集成 conda env 的 Snakemake 未正确安装

Question

我的snakemake管道中有一条规则来运行multiqc：

    rule summaryReport:
        input:
            fastqc_forward = expand(final_path + "/fastqc/{sample}_R1_fastqc.html", sample = samples),
            fastqc_rev = expand(final_path + "/fastqc/{sample}_R2_fastqc.html", sample = samples)
        output:
            report = final_path + "/fastqc/report_quality_control.html"
        params:
            path = final_path + "/fastqc"
        conda:
            "multiqc.yaml"
        shell:
            "multiqc {params.path} --filename {output.report}"

使用conda env文件multiqc.yaml：

name: multiqc 
channels:
  - conda-forge
  - bioconda
dependencies:
  - multiqc=1.12

当我运行管道时，出现以下错误：

Activating conda environment: /XXXX/.snakemake/conda/e8f3e6def45259d12dddd42fcd679657
Traceback (most recent call last):
  File "/XXXX/.snakemake/conda/e8f3e6def45259d12dddd42fcd679657/bin/multiqc", line 6, in <module>
    from multiqc.__main__ import multiqc
ModuleNotFoundError: No module named 'multiqc'

我已经测试过手动激活conda环境，确实有相同的情况运行 multiqc 时出错。

我已经测试过通过 Snakemake 外部的“multiqc.yaml”创建一个 conda 环境，在这种情况下 multiqc 运行正常。

如果有人对此有想法，那将对我有很大帮助！

先感谢您

Answer 1

您很可能还想安装 python，因为根据 docs 不建议使用系统范围的Python：

name: multiqc 
channels:
  - conda-forge
  - bioconda
dependencies:
  - python=3.7
  - multiqc=1.12