Genome Sampler installation

Library Plugin Support
1

Hi - thanks for this new plugin, it looks like it will be tremendously useful in paring down large datasets for phylogenetic analysis. I've been struggling with the conda installation - I get the error below when creating a conda environment, and it looks like it is a dead link. Is there a different directory it should be pointing too?

conda env create -n genome-sampler-2020.8 --file genome-sampler-py36-osx-conda.yml

Collecting package metadata (repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid.
  channel name: qiime2/latest/tested
  channel url: https://packages.qiime2.org/qiime2/latest/tested
  error code: 404

You will need to adjust your conda configuration to proceed.
Use `conda config --show channels` to view your configuration's current state,
and use `conda config --show-sources` to view config file locations.
2

Hi @duderostome,

Sorry for not seeing this post sooner.

It does looks like library has forgotten about the 2020.8 non-distro releases. So the current best bet would be to clone/download GitHub - caporaso-lab/genome-sampler and run:

pip install .

in your preferred QIIME 2 environment.

In the interim, I'll see about getting this into our new community distribution so that conda installs work as expected.

1 Like
3

Hi @ebolyen,

Thanks for your response - just tried it and so far so good. One thing I noticed was that the PyVCF module is not part of qiime2-2022.8 environment, but was easy enough to install via bioconda.

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