Cannot install bcftools-gtc2vcf-plugin using conda

Question

I have installed bioconda following the instructions at https://bioconda.github.io/user/install.html#set-up-channels. Then I tried

conda install bwa
conda install bcftools
conda install plink2

They all installed fine. However, when I tried

conda install bcftools-gtc2vcf-plugin

or

conda install -c bioconda bcftools-gtc2vcf-plugin 

as instructed at https://bioconda.github.io/recipes/bcftools-gtc2vcf-plugin/README.html, I got errors as follows:

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:

  - bcftools-gtc2vcf-plugin

Current channels:

  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

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.

Any help would be highly appreciated.

Thanks in advance!

Answer 1

I would advise (as of 2020-01-06) not to use the bcftools-gtc2vcf-plugin as it is an old version missing many features compared to the current version. I would advise either to compile from source (https://github.com/freeseek/gtc2vcf) or alternatively to download pre-compiled binaries (https://personal.broadinstitute.org/giulio/gtc2vcf) that should work on systems with ≥GLIBC_2.3 installed (and making sure you are running the latest version of BCFtools)

If you get the error:

No functional bcftools plugins were found in
    BCFTOOLS_PLUGINS="/Users/moxu/xbin/seq/bcftools/plugins".

- Is the plugin path correct?

- Run "bcftools plugin -lv" for more detailed error output.

Could not load "gtc2vcf".

(a bcftools plugin bug that the maintainers will fix soon), can you try to run one of the following commands instead:

$ bcftools plugin gtc2vcf -vv
$ bcftools +gtc2vcf -vv
$ bcftools plugin /Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so -vv
$ bcftools +/Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so -vv

You should get a reason for why the plugin is not loading. A typical error message could look like this:

/Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so:
    dlopen   .. /lib64/libc.so.6: version `GLIBC_2.3' not found (required by /Users/moxu/xbin/seq/bcftools/plugins/gtc2vcf.so)