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cruizperez / MicrobeAnnotator

Pipeline for metabolic annotation of microbial genomes
Artistic License 2.0
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Workarounds for bad conda installation #76

Open morgansobol opened 1 year ago

morgansobol commented 1 year ago

In case anyone else had the same issues as me with conda installation not working according to installation instructions maybe these steps will help:

  1. Do not do conda config --add channels cruizperez. This messed up my conda installation and I had to manually remove it from my .condarc file.

  2. First create environment only by conda create -n microbeannotator then activate env conda activate microbeannotator

  3. Install microbeannotator like this: conda install microbeannotator and hmmer like this: pip install hmmer==0.1.0

  4. Then for some reason my env did not have a lot of dependencies still, so I had to also pip install: wget, Bio, pandas, matplotlib, seaborn, psutil

Then I was finally able to successfully run microbeannotator -h

Hope it helps!

alegarritano commented 1 year ago

I second everything @morgansobol suggested.

I was having issues when installing the databases and didn't even think about an issue with the installation process as this is not very common using Conda.

When I tried running microbeanntator -h, I came across several modules that were not installed for some reason (matplot, seaborn and psutil). Once I pip installed all of them, I was able to correctly install the databases and the software worked.

Finally, I also had to install diamond as well