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Preprocessing installation fails #1
Description
For installation of the preprocessing I tried the code:
conda install preprocessing -c fasnicar
It returns:
Channels:
- fasnicar
- conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): -
done
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides bowtie2 >=2.0.0 needed by preprocessing-0.2.4-py_0
Could not solve for environment specs
The following package could not be installed
└─ preprocessing is not installable because it requires
└─ bowtie2 >=2.0.0 , which does not exist (perhaps a missing channel).
I installed bowtie2 with the most recent version, and that part works. I am not sure how to solve this problem.
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fasnicar commentedon Aug 6, 2024
If you installed bowtie2 separately from conda it won't be 'seen' by conda when installing the preprocessing as it is listed as a dependency. As suggested but the error message
You should also include the bioconda channel when installing the package (
-c bioconda), and that should solve the issue.Regards,
Francesco
KarvD commentedon Feb 21, 2025
Thank you that problem is somewhat solved now. However, I encountered another issue when trying to use the preprocessing, this is the output I get:
zsh:1: command not found: preprocess.sh
input: parallel -j NCPU 'preprocess.sh -i {}' :::
ls raw_data/When trying to solve this issue I also got this error, which might be useful:
ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-arm64: {MatchSpec("__win"), MatchSpec("xopen==2.0.2=pyh7428d3b_1")}
Encountered problems while solving:
Could not solve for environment specs
The following package could not be installed
└─ trim-galore is not installable because it requires
└─ cutadapt, which requires
└─ xopen >=1.6.0 but there are no viable options
├─ xopen 2.0.2 conflicts with any installable versions previously reported;
└─ xopen 2.0.2 would require
└─ __win, which is missing on the system.
I hope you can help me further.