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jodyphelan / malaria-profiler

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ImportError: cannot import name 'bam_profiler' from 'pathogenprofiler' #13

Open srinkadatta opened 1 week ago

srinkadatta commented 1 week ago

I am consistently encountering an import error that states it is unable to import bam_profiler from pathogenprofiler. After examining the pathogenprofiler package, I found that there is no script or module named bam_profiler.

Could you please advise on how to resolve this issue?

jodyphelan commented 1 week ago

Hi @srinkadatta we recently did an update of pathogenprofiler so this might have rise to the error. Are you running linux or macOS?

srinkadatta commented 1 week ago

Hi @srinkadatta we recently did an update of pathogenprofiler so this might have rise to the error. Are you running linux or macOS?

I am running on linux.

jodyphelan commented 1 week ago

Try this to create a new conda environment:

wget https://raw.githubusercontent.com/jodyphelan/pathogen-profiler/dev/conda/linux-latest.txt
mamba create --name mp --file linux-latest.txt
conda activate mp
pip install --force-reinstall git+https://github.com/jodyphelan/pathogen-profiler.git@dev
pip install --force-reinstall git+https://github.com/jodyphelan/malaria-profiler.git@dev
malaria-profiler update_db

After it should hopefully work for you.