我正在try 使用YAML文件创建一个Conda环境(通过Snakemake),以便运行MAGeCK Flute:

name: mageck_flute
channels: 
  - bioconda
dependencies:
  - bioconductor-mageckflute
  - bioconductor-clusterprofiler
  - r-ggplot2

我得到以下错误:

warning  libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY
Could not solve for environment specs
The following packages are incompatible
├─ bioconductor-clusterprofiler   is uninstallable because there are no viable options
│  ├─ bioconductor-clusterprofiler [2.4.3|3.0.4|...|4.6.0] would require
│  │  └─ r-magrittr   but there are no viable options
│  │     ├─ r-magrittr 1.5 would require
│  │     │  └─ r 3.2.2* , which does not exist (perhaps a missing channel);
│  │     ├─ r-magrittr 1.5 would require
│  │     │  └─ r 3.3.1* , which requires
│  │     │     └─ r-base [3.3.1 |3.3.1 6], which requires
│  │     │        └─ icu 54.* , which does not exist (perhaps a missing channel);
│  │     ├─ r-magrittr [1.5|2.0.1|2.0.2|2.0.3] conflicts with any installable versions previously reported;
│  │     ├─ r-magrittr 1.5 would require
│  │     │  └─ r-base 3.2.0* , which does not exist (perhaps a missing channel);
│  │     ├─ r-magrittr 1.5 would require
│  │     │  └─ r-base 3.2.1* , which does not exist (perhaps a missing channel);
│  │     └─ r-magrittr 1.5 would require
│  │        └─ r-base 3.2.2* , which does not exist (perhaps a missing channel);
│  ├─ bioconductor-clusterprofiler 3.0.5 would require
│  │  └─ r 3.3.1* , which cannot be installed (as previously explained);
│  └─ bioconductor-clusterprofiler [3.18.0|3.18.1] would require
│     ├─ r-base >=4.0,<4.1.0a0  with the potential options
│     │  ├─ r-base [4.0.0|4.0.1|4.0.2|4.0.3], which can be installed;
│     │  ├─ r-base [4.0.3|4.0.5] would require
│     │  │  └─ libcurl [>=7.75.0,<9.0a0 |>=7.76.1,<9.0a0 ] but there are no viable options
│     │  │     ├─ libcurl [7.75.0|7.76.0|...|7.81.0] would require
│     │  │     │  └─ libnghttp2 >=1.43.0,<2.0a0  but there are no viable options
│     │  │     │     ├─ libnghttp2 [1.46.0|1.47.0|1.51.0|1.52.0] would require
│     │  │     │     │  └─ c-ares >=1.18.1,<2.0a0 , which conflicts with any installable versions previously reported;
│     │  │     │     ├─ libnghttp2 1.52.0 conflicts with any installable versions previously reported;
│     │  │     │     ├─ libnghttp2 1.43.0 would require
│     │  │     │     │  └─ c-ares >=1.17.1,<2.0a0 , which conflicts with any installable versions previously reported;
│     │  │     │     ├─ libnghttp2 1.43.0 would require
│     │  │     │     │  └─ c-ares >=1.17.2,<2.0a0 , which conflicts with any installable versions previously reported;
│     │  │     │     └─ libnghttp2 1.46.0 conflicts with any installable versions previously reported;
│     │  │     ├─ libcurl [7.82.0|7.83.0|...|8.1.2] would require
│     │  │     │  └─ libnghttp2 [>=1.47.0,<2.0a0 |>=1.51.0,<2.0a0 |>=1.52.0,<2.0a0 ] but there are no viable options
│     │  │     │     ├─ libnghttp2 [1.46.0|1.47.0|1.51.0|1.52.0], which cannot be installed (as previously explained);
│     │  │     │     └─ libnghttp2 1.52.0 conflicts with any installable versions previously reported;
│     │  │     └─ libcurl [7.78.0|7.80.0|...|8.1.1] conflicts with any installable versions previously reported;
│     │  ├─ r-base [4.0.5|4.1.0|4.1.1|4.1.2|4.1.3] would require
│     │  │  └─ libtiff >=4.3.0,<4.5.0a0  but there are no viable options
│     │  │     ├─ libtiff 4.4.0 would require
│     │  │     │  └─ libdeflate >=1.12,<1.13.0a0 , which conflicts with any installable versions previously reported;
│     │  │     ├─ libtiff 4.4.0 would require
│     │  │     │  └─ libdeflate >=1.13,<1.14.0a0 , which conflicts with any installable versions previously reported;
│     │  │     ├─ libtiff [4.3.0|4.4.0] would require
│     │  │     │  └─ libdeflate >=1.10,<1.11.0a0 , which conflicts with any installable versions previously reported;
│     │  │     ├─ libtiff [4.4.0|4.5.0] would require
│     │  │     │  └─ libdeflate >=1.14,<1.15.0a0 , which conflicts with any installable versions previously reported;
│     │  │     ├─ libtiff 4.4.0 conflicts with any installable versions previously reported;
│     │  │     ├─ libtiff 4.3.0 would require
│     │  │     │  └─ libdeflate >=1.8,<1.9.0a0 , which conflicts with any installable versions previously reported;
│     │  │     └─ libtiff 4.3.0 would require
│     │  │        └─ libdeflate >=1.7,<1.8.0a0 , which conflicts with any installable versions previously reported;
│     │  └─ r-base [4.0.5|4.1.3] would require
│     │     └─ libtiff >=4.4.0,<4.5.0a0  but there are no viable options
│     │        ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│     │        ├─ libtiff 4.4.0, which cannot be installed (as previously explained);
│     │        ├─ libtiff [4.3.0|4.4.0], which cannot be installed (as previously explained);
│     │        ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│     │        └─ libtiff 4.4.0 conflicts with any installable versions previously reported;
│     ├─ r-dplyr   but there are no viable options
│     │  ├─ r-dplyr 0.5.0 would require
│     │  │  └─ r-bh >=1.58.0_1  but there are no viable options
│     │  │     ├─ r-bh 1.60.0_2 would require
│     │  │     │  └─ r-base 3.3.2*  but there are no viable options
│     │  │     │     ├─ r-base [3.3.1|3.3.2], which cannot be installed (as previously explained);
│     │  │     │     └─ r-base 3.3.2 conflicts with any installable versions previously reported;
│     │  │     ├─ r-bh [1.58.0_1|1.60.0_2] would require
│     │  │     │  └─ r-base 3.2.2* , which does not exist (perhaps a missing channel);
│     │  │     ├─ r-bh 1.60.0_2 would require
│     │  │     │  └─ r 3.3.1* , which cannot be installed (as previously explained);
│     │  │     ├─ r-bh [1.60.0_2|1.62.0_1|...|1.81.0_1] conflicts with any installable versions previously reported;
│     │  │     ├─ r-bh 1.58.0_1 would require
│     │  │     │  └─ r-base 3.2.0* , which does not exist (perhaps a missing channel);
│     │  │     └─ r-bh 1.58.0_1 would require
│     │  │        └─ r-base 3.2.1* , which does not exist (perhaps a missing channel);
│     │  ├─ r-dplyr 0.5.0 would require
│     │  │  └─ r-base 3.3.1* , which cannot be installed (as previously explained);
│     │  ├─ r-dplyr [0.4.3|0.5.0] conflicts with any installable versions previously reported;
│     │  ├─ r-dplyr [0.7.0|0.7.4|...|1.1.2] conflicts with any installable versions previously reported;
│     │  ├─ r-dplyr 0.4.2 would require
│     │  │  └─ r-base 3.2.0* , which does not exist (perhaps a missing channel);
│     │  ├─ r-dplyr [0.4.2|0.4.3] would require
│     │  │  └─ r-base 3.2.1* , which does not exist (perhaps a missing channel);
│     │  └─ r-dplyr 0.4.3 would require
│     │     └─ r-base 3.2.2* , which does not exist (perhaps a missing channel);
│     └─ r-magrittr   but there are no viable options
│        ├─ r-magrittr 1.5, which cannot be installed (as previously explained);
│        ├─ r-magrittr 1.5, which cannot be installed (as previously explained);
│        ├─ r-magrittr [1.5|2.0.1|2.0.2|2.0.3] conflicts with any installable versions previously reported;
│        ├─ r-magrittr 1.5, which cannot be installed (as previously explained);
│        ├─ r-magrittr 1.5, which cannot be installed (as previously explained);
│        └─ r-magrittr 1.5, which cannot be installed (as previously explained);
├─ bioconductor-mageckflute   is uninstallable because there are no viable options
│  ├─ bioconductor-mageckflute 1.10.0 would require
│  │  ├─ bioconductor-clusterprofiler >=3.18.0,<3.19.0 , which cannot be installed (as previously explained);
│  │  ├─ r-base >=4.0,<4.1.0a0  with the potential options
│  │  │  ├─ r-base [4.0.0|4.0.1|4.0.2|4.0.3], which can be installed;
│  │  │  ├─ r-base [4.0.3|4.0.5], which cannot be installed (as previously explained);
│  │  │  ├─ r-base [4.0.5|4.1.0|4.1.1|4.1.2|4.1.3], which cannot be installed (as previously explained);
│  │  │  └─ r-base [4.0.5|4.1.3], which cannot be installed (as previously explained);
│  │  └─ r-ggrepel   but there are no viable options
│  │     ├─ r-ggrepel 0.6.5 would require
│  │     │  └─ r-base 3.3.2*  but there are no viable options
│  │     │     ├─ r-base [3.3.1|3.3.2], which cannot be installed (as previously explained);
│  │     │     └─ r-base 3.3.2 conflicts with any installable versions previously reported;
│  │     ├─ r-ggrepel 0.5 would require
│  │     │  └─ r 3.2.2* , which does not exist (perhaps a missing channel);
│  │     ├─ r-ggrepel [0.5|0.6.5] would require
│  │     │  └─ r 3.3.1* , which cannot be installed (as previously explained);
│  │     └─ r-ggrepel [0.6.5|0.7.0|...|0.9.3] conflicts with any installable versions previously reported;
│  ├─ bioconductor-mageckflute [1.12.0|1.14.0] would require
│  │  └─ r-base >=4.1,<4.2.0a0  but there are no viable options
│  │     ├─ r-base [4.0.5|4.1.0|4.1.1|4.1.2|4.1.3], which cannot be installed (as previously explained);
│  │     ├─ r-base [4.0.5|4.1.3], which cannot be installed (as previously explained);
│  │     └─ r-base 4.1.3 would require
│  │        └─ libtiff >=4.5.0,<4.6.0a0  but there are no viable options
│  │           ├─ libtiff [4.4.0|4.5.0], which cannot be installed (as previously explained);
│  │           ├─ libtiff 4.5.0 would require
│  │           │  └─ libdeflate >=1.17,<1.18.0a0 , which conflicts with any installable versions previously reported;
│  │           ├─ libtiff 4.5.0 would require
│  │           │  └─ libdeflate >=1.16,<1.17.0a0 , which conflicts with any installable versions previously reported;
│  │           ├─ libtiff [4.5.0|4.5.1] would require
│  │           │  └─ libdeflate >=1.18,<1.19.0a0 , which conflicts with any installable versions previously reported;
│  │           └─ libtiff 4.5.0 conflicts with any installable versions previously reported;
│  ├─ bioconductor-mageckflute [1.2.2|1.2.3|1.4.2|1.6.0] would require
│  │  └─ r-ggextra  , which requires
│  │     └─ r-shiny >=0.13.0  but there are no viable options
│  │        ├─ r-shiny [1.0.3|1.0.5|1.1.0|1.2.0] would require
│  │        │  └─ r-htmltools >=0.3.5 , which conflicts with any installable versions previously reported;
│  │        ├─ r-shiny [1.3.0|1.3.2] would require
│  │        │  └─ r-htmltools >=0.3.6 , which conflicts with any installable versions previously reported;
│  │        ├─ r-shiny [1.4.0|1.4.0.2|1.5.0] would require
│  │        │  └─ r-htmltools >=0.4.0 , which conflicts with any installable versions previously reported;
│  │        ├─ r-shiny 1.6.0 would require
│  │        │  └─ r-digest >=0.6.25 , which conflicts with any installable versions previously reported;
│  │        ├─ r-shiny [1.7.0|1.7.1|1.7.2|1.7.3|1.7.4] would require
│  │        │  └─ r-htmltools >=0.5.2 , which conflicts with any installable versions previously reported;
│  │        └─ r-shiny [0.13.2|0.14.2|...|1.7.1] conflicts with any installable versions previously reported;
│  └─ bioconductor-mageckflute [1.8.0|2.2.0] would require
│     └─ r-msigdbr  , which requires
│        └─ r-dplyr >=0.7.0 , which conflicts with any installable versions previously reported;
└─ r-ggplot2   is uninstallable because there are no viable options
   ├─ r-ggplot2 2.2.1 would require
   │  └─ r-reshape2   but there are no viable options
   │     ├─ r-reshape2 [1.4.2|1.4.3|1.4.4] would require
   │     │  └─ r-stringr   but there are no viable options
   │     │     ├─ r-stringr 1.1.0 would require
   │     │     │  └─ r 3.3.1* , which cannot be installed (as previously explained);
   │     │     ├─ r-stringr [1.0.0|1.1.0|...|1.5.0] conflicts with any installable versions previously reported;
   │     │     ├─ r-stringr 1.0.0 would require
   │     │     │  └─ r-base 3.2.0* , which does not exist (perhaps a missing channel);
   │     │     ├─ r-stringr 1.0.0 would require
   │     │     │  └─ r-base 3.2.1* , which does not exist (perhaps a missing channel);
   │     │     └─ r-stringr 1.0.0 would require
   │     │        └─ r-base 3.2.2* , which does not exist (perhaps a missing channel);
   │     ├─ r-reshape2 1.4.1 would require
   │     │  └─ r-base 3.2.0* , which does not exist (perhaps a missing channel);
   │     ├─ r-reshape2 1.4.1 would require
   │     │  └─ r-base 3.2.1* , which does not exist (perhaps a missing channel);
   │     ├─ r-reshape2 1.4.1 would require
   │     │  └─ r-base 3.2.2* , which does not exist (perhaps a missing channel);
   │     └─ r-reshape2 [1.4.1|1.4.2|1.4.3|1.4.4] conflicts with any installable versions previously reported;
   ├─ r-ggplot2 [2.0.0|2.1.0] would require
   │  └─ r 3.2.2* , which does not exist (perhaps a missing channel);
   ├─ r-ggplot2 [2.1.0|2.2.0|2.2.1] would require
   │  ├─ r 3.3.1* , which cannot be installed (as previously explained);
   │  └─ r-base 3.3.1* , which cannot be installed (as previously explained);
   ├─ r-ggplot2 [2.1.0|2.2.0|...|3.4.2] conflicts with any installable versions previously reported;
   ├─ r-ggplot2 1.0.1 would require
   │  └─ r-base 3.2.0* , which does not exist (perhaps a missing channel);
   ├─ r-ggplot2 1.0.1 would require
   │  └─ r-base 3.2.1* , which does not exist (perhaps a missing channel);
   └─ r-ggplot2 1.0.1 would require
      └─ r-base 3.2.2* , which does not exist (perhaps a missing channel).

我已经在Conda基本环境中手动安装了这些R包,没有任何问题,但我想使用上面的YAML文件将其与Snakemake规则一起使用. 如何通过YAML文件安装这些包?

推荐答案

不建议只使用bioconda作为这样的频道,而应该使用:

name: mageck_flute
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - r-base=4.2  # specifying R version improves solve speed and consistency
  - bioconductor-mageckflute
  - bioconductor-clusterprofiler
  - r-ggplot2

请参见https://bioconda.github.io/.请注意,他们也推荐设置channel_priority: strict,但有些人发现flexible(默认设置)也是可靠的(参见 comments ).

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