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czbiohub-sf / MIDAS

Metagenomic Intra-Species Diversity Analysis (MIDAS)
MIT License
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Install from source needs additional channel #121

Closed mtisza1 closed 1 year ago

mtisza1 commented 1 year ago

I was successfully able to install MIDAS2 using the "From Source" instructions only after modifying the midas2.yml file to include your anaconda channel "zhaoc1"

https://midas2.readthedocs.io/en/latest/installation.html#from-source

Without the zhaoc1 channel, I get the following error beacuse midas2 conda package is only available from zhaoc1

Solving environment: failed

ResolvePackageNotFound: 
  - midas2=1.0.9

Additionally, the install provided under "Quickstart" didn't work for me. This was related to an issue with Python version (python 3.7.9 was installed, but python 3.9 was required for something). This may have something to do with v1.0.0 (which is indicated in these instructions) and v1.0.9.

https://midas2.readthedocs.io/en/latest/quickstart.html#install-midas2

Finally, the installation instructions under "Conda" didn't practically work for me as the "solving environment" step hung for several hours before I killed it.

https://midas2.readthedocs.io/en/latest/installation.html#conda

I look forward to using the tool.

Mike

zhaoc1 commented 1 year ago

Thanks for trying out MIDAS2. And you are right about the -c zhaoc1, I missed it in the midas2.yaml file.

I recently updated the MIDAS2 code base to v1.1.0 while the ReadTheDoc update is on my TODO list. The latest MIDAS2 requires Python3.9.

As for the conda install command, the following should work:

conda config --set channel_priority flexible
conda install -c zhaoc1 -c conda-forge -c bioconda-c anaconda -c defaults midas2

This takes a while to "solving environment", but it should not be stuck at this process.

Thanks, Chunyu

mtisza1 commented 1 year ago

Thanks so much for the quick response, Chunyu!

My conda tends to be a little slow, but I just tried the suggested conda install again, and it's been hanging on the solve step for over 90 minutes.

I'll close this now. Thanks!

zhaoc1 commented 1 year ago

Sure thing! I only tested the conda install on linux, and not sure about mac os. To my experience, the fatest way is to install from the source. And you mentioned, add -c zhaoc1 to the YML though.