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hall-lab / svtools

Tools for processing and analyzing structural variants.
MIT License
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Installation error with Pip because some packages rely on Python3 #300

Closed shangshanzhizhe closed 4 years ago

shangshanzhizhe commented 4 years ago

Hi, I used pip to install the SVtools in conda virtual env and encountered error, blew are the content of the log:

pip install svtools 2>&1 > error.log Requirement already satisfied: svtools in /data/00/user/user103/.local/lib/python2.7/site-packages/svtools-0.5.1-py2.7.egg Requirement already satisfied: svtyper==0.7.1 in /data/00/user/user103/miniconda2/lib/python2.7/site-packages (from svtools) Requirement already satisfied: numpy in /data/00/user/user103/.local/lib/python2.7/site-packages (from svtools) Requirement already satisfied: scipy in /data/00/user/user103/miniconda2/lib/python2.7/site-packages (from svtools) Requirement already satisfied: statsmodels in /data/00/user/user103/miniconda2/lib/python2.7/site-packages/statsmodels-0.11.1-py2.7-linux-x86_64.egg (from svtools)

AND final: statsmodels requires Python '>=3.5' but the running Python is 2.7.17

I'd like to know how to fix this problem on installing the SVtools. Thank you!

Best, Shangzhe

shangshanzhizhe commented 4 years ago

Hi,

Problem has just been solved. But I kept the issue, reminding other users that few dependency packages of SVtools only rely on Python3 right now. Such as statsmodels and cachetools. To solve this, you can install SVtools in a virtual enviornment. Before pip install svtools, you can install the older version of the statsmodels and cachetools, maybe statsmodels==0.90 cachetools==0.3.1 This worked for me. Hope above could help.

Best, Shangzhe

skchronicles commented 11 months ago

@shangshanzhizhe Do you mean statsmodels==0.9.0? I am not sure if that is a typo, but statsmodels==0.90 does not exist. I ran into some issues while installing svtools and installing statsmodels==0.9.0 prior to svtools fixed the issue.