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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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conda install not working #39

Closed lydiayliu closed 3 years ago

lydiayliu commented 3 years ago

Hi there,

Using the follow commands to install cnv_facets through conda

conda create --name facets --yes
conda activate facets
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda install -c bioconda -c conda-forge cnv_facets

I get the error

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  • cnv_facets

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

I found the cnv_facets page on Anaconda: https://anaconda.org/bioconda/cnv_facets

I've tried both of the commands listed on the anaconda page

conda install -c bioconda cnv_facets
conda install -c bioconda/label/cf201901 cnv_facets

and both give the same error.

Is there anything I'm missing? Thanks!

lydiayliu commented 3 years ago

Taken the workaround inspired by #35

Here's the docker file in case it helps anyone:

FROM mambaorg/micromamba

RUN micromamba install -y -n base -c conda-forge -c bioconda 'r-facets>=0.6.1' 'r-data.table' 'r-ggplot2' 'r-argparse>=2' 'snp-pileup>=0.6.1' 'r-gridextra' 'bioconductor-rsamtools' 'samtools' 'bcftools >=1.9' && \
    micromamba clean --all --yes

COPY cnv_facets.R /usr/local/bin/

WORKDIR /data/

CMD ["cnv_facets.R"]