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Hydro3639 / NanoPhase

Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and short reads (hybrid strategy)
MIT License
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install problem #3

Closed yikiii closed 1 year ago

yikiii commented 1 year ago

hi, something wrong with installation.

install via mamba： mamba create -n nanophase python=3.8 -y mamba activate nanophase mamba install -c nanophase nanophase -y

but：

Could not solve for environment specs Encountered problems while solving:

yikiii commented 1 year ago

I found type conda config --set channel_priority flexible first maybe work

Hydro3639 commented 1 year ago

Good to know you fix this. I would suggest adding channels of defaults, conda-forge, and bioconda to avoid some similar errors. Please let me know if you need more help.

yikiii commented 1 year ago

Thanks for your reply.

something wrong with metawrap refinement:

from Bio import SeqIO
ImportError: No module named Bio

I'm sure the package is installed.

Python 3.8.15 | packaged by conda-forge | (default, Nov 22 2022, 08:46:39) 
[GCC 10.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import SeqIO
>>>

I modify the file nanophase.meta to use my conda env metawrap-env installed before, it works.

by the way, where is medaka_model' directory, in case I want to download new model from https://github.com/nanoporetech/medaka/tree/master/medaka/data to use

Hydro3639 commented 1 year ago

Yes, currently, the medaka was not the latest one. I will update medaka and other packages in the next release. Currently, I will suggest to uninstall medaka first in nanophase env, then install medaka (v1.7.2), which you can use all new models. Hope it helps.

yikiii commented 1 year ago

I'll try. Thanks for all your work!