Thank you for the development of MAGpy, it is a great tool.
Using the pipeline with the rule specific conda packages (--use-conda, following your instructions), I had to adapt the call to python in a few rules. Somehow the 'python' symlink was missing and therefore 'python3' had to be called directly. Personally, I solved the issue by not changing the shebang of the scripts, but by calling the python scripts with python in the rules, e.g.:
$ python3 script.py
There is also a small error in the readme. To run the pipeline, you have to call
$ snakemake -rp -s MAGpy --use-conda
without the ‘MAGpy’. I assume that this rule name has changed to ‘all’.
Thank you for the development of MAGpy, it is a great tool.
Using the pipeline with the rule specific conda packages (--use-conda, following your instructions), I had to adapt the call to python in a few rules. Somehow the 'python' symlink was missing and therefore 'python3' had to be called directly. Personally, I solved the issue by not changing the shebang of the scripts, but by calling the python scripts with python in the rules, e.g.:
$ python3 script.py
There is also a small error in the readme. To run the pipeline, you have to call
$ snakemake -rp -s MAGpy --use-conda
without the ‘MAGpy’. I assume that this rule name has changed to ‘all’.