sgt_constructor.py not able to resolve env location

[jeanmattique]

Hi,

I am trying to run the "Detailed Workflow" pipeline that is described here: https://thebrownlab.github.io/phylofisher-pages/detailed-example-workflow/step3-project-dir and I am running into an error I cannot resolve. When I try to run sgt_constructor.py I get the following error message:

WorkflowError:
Failed to open source file /Users/jmattick/miniconda3/envs/fisher/bin/envs/mafft.yaml
FileNotFoundError: [Errno 2] No such file or directory: '/Users/jmattick/miniconda3/envs/fisher/bin/envs/mafft.yaml'
File "/Users/jmattick/miniconda3/envs/fisher/lib/python3.7/site-packages/snakemake/deployment/conda.py", line 228, in create
File "/Users/jmattick/miniconda3/envs/fisher/lib/python3.7/site-packages/snakemake/deployment/conda.py", line 99, in hash
File "/Users/jmattick/miniconda3/envs/fisher/lib/python3.7/site-packages/snakemake/deployment/conda.py", line 81, in content
File "/Users/jmattick/miniconda3/envs/fisher/lib/python3.7/site-packages/snakemake/deployment/conda.py", line 68, in _get_content
Traceback (most recent call last):
File "/Users/jmattick/miniconda3/envs/fisher/bin/sgt_constructor.py", line 150, in
run_snakemake(length_filter=False)
File "/Users/jmattick/miniconda3/envs/fisher/bin/sgt_constructor.py", line 85, in run_snakemake
f'--config {make_config(length_filter)}',
File "/Users/jmattick/miniconda3/envs/fisher/bin/sgt_constructor.py", line 49, in make_config
f'genes={",".join(get_genes(length_filter))}',
File "/Users/jmattick/miniconda3/envs/fisher/bin/sgt_constructor.py", line 27, in get_genes
bmge_out_files = [file for file in os.listdir(len_filt_bmge_dir) if file.endswith('.bmge')]
FileNotFoundError: [Errno 2] No such file or directory: '/Users/jmattick/Documents/PhyloFisherTest/sgt_constructor_out_Jan.11.2023/length_filtration/bmge'

When I check, there is no directory /Users/jmattick/miniconda3/envs/fisher/bin/envs/mafft.yaml, but there is a directory containing /Users/jmattick/miniconda3/envs/fisher/bin/mafft.yaml

I am not sure how to tell sgt_constructor.py to point to bin/ for the environment, rather than bin/envs. I have installed phylofisher exactly as described using conda in https://thebrownlab.github.io/phylofisher-pages/getting-started/installation/ and I am running on macOS Monterey v. 12.4 on a MacBook Pro.

Thank you for any help you can provide,
Regards,
John

[robert-ervin-jones]

Hi John,

Thank you for reaching out.

This issue was addressed in Issue 63, and the solution will be included in v1.2.5.

If you have any more questions, concerns, or issues, please don't hesitate to reach out.

Best,
Robert