Using pip in conda for SCCmecfinder install from CGE errors

Question

I want to install SCCmecfinder from CGE (bitbucket). Im in Ubuntu (18.04.2) and using conda (4.7.5) with pip to install. Is this the best way to go about it, or directly using python outside of conda be better? (NB: I'm very new to all of this and learning on the fly with low skill level, so please explain clearly and simply.)

I created a new environment in Anaconda3/envs/SCCmecfinder, activated it and used:

pip install git+https://bitbucket.org/genomicepidemiology/sccmecfinder

this returned error code:

python setup.py egg_info" failed with error code 1 in /tmp/pip-req-build-92mzn1kf/

I followed feedback from others and used:

pip install --upgrade setuptools

retried the install instruction as above and this returned error code:

"python setup.py egg_info" failed with error code 1 in /tmp/pip-req-build-92mzn1kf/

I deactivated the environment, installed pip into it, reactivated it and retried the installation line again. New error returned - see below:

final error message:

ERROR: Complete output from command python setup.py egg_info:

ERROR: Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/home/sharb/anaconda3/envs/SCCmecfinder/lib/python3.7/tokenize.py", line 447, in open

    buffer = _builtin_open(filename, 'rb')

FileNotFoundError: [Errno 2] No such file or directory: '/tmp/pip-req-build-pobis9bg/setup.py'

----------------------------------------

ERROR: Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-req-build-pobis9bg/

phd phd · Accepted Answer · 2019-07-15T03:54:35

The repository at https://bitbucket.org/genomicepidemiology/sccmecfinder doesn't have setup.py so it's not pip-installable.

All files in the repository are scripts (not libraries) so just copy them to any directory in your $PATH and make them executable.

Using pip in conda for SCCmecfinder install from CGE errors

1 Answers