search

ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
115 stars 14 forks source link

conda install issues with numpy and samtools #94

Closed seanharrington256 closed 6 months ago

seanharrington256 commented 8 months ago

I installed pixy via conda on a Linux cluster using: 

conda create -n pixy -y
conda activate pixy
conda install --yes -c conda-forge pixy python=3.8
conda install --yes -c bioconda htslib

Attempting to run pixy --version caused an error: AttributeError: module 'numpy' has no attribute 'typeDict'

I fixed this by downgrading numpy: conda install numpy=1.21

When trying to actually run pixy, I then ran into an issue with tabix:

tabix: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

I managed to fix this by installing samtools 1.9:

conda install -c bioconda samtools=1.9 --force-reinstall -y

It now seems to be running well and is able to generate output.

ksamuk commented 6 months ago

Thanks Sean, I am going to update the installation procedure to make sure these issues no longer arise.