Circos into workflow

Nay

6/20/24, 11:25 AM

I'm trying to use the proteny tool that is implemented in the Snakemake framework. I started with the example, but I can't make it run. This is the error that I get.

*File "/root/mambaforge/envs/snakemake/bin/snakemake", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/root/mambaforge/envs/snakemake/lib/python3.11/site-packages/snakemake/__init__.py", line 3030, in main
    success = snakemake(
              ^^^^^^^^^^
  File "/root/mambaforge/envs/snakemake/lib/python3.11/site-packages/snakemake/__init__.py", line 554, in snakemake
    update_config(overwrite_config, load_configfile(f))
                                    ^^^^^^^^^^^^^^^^^^
  File "/root/mambaforge/envs/snakemake/lib/python3.11/site-packages/snakemake/io.py", line 1715, in load_configfile
    config = _load_configfile(configpath)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/root/mambaforge/envs/snakemake/lib/python3.11/site-packages/snakemake/io.py", line 1689, in _load_configfile
    obj = open(configpath_or_obj, encoding="utf-8")
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'circos'*

I am pretty sure that circos is installed in the main directory. I even put circos PATH into the bashrc file, and I'm still having the issue. Mambaforge, conda, and Snakemake are updated.

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EN: Circos into workflow

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