Installation issues

[TommyH-Tran]

Summary:

pyani: command not found

Description:

I have followed the steps to install pyani using conda in Ubuntu. After I make the enviornment, install pyani and third party packages I cannot run the command pyani.

I followed the installation guide here: https://pyani.readthedocs.io/en/latest/installation.html
I also tried following the one on Github but still encountered the same problem.

Reproducible Steps:

conda create --name pyani --yes python=3.7
conda activate pyani
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda install --yes pyani

(pyani) tom@DESKTOP-TBQ1J5R:~/miniconda3/envs/pyani/bin$ pyani --version
pyani: command not found

(pyani) tom@DESKTOP-TBQ1J5R:~/miniconda3/envs/pyani/bin$ average_nucleotide_identity.py --version
average_nucleotide_identity.py: pyani 0.2.12

Current Output:

(pyani) tom@DESKTOP-TBQ1J5R:~/miniconda3/envs/pyani/bin$ pyani --version
pyani: command not found

Expected Output:

$ pyani --version
pyani 0.2.9

Operating System: WSL2 Ubuntu on Windows

[widdowquinn]

Hi @TommyH-Tran - this is the same issue as #419 #412 #411 etc.

Installing pyani via conda install pyani gives you v0.2.x which is run using the average_nucleotide_identity.py command. Please see the https://github.com/widdowquinn/pyani/blob/master/README_v_0_2_x.md for relevant documentation.

Cheers,

L.

[nahanoo]

Hi!
You are missing intervaltree in your requirment files. This causes to fail python setup.py install.

[widdowquinn]

Hi! You are missing intervaltree in your requirment files. This causes to fail python setup.py install.

Hi @nahanoo - thanks for using pyani. I see intervaltree in the requirements.txt file here: https://github.com/widdowquinn/pyani/blob/master/requirements.txt

Please might you raise a separate issue for your own problem with more information about how you come to this error, or maybe clone the current repo, which ought not to throw this?