use command instead of locate
EricDeveaud opened this issue · 4 comments
EricDeveaud commented
Hello,
you may want to use 'command' instead of locate in order to find the path of auxiliary binaries
command is posix and available on all unices.
locate is not always available, eg on our cluster it is not, and won't be.
444thLiao commented
maybe replace sh.locate with sh.find in phigaro/helper.py would fix your problem..
EricDeveaud commented
nop find is not acceptable
to check for binaries, just check on the PATH
snayfach commented
$ phigaro-setup --no-updatedb
Traceback (most recent call last):
File "/global/home/users/snayfach/.conda/envs/phigaro_env/bin/phigaro-setup", line 8, in <module>
sys.exit(main())
File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/cli/helper.py", line 121, in main
force=args.force,
File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/cli/helper.py", line 29, in create_config
config = helper.setup()
File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/helper.py", line 160, in setup
prodigal_params = self._setup_prodigal()
File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/helper.py", line 143, in _setup_prodigal
raise_if_not_found=ProdigalNotFound.message,
File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/helper.py", line 123, in _find_binary
'-b', '-r', '^{}$'.format(name)
File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/phigaro/helper.py", line 117, in _locate
return [s.rstrip() for s in sh.locate(*args, **kwargs)]
File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/sh.py", line 3581, in __getattr__
return self.__env[name]
File "/global/home/users/snayfach/.conda/envs/phigaro_env/lib/python3.7/site-packages/sh.py", line 3378, in __getitem__
raise CommandNotFound(k)
sh.CommandNotFound: locate