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snayfach / IGGsearch

Metagenomic species profiling with enhanced coverage of the human gut microbiome

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Make possible to install using pip or conda

boulund opened this issue · comments

commented

Are there any plans to make the tool installable via pip or conda?

commented

Just noticed that the install instructions in the README are incorrect. They currently state:

Clone the repo from github: git clone https://github.com/snayfach/IGGsearch

Update your environment:
export PYTHONPATH=$PYTHONPATH:/path/to/IGGsearch
export PATH=$PATH:/path/to/IGGsearch

But following these instructions leads to:

Traceback (most recent call last):
  File "IGGsearch/run_iggsearch.py", line 30, in <module>
    from iggsearch import download
  File "/home/analyses/06.iggsearch_test_20190730_FB/IGGsearch/iggsearch/download.py", line 3, in <module>
    import os, sys, subprocess as sp, numpy as np, time, shutil, utility
ModuleNotFoundError: No module named 'utility'

The correct instruction should probably be export PYTHONPATH=$PYTHONPATH:/path/to/IGGsearch/iggsearch. This would of course not be a problem if the package was installable via pip or conda.

commented

Yes of course, thank you! That will be fixed shortly.

There are not currently any plans to make the tool available via pip/conda, but I agree that would be a good thing. I'll look into it if I find the time and will leave the ticket open while that issue remains.