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snayfach / IGGsearch

Metagenomic species profiling with enhanced coverage of the human gut microbiome
GNU General Public License v3.0
24 stars 8 forks source link

Make possible to install using pip or conda #30

Open boulund opened 5 years ago

boulund commented 5 years ago

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

boulund commented 5 years ago

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.

snayfach commented 5 years ago

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.