gem-pasteur / Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes
GNU General Public License v3.0
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Installing from pip not working #74

Closed leaemiliepradier closed 5 years ago

leaemiliepradier commented 5 years ago

Hello, i'm unable to install integron_finder from pip following the directions in your README.md

Version of Integron_Finder:

integron_finder-1.5.1

OS

Expected behavior

Showing an error or minimalistic help when executing the command integron_finder using a python2.7 environment

The installation with python 3.5 and 3.6 simply fails, as shown below. pip install integron_finder

Actual behavior

With a virtual environment running with python 3.6, the command pip install integron_finder yields:

    ERROR: Command errored out with exit status 1:
     command: /home/irene/envs/py36/bin/python3.5 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-k5znen5k/integron-finder/setup.py'"'"'; __file__='"'"'/tmp/pip-install-k5znen5k/integron-finder/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-k5znen5k/integron-finder/pip-egg-info
         cwd: /tmp/pip-install-k5znen5k/integron-finder/
    Complete output (1 lines):
    Sorry, Python 3 is not supported yet
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

With a virtual environment running with python2.7, the previous command works. But integron_finder yields:

Traceback (most recent call last):
  File "/home/irene/envs/py27/bin/integron_finder", line 1403, in <module>
    or define INTEGRON_HOME environment variable.""")
Exception: cannot find integron_finder data check your installation
or define INTEGRON_HOME environment variable.

The command integron_finder -h yields the same.

jeanrjc commented 5 years ago

Duplicate of #57 #63 #64

leaemiliepradier commented 5 years ago

Don't you want to add that to the README.md ? This is the one that worked in a py 3.6 environment pip install git+https://github.com/gem-pasteur/Integron_Finder/#egg=integron_finder

jeanrjc commented 5 years ago

You're right, it's done. Thanks.