scIB pipeline error

Question

[Andy]

Hello everyone,

Andy again.

I am trying to run the scib pipeline, which published in nature method in 2022.

I got the environment down, but I got into trouble in the last few steps. I run everything based on the tutorial, and the the tutorial GitHub page is: https://github.com/theislab/scib-pipeline/blob/main/.github/workflows/pipeline.yml.

I am currently trying to run

snakemake metrics --configfile configs/test_data-R${{ matrix.R }}_small.yaml -kc1

However, I got following error messages:

>Traceback (most recent call last):
  >File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/snakemake/io.py", line 1340, in _load_configfile
    with open(configpath) as f:
>FileNotFoundError: [Errno 2] No such file or directory: 'configs/test_data-R3.6.yaml'

>During handling of the above exception, another exception occurred:

>Traceback (most recent call last):
  File "/risapps/rhel7/python/3.7.3/bin/snakemake", line 10, in <module>
    sys.exit(main())
  File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/snakemake/__init__.py", line 2119, in main
    log_handler=log_handler,
  File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/snakemake/__init__.py", line 405, in snakemake
    overwrite_config.update(load_configfile(f))
  File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/snakemake/io.py", line 1370, in load_configfile
    config = _load_configfile(configpath)
  File "/risapps/rhel7/python/3.7.3/lib/python3.7/site-packages/snakemake/io.py", line 1365, in _load_configfile
    raise WorkflowError("{} file {} not found.".format(filetype, configpath))
snakemake.exceptions.WorkflowError: Config file configs/test_data-R3.6.yaml not found.

I am wondering if you guys could help me out.

Thanks Andy

[GenoMax]

No such file or directory: 'configs/test_data-R3.6.yaml'

Adjust the path if the file exists.

[Andy]

Yes. Now I think I understand where I got run. I need conda install the snakemake then run the code.....