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scikit-bio dependency #26
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Thanks for that John, I'll fix this in future upon the next update. There was a change in some of the required dependencies and I think I might have messed up the conda recipe in the process of trying to trim back on rosella's requirements. I'll close this once the conda recipe is updated. Cheers, |
thanks! But now after creating a new dedicated conda environment for this, i realize that the actual problem is actually with the shebang of the main script of flight (which uses the system python interpreter instead of that of the current conda environment) |
ok now i got it installed and running! the first problem (exclusively on my side) was that my conda (although updated) still installs python=2 per default, if not otherwise specified in the recipe. I solved this by explicitely specifying python3 (most more recent conda setups should not do this, but still it may be a good idea to specify python3 as a dependency in the conda recipe?) The other problem was that the most recent version sci-kit bio in conda does not work wth the most recent version of scipy in conda. So i had to explicitely specify scipy=1.8.1 The other dependencies i thought were necessary are not actually needed to be explicitely specified. So the updated installation procedure that worked for me is (in case anybody else has the same problem):
|
Thanks for working through this, I'll update the setup.py for flight, that should solve any issues |
when trying to run rosella i got an error during the short read processing step with flight, complaining about the missing
skbio
module:I did follow the installation procedure given in the readme.md, including installing flight from github using pip:
```pip install git+https://github.com/rhysnewell/flight.git#egg=flight-genome``´
I guess this means that skbio may have to be added to the dependencies? I guess this would be easiest to do by adding it to the conda recipe for rosella?
Edit: also, looking at issue #21 I guess the same applies for matplotlib, seaborn, umap, numba? Maybe it is easiest for now to just change the installation instructions to:
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