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tsailabSJ / changeseq

CHANGE-seq analysis pipeline
GNU Affero General Public License v3.0
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Problems with non-conda install #8

Open lfrancioli opened 3 years ago

lfrancioli commented 3 years ago

Hi,

I just tried to install changeseq following the procedure described in the README using git clone, not conda) and have experienced a couple of issues:

  1. biopython==1.76 and pandas seem to be missing from requirements.txt (I've been installing the latest versions compatible with python2). Also statsmodel<=0.10.0 (getting import errors that look like version incompatibility with later versions) and HTSeq<=12.4 (later versions dropped python2 support).
  2. when running python setup.py install, I'm getting the following error 
    Extracting changeseq-1.2.9.1-py3.8.egg to /cluster/home/franciol/venv/change_seq/lib/python3.8/site-packages
File "/cluster/home/franciol/venv/change_seq/lib/python3.8/site-packages/changeseq-1.2.9.1-py3.8.egg/changeseq/refseq_gene_name.py", line 2
NM_000299   PKP1

I'm using python 2.7.18 with a clean virtual env.

As far as I can tell, I'm still able to use changeseq using python changeseq/changeseq.py though.

Also, any plans for python 3 support?

Hope this helps, Laurent

YichaoOU commented 3 years ago

Hi Laurent,

  1. pip installation. Sorry, I didn't really check requirements.txt since CHANGE-seq 1.0. Conda installation should work.

  2. Yeah, this error occurs in python 3. Did you have this problem in python 2?

Yes. We will upgrade to python 3 in a month or so.

Best, Yichao