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daler / pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
http://daler.github.io/pybedtools
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pybedtools from conda use version 2.26 not 2.3 #371

Closed udiland closed 1 year ago

udiland commented 1 year ago

Hi, I want to use the 'getfasta' with 'nameOnly' parameter. I get the error: ERROR: Unrecognized parameter: -nameOnly The output also show that the version of bedTools use is Version: v2.26.0, so there is no such argument. Is there a way to get pybedtools with Version 2.3? (this is what the online manual show) Thanks,

udiland commented 1 year ago

I now see that this happen only when I run in pycharm ide with remote interpreter to a server with conda environment but when I run the code directly in the server it give the expected results

daler commented 1 year ago

Seems like a path issue with pycharm on remote rather than a pybedtools issue then?

udiland commented 1 year ago

Looks like it, couldn't figure out exactly what is is going on. Thanks.