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sigven / pcgr

Personal Cancer Genome Reporter (PCGR)
https://sigven.github.io/pcgr
MIT License
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cyvcf2 not bundled with latest pcgr vesion #177

Closed adbeggs closed 2 years ago

adbeggs commented 2 years ago

Just to flag up - cyvcf2 does not bundle with the default pcgr conda - works fine when add it in the Environment.yml

pdiakumis commented 2 years ago

@adbeggs thanks for the report. Yep, that's intentional. The pcgr conda pkg bundles just the Python code. The dependencies (cyvcf2, ensemble-vep etc.) get brought in via the environment file.

adbeggs commented 2 years ago

It's more if you build a singularity image, I exported the environment.yml from a machine where I installed it with conda. When I build the singularity image it builds the conda environment correctly but cyvcf2 seems to be left out in the environment.ym

pdiakumis commented 2 years ago

@adbeggs may I ask which commands you're using to set up the environments? I think the simplest way to install them is with:

PCGR_VERSION="0.10.14"
PCGR_REPO="https://raw.githubusercontent.com/sigven/pcgr/v${PCGR_VERSION}/conda/env/lock/"
PLATFORM="linux" # or "osx"

mamba create --file ${PCGR_REPO}/pcgr-${PLATFORM}-64.lock --prefix ./pcgr
mamba create --file ${PCGR_REPO}/pcgrr-${PLATFORM}-64.lock --prefix ./pcgrr
conda activate ./pcgr

# test that it works
pcgr --version

Using the --prefix option installs those envs in the local directory, but I suppose you could also use -n/--name pcgr to install those in your central conda location.

Thanks for filing these issues, very helpful!