung" for 2 of the samples, and "K562" has a space in front of every sample).

nsheff commented 4 years ago

also:

sample_name output_file_path file_name
GSE105587_ENCFF018NNF_conservative_idr_thresholded_peaks_GRCh38 source1 78c0e4753d04b238fc07e4ebe5a02984
GSE105977_ENCFF617QGK_optimal_idr_thresholded_peaks_GRCh38 source1 fdd94ac0787599d564b07193e4ec41fd

let's just change file_name to md5sum -- and then use that as the filename. just rename the column, its weird to see it like that.

joseverdezoto commented 4 years ago

@nsheff

2 issues with the demo PEP you can download from bedhost:

1. The auto PEP for bedsets says: `  output_dir: $HOME`.  we should at least give it a bedset-specific name.

2. There are spaces in some of the values. (" Lung" for 2 of the samples, and "K562" has a space in front of every sample).

In item 1, do you mean a bedset specific directory where pipeline logs would be stored? Maybe it makes sense to keep the bedbuncher pipeline logs together with the bedset outputs. Right now they're stored in a separate logs directory. I feel like that would make it less confusing for the user to navigate results?

joseverdezoto commented 4 years ago

Config output_dir updated and bedset PEP annotation sheet fixed.