snakemake环境变量未传递给集群执行（snakemake抛出错误）

Question

我将envvars定义为传递给shell脚本

envvars:
    "PASS"

如果我忘记在shell中指定它们，那么使用snakemake -n的试运行将提醒我设置它。在我的本地机器上执行效果很好，但我无法将envvars传递到集群环境。尽管我设置了环境变量，但在集群执行之后，我遇到了以下snakemake错误。由于snakemake错误，作业从未启动

WorkflowError in line 10 of /home/workflows/Snakefile:
The following environment variables are requested by the workflow but undefined. Please make sure that they are correctly defined before running Snakemake:
PASS
  File "/home/workflows/Snakefile", line 11, in <module>

在使用snakemake --jobs 2 --latency-wait 30 --cluster "qsub ..."执行snakemake之后。显式指定环境变量没有帮助：snakemake --jobs 2 --latency-wait 30 --cluster "qsub ..." --envvars PASS

snakemake是否在与初始snakemake客户端shell不同的shell中再次执行

Answer 1

看起来您需要添加flag ^{} to qsub以使环境变量可用于qsub作业

-V    Declares that all environment variables in the qsub commands environment are to be exported to the batch job.