Snakemake:我一直在获取'conda'命令在$ PATH中不可用.在SGE群集上运行时 [英] Snakemake: I keep getting The 'conda' command is not available in $PATH. when running on SGE cluster

问题描述

我在这里扯头发，希望有人可以帮助我.

I'm tearing my hair out here, hopefully someone can help me.

运行snakemake 4.8.0

Running snakemake 4.8.0

我有一个snakemake管道，该管道与两个conda envs和--use-conda一起运行，并且在作为独立管道运行时可以正常工作.

I have a snakemake pipeline, which I run with two conda envs and --use-conda and it works fine when run as a standalone pipeline.

但是，当我在集群上运行时，出现错误:

However, when I run on our cluster, I get the error:

'conda'命令在$ PATH中不可用."

"The 'conda' command is not available in $PATH."

现在.Anaconda已安装在我们的群集上，但是我们需要使用以下命令在节点上将其激活:

Now. Anaconda is installed on our cluster, but we need to activate it on nodes with:

module load anaconda

此外，模块被定义为一个函数，因此我首先要介绍一些东西.因此，在我的snakefile的顶部，我有:

Also, module is defined as a function, so I have source a couple of things first. Therefore, at the top of my snakefile, I have:

shell.prefix("source $HOME/.bashrc; source /etc/profile; module load anaconda; )

这不能解决问题.

我什至在 .bashrc 中放入了 module load anaconda ，但这仍然行不通.仅在集群执行时，我收到关于找不到conda的错误.

I even put module load anaconda in my .bashrc, and that still doesn't work. Only on cluster execution, I get the error about conda not being found.

我的 .bashrc 的其他更改被蛇形拾取并拾取，所以我不知道为什么它在conda上有问题.

Other changes to my .bashrc are picked up and are picked up by snakemake, so I have no idea why it is having problems with conda.

我什至创建了一个conda env，将snakemake和conda加载到该env中，在提交脚本和Snakefile中激活该env:

I even created a conda env, loaded snakemake and conda into that env, activate the env in the submission script and in the Snakefile:

shell.prefix("source $HOME/.bashrc; source /etc/profile; module load anaconda; source activate MAGpy-3.5; ")

并且它 still 说:'conda'命令在$ PATH中不可用."

And it still says "The 'conda' command is not available in $PATH."

从字面上将我的头发扯掉.

Literally tearing my hair out.

顺便说一句，我使用 qsub -S/bin/bash 提交，还使用 shell.executable("/bin/bash")，但使用临时shell脚本在 .snakemake 中创建的文件由/bin/sh 运行-可以吗?

As an aside, I submit using qsub -S /bin/bash and also use shell.executable("/bin/bash") but the temp shell scripts created in .snakemake are run by /bin/sh - is that expected?

请帮助我！

推荐答案

您可以提供自定义的"jobscript模板"，您尝试过吗?默认值如下:

You can provide a custom "jobscript template", have you tried that? The default one looks like this:

#!/bin/sh
# properties = {properties}
{exec_job}

所以也许您的样子可能是这样的:

So perhaps yours could look this like:

#!/bin/bash
# properties = {properties}
module add anaconda
{exec_job}

，然后在运行snakemake时使用-jobscript 参数引用该文件.

and then you refer to this file with the --jobscript parameter when you run snakemake.

P.S.如果您在代码中查找，则在没有任何 PATH 设置的情况下，调用 python -m snakemake 来填充 {exec_job} 导致您看到的错误.

P.S. if you look in the code the {exec_job} is filled in with a call to python -m snakemake without any PATH setting, which I think contributes to the error you are seeing.

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