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Option to change bedgraphToBigwig path #124

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agalitsyna opened this issue Oct 10, 2022 · 0 comments
Closed

Option to change bedgraphToBigwig path #124

agalitsyna opened this issue Oct 10, 2022 · 0 comments
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@agalitsyna
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I usually run notebooks with bioframe in other environments from running notebooks, and there is no simple way to change the path to some binaries run as subprocessed in bioframe, e.g. here:

p = subprocess.run(
["bedGraphToBigWig", f.name, cs.name, outpath],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)

Having an option to pass the path will be great.

agalitsyna added a commit that referenced this issue Oct 10, 2022
gfudenberg pushed a commit that referenced this issue Oct 10, 2022
* Resolving #124

* adds path_to_binary argument to enable user specification when working in various conda environments
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