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bobeobibo / phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages
MIT License
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Wrong paths are used when installing figaro via conda #39

Closed kabilov closed 5 months ago

kabilov commented 1 year ago

Dear colleagues,

I installed phigaro via conda, creating a separate environment (phigaro). But the software does not work, because it accesses programs using the wrong path.

Traceback (most recent call last): File "/home/user/anaconda3/envs/phigaro/bin/phigaro", line 10, in sys.exit(main()) File "/home/user/anaconda3/envs/phigaro/lib/python3.6/site-packages/phigaro/cli/batch.py", line 232, in main substitutions, ProdigalTask, preprocess_task=preprocess_task File "/home/user/anaconda3/envs/phigaro/lib/python3.6/site-packages/phigaro/cli/batch.py", line 35, in create_task task = task_class(*args, **kwargs) File "/home/user/anaconda3/envs/phigaro/lib/python3.6/site-packages/phigaro/batch/task/prodigal.py", line 14, in init self.prodigal = sh.Command(self.config['prodigal']['bin']).bake( File "/home/user/anaconda3/envs/phigaro/lib/python3.6/site-packages/sh.py", line 788, in init raise CommandNotFound(path) sh.CommandNotFound: /home/user/anaconda3/bin/prodigal

But path must be /home/kabilov/anaconda3/envs/phigaro/bin/prodigal

PollyTikhonova commented 5 months ago

I believe an option of manual providing the paths/config file would solve the issue.