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Ken Hsu
Ken Hsu

Reputation: 441

dyld: Library not loaded: @rpath/libdeflate.so

enter image description hereI am a mac user with operating system, macOS Mojave 10.14.6. I have installed bcftools in my conda environment py3.9 (Python 3.9). The following code is my installing command line:

conda install -c bioconda bcftools

but when I try to use it, the shell told me there is something wrong with it.

dyld: Library not loaded: @rpath/libdeflate.so
Referenced from: /opt/anaconda3/envs/py3.9/bin/bcftools
Reason: image not found
Abort trap: 6

when I went the path (/opt/anaconda3/envs/py3.9/bin/bcftools), I found there is only a binary file. I hope that someone can help me, thanks!

Upvotes: 1

Views: 1019

Answers (1)

merv
merv

Reputation: 76810

Bioconda has very specific channel requirements, namely, it builds packages using Conda Forge builds, not Anaconda (defaults). The correct ad hoc installation command for Bioconda packages is:

conda install -c conda-forge -c bioconda -c defaults bcftools

However, if you have an Anaconda base (as opposed to Miniforge), it is usually not a good idea to prioritize the conda-forge channel when installing in base (can lead to lots of channel switching and long solves). Instead, create a new environment and configure it to use the correct channels:

# create new environment
conda create -n my_env

# activate environment
conda activate my_env

# set channels for environment
conda config --env --add channels defaults
conda config --env --add channels bioconda
conda config --env --add channels conda-forge

# no need to use ad hoc `-c` flags
conda install bcftools

Upvotes: 2

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