nf-core / nf-core/tools

Conda install nf-core cli on mac arm64 fails

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bug
Dominant language
Python
Stars
322
Forks
255
Avg merge
2d 3h
Merged PRs (30d)
5

Description

Description of the bug

Following the instructions here: https://nf-co.re/docs/nf-core-tools/installation#bioconda i.e. conda install nf-core, fails with the following error:

Error while loading conda entry point: conda-libmamba-solver (dlopen(/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/bindings.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.20.dylib                                                                                                                                                              
  Referenced from: <496442DC-0EDE-3705-A2B5-401A4FC0D733> /Users/nathanjohnson/miniconda3/lib/libmamba.2.0.0.dylib                                                                               
  Reason: tried: '/Users/nathanjohnson/miniconda3/lib/libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/bin/../lib/libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/bin/../lib/libarchive.20.dylib' (no such file), '/usr/local/lib/libarchive.20.dylib' (no such file), '/usr/lib/libarchive.20.dylib' (no such file, not in dyld cache))  

A little googling led me to try the following to force install of the dependencies from the same channel, this takes a while to find a successful resolution, but does eventually work:

conda install --solver=classic conda-forge::conda-libmamba-solver conda-forge::libmamba conda-forge::libmambapy conda-forge::libarchive

This is on a very new M4 mac:

uname -a
Darwin Nathans-MBP.fritz.box 24.1.0 Darwin Kernel Version 24.1.0: Thu Nov 14 18:15:21 PST 2024; root:xnu-11215.41.3~13/RELEASE_ARM64_T6041 arm64 arm Darwin
Command used and terminal output
conda install nf-core
...
Error while loading conda entry point: conda-libmamba-solver (dlopen(/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/bindings.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.20.dylib                                                                                                                                                              
  Referenced from: <496442DC-0EDE-3705-A2B5-401A4FC0D733> /Users/nathanjohnson/miniconda3/lib/libmamba.2.0.0.dylib                                                                               
  Reason: tried: '/Users/nathanjohnson/miniconda3/lib/libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/bin/../lib/libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/bin/../lib/libarchive.20.dylib' (no such file), '/usr/local/lib/libarchive.20.dylib' (no such file), '/usr/lib/libarchive.20.dylib' (no such file, not in dyld cache))  
System information

No response

Contributor guide

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First steps

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Research direction

The issue names the Bioconda installation instructions and the conda install nf-core command; start by reproducing that command on macOS arm64 and compare the documented installation path with the reported dependency error. Done means the documented install succeeds on the affected platform, or the instructions clearly identify the supported workaround.

Written by the indexing model from the issue text.

Assessment

Tech stack
macos, python
Domain
cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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