qiime1.9.1 pip install fails "Title seems unclear, most of the words contain the same letters over and over?"


pip install --user numpy
[installs fine]

pip install --user qiime

Collecting qiime
  Using cached qiime-1.9.1.tar.gz (19.5 MB)
    ERROR: Command errored out with exit status 1:
     command: /opt/apps/apps/binapps/anaconda3/2020.07/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-agkb1t_2/qiime/setup.py'"'"'; __file__='"'"'/tmp/pip-install-agkb1t_2/qiime/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-pip-egg-info-2hj6d4th
         cwd: /tmp/pip-install-agkb1t_2/qiime/
    Complete output (6 lines):
    Traceback (most recent call last):
      File "", line 1, in 
      File "/tmp/pip-install-agkb1t_2/qiime/setup.py", line 363
        if all([e not in sys.argv for e in 'egg_info', 'sdist', 'register']):
    SyntaxError: invalid syntax
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Any advice?


I am glad that you are interested in using Qiime. While you may find support from another member on this forum, we currently only officially support QIIME 2, specifically only the 2021.2 and 2021.4 releases. Have you considered switching to QIIME 2? If so, check out the install page.


An off-topic reply has been split into a new topic: Issues with glibc compatibility when install QIIME 2 2021.4

Please keep replies on-topic in the future.

I'd highly suggest migrating to qiime2.

Are you installing it in an environment with python 2.7?
You may also just want to install it with anaconda: https://anaconda.org/bioconda/qiime