gbouras13/coatofarms

ONT Long-read 16S Snakemake pipeline using Emu

coatofarms's Issues

specifiying rank in parse_silva_output.py

Hello,

is it possible to specifiy the desired rank in the parse_silva_output.py script, as can be done with the emu combine-output command?

In the python script, I see that the variable "rank" is an argument of the function, but I cannot seem to use it when running the script.

If I run (in command line linux) python parse_silva_output.py -h it shows me the -d argument (for the directory of the .tsv files), but no rank argument

Script for Krona

Hello !
Thank you for your efforts in writing this nice tools. I have two comments:
1-On our machine, the path to files needs to be provided in their absolute form (we do not use slurm)
2-The krona script in the workflow is not executed due to a typo in the code : in the workflow folder, the folder Scripts is written with an uppercase S but it is called scripts (lowercase S) in the code

All the best,
Nicolas

Could not create conda environment from .yaml files

Hi,
I'm working on a linux HPC cluster. I have all the files installed for coatofarms and snakemake, but when I run coatofarms it fails. My guess is that this happens because of platform incompatibilities of linux vs osx-64. I cannot find where to specify linux as the platform for creating envs using the .yaml files.

Below is the error I get:

Creating conda environment ../coatofarms/coatofarms/workflow/envs/emu.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /home/ang425/coatofarms/coatofarms/workflow/rules/../envs/emu.yaml:
Command:
conda env create --quiet --file "/home/ang425/coatofarms/coatofarms/workflow/conda/6a95845d5d8e9542247bd9017b085649_.yaml" --prefix "/home/ang425/coatofarms/coatoofarms/workflow/conda/6a95845d5d8e9542247bd9017b085649_"
Output:
Channels:

• conda-forge
• bioconda
• defaults
  Platform: osx-64
  Collecting package metadata (repodata.json): ...working... done
  Solving environment: ...working... done
  Preparing transaction: ...working... done
  Verifying transaction: ...working... done
  Executing transaction: ...working... done
  Installing pip dependencies: ...working... Pip subprocess error:
  /home/ang425/coatofarms/coatofarms/workflow/conda/6a95845d5d8e9542247bd9017b085649_/.tmpft9wx1mc: line 3: /home/ang425/coatofarms/coatofarms/workflow/conda/6a958445d5d8e9542247bd9017b085649_/bin/python: cannot execute binary file

Ran pip subprocess with arguments:
['/home/ang425/coatofarms/coatofarms/workflow/conda/6a95845d5d8e9542247bd9017b085649_/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/ang425/coatofarms/cooatofarms/workflow/conda/condaenv.0ksj7a8q.requirements.txt', '--exists-action=b']
Pip subprocess output:

failed

CondaEnvException: Pip failed