Failed to create Conda environment in the test run

[camillevleal]

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?

  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

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

[jfy133]

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 😅)

[camillevleal]

Thank you @jfy133. I will try it using Docker and see if its works.

[jfy133]

I will assume this worked :) feel free to reopen if you still had issues with docker