Question

我已按照https://bioconda.github.io/user/install.html#set-up-channels上的说明安装了bioconda。然后我尝试了

conda install bwa
conda install bcftools
conda install plink2

它们都安装良好。但是，当我尝试

conda install bcftools-gtc2vcf-plugin

或

conda install -c bioconda bcftools-gtc2vcf-plugin

按照https://bioconda.github.io/recipes/bcftools-gtc2vcf-plugin/README.html的指示，出现以下错误：

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.

任何帮助将不胜感激。

谢谢！

Answer 1

我建议（从2020年1月6日开始）不要使用bcftools-gtc2vcf-plugin，因为它是一个旧版本，与当前版本相比缺少许多功能。我建议要么从源代码编译（https://github.com/freeseek/gtc2vcf，要么下载可以在安装了≥GLIBC_2.3的系统上运行的预编译二进制文件（https://personal.broadinstitute.org/giulio/gtc2vcf）（并确保您正在运行最新的二进制文件）。版本的BCFtools）

如果出现错误：

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".

（维护者即将修复的bcftools插件错误），您可以尝试改为运行以下命令之一吗？

$ 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

您应了解为什么未加载插件的原因。典型的错误消息可能如下所示：

/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)

无法使用conda安装bcftools-gtc2vcf-plugin

1 个答案: