正确访问cluster_config“__default__价值观

Question

我有一个cluster.json文件看起来像这样：

{ 
    "__default__": 
    { 
     "queue":"normal", 
     "memory":"12288", 
     "nCPU":"1", 
     "name":"{rule}_{wildcards.sample}", 
     "o":"logs/cluster/{wildcards.sample}/{rule}.o", 
     "e":"logs/cluster/{wildcards.sample}/{rule}.e", 
     "jvm":"10240m" 
    }, 
    "aln_pe": 
    { 
     "memory":"61440", 
     "nCPU":"16" 
    }, 
    "GenotypeGVCFs": 
    { 
     "jvm":"102400m", 
     "memory":"122880" 
    } 
} 

在我snakefile我有尝试访问他们的PARAMS的cluster_config对象几条规则

params: 
    memory=cluster_config['__default__']['jvm'] 

但是，这会给我一个“KeyError异常”

KeyError in line 27 of home/bwubb/projects/Germline/S0330901/haplotype.snake: 
'__default__' 

这是否有事可做'__default__'是一个特殊的对象？它在一个视觉吸引人的字典中打印，其他人标记为OrderDict，但是当我看着json时，它看起来是一样的。

如果我的json没有问题，那么我应该不要访问'__default__'？

Answer 1

的默认值是通过关键字 “集群” 访问，不

__default__ 

See here in this example in the tutorial:

{ 
"__default__" : 
{ 
    "account" : "my account", 
    "time" : "00:15:00", 
    "n" : 1, 
    "partition" : "core" 
}, 
"compute1" : 
{ 
    "time" : "00:20:00" 
} 
} 

The JSON list in the URL above and listed above is the one being accessed in this example. It's unfortunate they are not on the same page. To access time, J.K. uses the following call.

#!python 

#!/usr/bin/env python3 
import os 
import sys 

from snakemake.utils import read_job_properties 

jobscript = sys.argv[1] 
job_properties = read_job_properties(jobscript) 

# do something useful with the threads 
threads = job_properties[threads] 

# access property defined in the cluster configuration file (Snakemake >=3.6.0) 
job_properties["cluster"]["time"] 

os.system("qsub -t {threads} {script}".format(threads=threads, script=jobscript))