biom-format not found

[Nazzy87]

Solving environment fails when installing picrust2. I am using mac m1 and I get below error when I try to install picrust2 env using conda env create -f picrust2-env.yaml. Any way around pls? thanks

Solving environment: failed

ResolvePackageNotFound:

• biom-format[version='>=2.1.10']
• hmmer[version='>=3.1b2,<=3.2.1']
• sepp=4.3.10
• gappa=0.8.0
• r-castor[version='>=1.7.2']
• epa-ng=0.3.8

[gavinmdouglas]

Hi there,

I can confirm that I can install PICRUSt2 with conda on my M1 Mac, so I don't think this is a Mac OS X problem. Are you using the latest version of conda?

Cheers,

Gavin

[lcamVz]

Hi Gavin,

Would you mind sharing your conda version I had picrust2 running on my intel desktop but since I updated my OSX and conda I am having issues. I also have an M1 Mac and am interested on installing it in there.

Best regard

[R-Wright-1]

Hi there,

I just looked into installation on my M1 mac and found that I was getting similar errors initially.

But everything seems to work fine if I first of all run: conda config --add subdirs osx-64

So for reference, everything that I ran to install PICRUSt2 from source:

wget https://github.com/picrust/picrust2/archive/v2.5.2.tar.gz
tar xvzf  v2.5.2.tar.gz
cd picrust2-2.5.2/
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add subdirs osx-64
conda env create -n picrust2-src -f picrust2-env.yaml
conda activate picrust2-src
pip install --editable .

When I initially ran pytest, it failed with the same error mentioned in #330, but the fix given there works: pip install dendropy==4.5.2

After installing this version of dendropy, pytest ran fine. Also note that I called my environment picrust2-src, but you don't need that option.

Robyn

[R-Wright-1]

I'm closing this issue now, but please let me know if there are additional issues or if this doesn't fix it.