Conda install nf-core cli on mac arm64 fails
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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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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