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click CLI - positional argument missing 'test' #35

MikeDMorgan opened this Issue Jan 4, 2018 · 1 comment


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MikeDMorgan commented Jan 4, 2018

I'm attempting to run Velocyto within a condo environment, a la issue #32. Upon calling the run command, I get a missing argument error that appears to originate from the click module:

velocyto run bam.dir/Uber_sort.bam mm10_genes.gtf

Traceback (most recent call last):
File "/home/morgan02/.local/bin/velocyto", line 11, in
File "/Users/morgan02/miniconda3/lib/python3.6/site-packages/click/", line 722, in call
return self.main(*args, **kwargs)
File "/Users/morgan02/miniconda3/lib/python3.6/site-packages/click/", line 697, in main
rv = self.invoke(ctx)
File "/Users/morgan02/miniconda3/lib/python3.6/site-packages/click/", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/morgan02/miniconda3/lib/python3.6/site-packages/click/", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/morgan02/miniconda3/lib/python3.6/site-packages/click/", line 535, in invoke
return callback(*args, **kwargs)
TypeError: run() missing 1 required positional argument: 'test'

gioelelm added a commit that referenced this issue Jan 4, 2018


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gioelelm commented Jan 4, 2018

Should be fixed now, feel free to reopen in case there are still encountering problems

@gioelelm gioelelm closed this Jan 4, 2018

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