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I just installed the Nextflow and I am trying to do the test but I am getting the error pasted below. It's seems nextflow are trying to install Bowtie2, v. 2.4.2 but the package is not found in conda. How can I solve it?
ERROR ~ Error executing process > 'NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_BUILD'
Caused by:
Failed to create Conda environment
command: conda create --mkdir --yes --quiet --prefix /Users/lealc/Library/CloudStorage/OneDrive-SmithsonianInstitution/Documents/Metagenomic/NextFlow/work/conda/env-d3f92820d6bc94caabb085b70037215a -c conda-forge -c bioconda -c defaults bioconda::bowtie2=2.4.2
status : 1
message:
Channels:
- conda-forge
- bioconda
- defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed
PackagesNotFoundError: The following packages are not available from current channels:
- bioconda::bowtie2==2.4.2
Current channels:
- https://conda.anaconda.org/conda-forge
- https://conda.anaconda.org/bioconda
- defaults
- https://conda.anaconda.org/bioconda
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
-[nf-core/mag] Pipeline completed with errors-
Command used and terminal output
nextflow run nf-core/mag -profile test,conda --outdir test
This is likely a combination of you using a recent OSX Operation and we possibly have quite an old version of Bowtie2 that doesn't have conda support for osx-arm64
I will try and send you a work around to try soon (I'm off work this week, or you could ask on the nf-core slack how to replace a conda version in a module) but there is a large possibility that many of the tools won't work because of the same reason, the osx-arm64 support is relatively recently.
If you continue to test after the workaround, it would be great to get a list of tools that don't work.
Otherwise, the faster way to get the pipeline running is too use docker rather than conda, where this should not be an issue™️ (I run Linux so don't know for sure 😅)
Description of the bug
I just installed the Nextflow and I am trying to do the test but I am getting the error pasted below. It's seems nextflow are trying to install Bowtie2, v. 2.4.2 but the package is not found in conda. How can I solve it?
Command used and terminal output
nextflow run nf-core/mag -profile test,conda --outdir test
Relevant files
nextflow.log
System information
Nextflow: version 23.04.4
Hardware: Macbook Pro
Executor: local
Container engine: Conda
OS: macOS Somona 14.6.1
Version of nf-core/mag: 3.0.2
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