Question: conda/bioconda installation of plink fails
0
gravatar for gary.napier
7 months ago by
gary.napier20
gary.napier20 wrote:

I'm trying to install the latest version of plink using conda install, as per the instructions here: https://anaconda.org/bioconda/plink

So I have tried

conda install -c bioconda plink

and

conda install -c bioconda/label/cf201901 plink

But I keep getting the error

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

If I wait then it says

Found conflicts! Looking for incompatible packages.

then

UnsatisfiableError: The following specifications were found to be incompatible with each other:

then

Package mkl conflicts for:

and a big list of things I don't understand, but they mention numpy a lot.

I thought plink and numpy would have nothing to do with each other.

How do I install the latest version of plink in the easiest way possible, preferably using conda/bioconda?

Thanks

ADD COMMENTlink modified 7 months ago by curious430 • written 7 months ago by gary.napier20
2
gravatar for curious
7 months ago by
curious430
curious430 wrote:

try a a fresh enviornment with conda conda create -n new_env. If not activated then probably conda activate new_env then try to install.

Otherwise maybe google plink binary and download newest if you cna't get conda to work.

ADD COMMENTlink modified 7 months ago • written 7 months ago by curious430

Amazing! It worked. Thank you so much. What is the explanation for this? Thanks

ADD REPLYlink written 7 months ago by gary.napier20
2

Your install of numpy is probably pinned against MKL and blas, whereas plink is pinned against openblas (and having MKL/blas and openblas in the same env may cause some problems). There is a way to tell conda to use openblas whereever it wants blas: https://github.com/conda-forge/numpy-feedstock/issues/108 .

ADD REPLYlink written 7 months ago by russhh5.5k

Thanks. It's going to take a lot of Googling to understand this, but thanks!

ADD REPLYlink written 7 months ago by gary.napier20

I don't know, the idea of environments is to keep things isolated so you don't get conflicts. Trying in a fresh environment is like the equivalent of "did you try turning it off and on again"

ADD REPLYlink written 7 months ago by curious430
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