我想使用 snakemake 实用程序 (5.6.0( 来使用存储在 EGA 上的文件。首先我想尝试官方文档中编写的代码，所以我尝试了这个：
import snakemake.remote.EGA as EGA
ega = EGA.RemoteProvider()
rule get_remote_file_ega:
input:
ega.remote("ega/dataset_id/foo.bam")
output:
"data/foo.bam"
shell:
"cp {input} {output}"
在执行脚本之前，我根据需要创建了环境变量(EGA_USERNAME和EGA_PASSWORD(。
然后我收到以下错误：
me:~/scripts$ snakemake -s test_ega.smk
Building DAG of jobs...
Traceback (most recent call last):
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/__init__.py", line 551, in snakemake
export_cwl=export_cwl)
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/workflow.py", line 433, in execute
dag.init()
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/dag.py", line 122, in init
job = self.update([job], progress=progress)
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/dag.py", line 603, in update
progress=progress)
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/dag.py", line 655, in update_
missing_input = job.missing_input
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/jobs.py", line 396, in missing_input
for f in self.input
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/jobs.py", line 397, in <genexpr>
if not f.exists and not f in self.subworkflow_input)
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/io.py", line 208, in exists
return self.exists_remote
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/io.py", line 119, in wrapper
v = func(self, *args, **kwargs)
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/io.py", line 258, in exists_remote
return self.remote_object.exists()
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 173, in exists
return self.parts.path in self.provider.get_files(self.parts.dataset)
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 126, in get_files
"data/metadata/datasets/{dataset}/files".format(dataset=dataset))
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 96, in api_request
headers["Authorization"] = "Bearer {}".format(self.token)
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 77, in token
self._login()
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 45, in _login
"client_id" : self._client_id(),
File "/home/puissant/miniconda3/lib/python3.7/site-packages/snakemake/remote/EGA.py", line 151, in _client_id
return self._credentials("EGA_CLIENT_ID")
NameError: name 'self' is not defined
涉及的代码部分在那里(EGA.py 第 151 行(：
1 @classmethod
2 def _client_id(cls):
3 return self._credentials("EGA_CLIENT_ID")
错误可能来自第 3 行的"自我"而不是"cls"吗？因为在将其更改为"cls"后，错误移动到下一个块，以相同的方式构建。我对python对象的理解是有限的，我希望我不要说大荒谬。
我是否忘记了任何步骤或误解了其中任何一个？
你是对的，你应该使用cls(这里大概代表"类"(而不是self。self通常是用于类实例(即对象(的名称。如果您在函数中的其他地方使用self，则需要将它们切换到cls.