How can I install the Bioconductor package "liftOver" in a conda environment?-CodePudding

I'm trying to install the Bioconductor package liftOver using conda. I'm creating a conda environment using a .yml file like this: conda env create -f coo_environment.yml

When I do this, I get:

Collecting package metadata: done
Solving environment: failed

ResolvePackageNotFound:
  - bioconductor-liftover

The relevant contents of coo_environment.yml are shown below

name: coo

channels:
        - conda-forge
        - bioconda
dependencies:
        # R
        - bioconductor-exomeCopy
        - bioconductor-rtracklayer
        - bioconductor-liftOver

CodePudding user response：

pyliftover is python implementation of UCSC liftOver genome coordinate conversion. So change the last line in your yml to pyliftover. Alternatively, you can also use ucsc-liftover.

CodePudding user response：

The Bioconductor liftOver reimplementation is provided as part of the rtracklayer package, so the bioconductor-rtracklayer is sufficient.

You can access the function in R with

rtracklayer::liftOver