Code Monkey home page Code Monkey logo

Comments (2)

yingeddi2008 avatar yingeddi2008 commented on August 23, 2024

So I was able to fix the snakemake() got an unexpected keyword argument 'configfile' error message by adding "s" to the configfile argument in the workflow.py line 7 (so inside snakemake command, configfiles = configfile).  However, another error popped up about the configpath in the snakemake package.

$ mgefinder workflow toydir/
#### PARAMETERS ###
command: workflow
workdir: toydir/
snakefile: /home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/mgefinder/workflow/Snakefile
configfile: /home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/mgefinder/workflow/config.yml
cores: 1
memory: 16000
unlock: False
rerun_incomplete: False
keep_going: False
###################
Traceback (most recent call last):
  File "/home/dfi_user/miniconda3/envs/mgefinder/bin/mgefinder", line 11, in <module>
    sys.exit(cli())
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/mgefinder/main.py", line 46, in workflow
    _workflow(workdir, snakefile, configfile, cores, memory, unlock, rerun_incomplete, keep_going)
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/mgefinder/workflow.py", line 6, in _workflow
    force_incomplete=rerun_incomplete, keepgoing=keep_going)
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/snakemake/__init__.py", line 394, in snakemake
    overwrite_config.update(load_configfile(f))
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/snakemake/io.py", line 1311, in load_configfile
    config = _load_configfile(configpath)
  File "/home/dfi_user/miniconda3/envs/mgefinder/lib/python3.7/site-packages/snakemake/io.py", line 1273, in _load_configfile
    with open(configpath) as f:
IsADirectoryError: [Errno 21] Is a directory: '/'

The path to the config file is correct, but somehow, it is not working. I am sincerely grateful if you could provide some hints.

Thanks,

Eddi

from mgefinder.

durrantmm avatar durrantmm commented on August 23, 2024

Hey Eddi, I am working on improving the README, it is not up to date. How about we set up a google hangout call so I can help you through this specifically? Please email me at [email protected].

from mgefinder.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.